3ZPI | pdb_00003zpi

PikC D50N mutant in P21 space group

PDB DOI: https://doi.org/10.2210/pdb3ZPI/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Streptomyces venezuelae
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2013-02-27 Released: 2014-03-19
Deposition Author(s): Podust, L.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free:
0.219 (Depositor), 0.220 (DCC)
R-Value Work:
0.174 (Depositor), 0.170 (DCC)
R-Value Observed:
0.176 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Recognition of Synthetic Substrates by P450 Pikc

Podust, L.M.

To be published.

Macromolecule Content

Total Structure Weight: 98.81 kDa
Atom Count: 7,302
Modeled Residue Count: 792
Deposited Residue Count: 872
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CYTOCHROME P450 HYDROXYLASE PIKC	A, B	436	Streptomyces venezuelae	Mutation(s): 1 EC: 1.14.15.33
UniProt
Find proteins for O87605 (Streptomyces venezuelae) Explore O87605 Go to UniProtKB: O87605
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O87605
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain P [auth B] MOL2 format, chain C [auth A] MOL2 format, chain P [auth B] mmCIF format, chain C [auth A] mmCIF format, chain P [auth B]	C [auth A], P [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain P [auth B] Interactions & Density Focus chain C [auth A] Focus chain P [auth B]
TLA Query on TLA Download Ideal Coordinates CCD File SDF format, chain O [auth A] MOL2 format, chain O [auth A] mmCIF format, chain O [auth A]	O [auth A]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain O [auth A] Interactions & Density Focus chain O [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain V [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain V [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain V [auth B]	F [auth A] G [auth A] J [auth A] K [auth A] M [auth A] F [auth A], G [auth A], J [auth A], K [auth A], M [auth A], R [auth B], S [auth B], V [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain V [auth B] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain V [auth B]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth A] SDF format, chain Q [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	D [auth A] E [auth A] H [auth A] I [auth A] L [auth A] D [auth A], E [auth A], H [auth A], I [auth A], L [auth A], Q [auth B], T [auth B], U [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth A] Focus chain Q [auth B] Focus chain T [auth B] Focus chain U [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.63 Å
R-Value Free: 0.219 (Depositor), 0.220 (DCC)
R-Value Work: 0.174 (Depositor), 0.170 (DCC)
R-Value Observed: 0.176 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.085	α = 90
b = 59.784	β = 95.81
c = 91.267	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-03-19

Deposition Author(s):

Podust, L.M.

Revision History (Full details and data files)

Version 1.0: 2014-03-19
Type: Initial release
Version 1.1: 2023-12-20
Changes: Data collection, Database references, Derived calculations, Other, Refinement description