4IRW | pdb_00004irw

Co-crystallization of streptavidin-biotin complex with a lanthanide-ligand complex gives rise to a novel crystal form

PDB DOI: https://doi.org/10.2210/pdb4IRW/pdb

Classification: BIOTIN BINDING PROTEIN
Organism(s): Streptomyces avidinii
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-01-15 Released: 2014-01-29
Deposition Author(s): Bandara, R.A.M.S.S., Liu, D.Q., Hindupur, A., Tesh, K.F., Fox, R.O.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free:
0.154 (Depositor), 0.170 (DCC)
R-Value Work:
0.123 (Depositor), 0.140 (DCC)
R-Value Observed:
0.126 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Co-crystallization of streptavidin-biotin complex with a lanthanide-ligand complex gives rise to a novel crystal form

Bandara, R.A.M.S.S., Liu, D.Q., Hindupur, A., Tesh, K.F., Fox, R.O.

To be published.

Macromolecule Content

Total Structure Weight: 16.48 kDa
Atom Count: 1,193
Modeled Residue Count: 123
Deposited Residue Count: 129
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Streptavidin	A	129	Streptomyces avidinii	Mutation(s): 0
UniProt
Find proteins for P22629 (Streptomyces avidinii) Explore P22629 Go to UniProtKB: P22629
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22629
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
BTN Query on BTN 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]	BIOTIN C₁₀ H₁₆ N₂ O₃ S YBJHBAHKTGYVGT-ZKWXMUAHSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
PDC Query on PDC Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain I [auth A] SDF format, chain H [auth A] SDF format, chain G [auth A] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] SDF format, chain B [auth A] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain B [auth A] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain B [auth A]	B [auth A] C [auth A] D [auth A] E [auth A] F [auth A] B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	PYRIDINE-2,6-DICARBOXYLIC ACID C₇ H₅ N O₄ WJJMNDUMQPNECX-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Interactions & Density Focus chain B [auth A] Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A]
TB Query on TB Download Ideal Coordinates CCD File SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A]	O [auth A], P [auth A], Q [auth A], R [auth A], S [auth A]	TERBIUM(III) ION Tb HKCRVXUAKWXBLE-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain T [auth A] MOL2 format, chain T [auth A] mmCIF format, chain T [auth A]	T [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain T [auth A] Interactions & Density Focus chain T [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
BTN	BindingDB: 4IRW	Kd: 0 (nM) from 1 assay(s)
BTN	BindingDB: 4IRW	ΔH: min: -1.23e+2, max: -6.69e+1 (kJ/mol) from 12 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.40 Å
R-Value Free: 0.154 (Depositor), 0.170 (DCC)
R-Value Work: 0.123 (Depositor), 0.140 (DCC)
R-Value Observed: 0.126 (Depositor)

Space Group: C 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.423	α = 90
b = 71.395	β = 90
c = 55.494	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
PHENIX	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-01-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-01-29
Type: Initial release
Version 1.1: 2024-02-28
Changes: Advisory, Data collection, Database references, Derived calculations