6CMZ | pdb_00006cmz

2.3 Angstrom Resolution Crystal Structure of Dihydrolipoamide Dehydrogenase from Burkholderia cenocepacia in Complex with FAD and NAD

PDB DOI: https://doi.org/10.2210/pdb6CMZ/pdb

Classification: OXIDOREDUCTASE
Organism(s): Burkholderia cenocepacia J2315
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2018-03-06 Released: 2018-03-21
Deposition Author(s): Minasov, G., Shuvalova, L., Dubrovska, I., Kiryukhina, O., Grimshaw, S., Kwon, K., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.253 (Depositor), 0.250 (DCC)
R-Value Work:
0.199 (Depositor), 0.200 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

2.3 Angstrom Resolution Crystal Structure of Dihydrolipoamide Dehydrogenase from Burkholderia cenocepacia in Complex with FAD and NAD.

Minasov, G., Shuvalova, L., Dubrovska, I., Kiryukhina, O., Grimshaw, S., Kwon, K., Anderson, W.F., Satchell, K.J.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

To be published.

Macromolecule Content

Total Structure Weight: 202.37 kDa
Atom Count: 14,440
Modeled Residue Count: 1,842
Deposited Residue Count: 1,864
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dihydrolipoyl dehydrogenase	A, B, C, D	466	Burkholderia cenocepacia J2315	Mutation(s): 0 Gene Names: lpdV, BCAL1215 EC: 1.8.1.4
UniProt
Find proteins for B4EEF2 (Burkholderia cenocepacia (strain ATCC BAA-245 / DSM 16553 / LMG 16656 / NCTC 13227 / J2315 / CF5610)) Explore B4EEF2 Go to UniProtKB: B4EEF2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B4EEF2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FAD (Subject of Investigation/LOI) Query on FAD Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain P [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain P [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain P [auth D]	F [auth A], G [auth A], J [auth B], M [auth C], P [auth D]	FLAVIN-ADENINE DINUCLEOTIDE C₂₇ H₃₃ N₉ O₁₅ P₂ VWWQXMAJTJZDQX-UYBVJOGSSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain P [auth D]
NAD Query on NAD Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C₂₁ H₂₇ N₇ O₁₄ P₂ BAWFJGJZGIEFAR-NNYOXOHSSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
FMN (Subject of Investigation/LOI) Query on FMN Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
ADP Query on ADP Download Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D]	K [auth B], N [auth C], Q [auth D]	ADENOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₀ P₂ XTWYTFMLZFPYCI-KQYNXXCUSA-N		Interactions Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Interactions & Density Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D]
MLT Query on MLT Download Ideal Coordinates CCD File SDF format, chain O [auth D] MOL2 format, chain O [auth D] mmCIF format, chain O [auth D]	O [auth D]	D-MALATE C₄ H₆ O₅ BJEPYKJPYRNKOW-UWTATZPHSA-N		Interactions Focus chain O [auth D] Interactions & Density Focus chain O [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth C] MOL2 format, chain E [auth A] MOL2 format, chain L [auth C] mmCIF format, chain E [auth A] mmCIF format, chain L [auth C]	E [auth A], L [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth A] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain L [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.253 (Depositor), 0.250 (DCC)
R-Value Work: 0.199 (Depositor), 0.200 (DCC)
R-Value Observed: 0.201 (Depositor)

Diffraction Data: https://doi.org/10.18430/m36cmz

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.565	α = 90
b = 107.246	β = 106.09
c = 105.427	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MoRDa	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2018-03-21

Deposition Author(s):

Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History (Full details and data files)

Version 1.0: 2018-03-21
Type: Initial release
Version 1.1: 2023-10-04
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-30
Changes: Structure summary