5H5X | pdb_00005h5x

Crystal structure of NADH bound carbonyl reductase from Streptomyces coelicolor

PDB DOI: https://doi.org/10.2210/pdb5H5X/pdb

Classification: OXIDOREDUCTASE
Organism(s): Streptomyces coelicolor A3(2)
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-11-10 Released: 2017-05-10
Deposition Author(s): Kong, X.-D., Xu, J.-H., Zhou, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.243 (Depositor), 0.244 (DCC)
R-Value Work:
0.179 (Depositor), 0.182 (DCC)
R-Value Observed:
0.182 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal structure of NADH bound carbonyl reductase from Streptomyces coelicolor

Li, M., Kong, X.-D., Zhou, J., Yu, H.-L., Zhang, Z.-J., Xu, J.-H.

To be published.

Macromolecule Content

Total Structure Weight: 326.5 kDa
Atom Count: 23,002
Modeled Residue Count: 3,017
Deposited Residue Count: 3,156
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative oxidoreductase	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	263	Streptomyces coelicolor A3(2)	Mutation(s): 0 Gene Names: SCO7363
UniProt
Find proteins for Q9KYM4 (Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145)) Explore Q9KYM4 Go to UniProtKB: Q9KYM4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9KYM4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAI Query on NAI Download:Ideal Coordinates CCD File SDF format, chain Z [auth E] SDF format, chain WA [auth L] SDF format, chain W [auth D] SDF format, chain TA [auth K] SDF format, chain S [auth C] SDF format, chain RA [auth J] SDF format, chain P [auth B] SDF format, chain NA [auth I] SDF format, chain M [auth A] SDF format, chain JA [auth H] SDF format, chain GA [auth G] SDF format, chain DA [auth F] MOL2 format, chain Z [auth E] MOL2 format, chain WA [auth L] MOL2 format, chain W [auth D] MOL2 format, chain TA [auth K] MOL2 format, chain S [auth C] MOL2 format, chain RA [auth J] MOL2 format, chain P [auth B] MOL2 format, chain NA [auth I] MOL2 format, chain M [auth A] MOL2 format, chain JA [auth H] MOL2 format, chain GA [auth G] MOL2 format, chain DA [auth F] mmCIF format, chain Z [auth E] mmCIF format, chain WA [auth L] mmCIF format, chain W [auth D] mmCIF format, chain TA [auth K] mmCIF format, chain S [auth C] mmCIF format, chain RA [auth J] mmCIF format, chain P [auth B] mmCIF format, chain NA [auth I] mmCIF format, chain M [auth A] mmCIF format, chain JA [auth H] mmCIF format, chain GA [auth G] mmCIF format, chain DA [auth F]	DA [auth F] GA [auth G] JA [auth H] M [auth A] NA [auth I] DA [auth F], GA [auth G], JA [auth H], M [auth A], NA [auth I], P [auth B], RA [auth J], S [auth C], TA [auth K], W [auth D], WA [auth L], Z [auth E]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C₂₁ H₂₉ N₇ O₁₄ P₂ BOPGDPNILDQYTO-NNYOXOHSSA-N		Interactions Focus chain DA [auth F] Focus chain GA [auth G] Focus chain JA [auth H] Focus chain M [auth A] Focus chain NA [auth I] Focus chain P [auth B] Focus chain RA [auth J] Focus chain S [auth C] Focus chain TA [auth K] Focus chain W [auth D] Focus chain WA [auth L] Focus chain Z [auth E] Interactions & Density Focus chain DA [auth F] Focus chain GA [auth G] Focus chain JA [auth H] Focus chain M [auth A] Focus chain NA [auth I] Focus chain P [auth B] Focus chain RA [auth J] Focus chain S [auth C] Focus chain TA [auth K] Focus chain W [auth D] Focus chain WA [auth L] Focus chain Z [auth E]
IPA Query on IPA Download:Ideal Coordinates CCD File SDF format, chain ZA [auth L] SDF format, chain YA [auth L] SDF format, chain X [auth D] SDF format, chain VA [auth K] SDF format, chain V [auth C] SDF format, chain UA [auth K] SDF format, chain T [auth C] SDF format, chain SA [auth J] SDF format, chain R [auth B] SDF format, chain QA [auth I] SDF format, chain Q [auth B] SDF format, chain PA [auth I] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain MA [auth H] SDF format, chain LA [auth H] SDF format, chain IA [auth G] SDF format, chain HA [auth G] SDF format, chain FA [auth F] SDF format, chain EA [auth F] SDF format, chain CA [auth E] SDF format, chain BA [auth E] MOL2 format, chain ZA [auth L] MOL2 format, chain YA [auth L] MOL2 format, chain X [auth D] MOL2 format, chain VA [auth K] MOL2 format, chain V [auth C] MOL2 format, chain UA [auth K] MOL2 format, chain T [auth C] MOL2 format, chain SA [auth J] MOL2 format, chain R [auth B] MOL2 format, chain QA [auth I] MOL2 format, chain Q [auth B] MOL2 format, chain PA [auth I] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain MA [auth H] MOL2 format, chain LA [auth H] MOL2 format, chain IA [auth G] MOL2 format, chain HA [auth G] MOL2 format, chain FA [auth F] MOL2 format, chain EA [auth F] MOL2 format, chain CA [auth E] MOL2 format, chain BA [auth E] mmCIF format, chain ZA [auth L] mmCIF format, chain YA [auth L] mmCIF format, chain X [auth D] mmCIF format, chain VA [auth K] mmCIF format, chain V [auth C] mmCIF format, chain UA [auth K] mmCIF format, chain T [auth C] mmCIF format, chain SA [auth J] mmCIF format, chain R [auth B] mmCIF format, chain QA [auth I] mmCIF format, chain Q [auth B] mmCIF format, chain PA [auth I] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain MA [auth H] mmCIF format, chain LA [auth H] mmCIF format, chain IA [auth G] mmCIF format, chain HA [auth G] mmCIF format, chain FA [auth F] mmCIF format, chain EA [auth F] mmCIF format, chain CA [auth E] mmCIF format, chain BA [auth E]	BA [auth E] CA [auth E] EA [auth F] FA [auth F] HA [auth G] BA [auth E], CA [auth E], EA [auth F], FA [auth F], HA [auth G], IA [auth G], LA [auth H], MA [auth H], N [auth A], O [auth A], PA [auth I], Q [auth B], QA [auth I], R [auth B], SA [auth J], T [auth C], UA [auth K], V [auth C], VA [auth K], X [auth D], YA [auth L], ZA [auth L]	ISOPROPYL ALCOHOL C₃ H₈ O KFZMGEQAYNKOFK-UHFFFAOYSA-N		Interactions Focus chain BA [auth E] Focus chain CA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain HA [auth G] Focus chain IA [auth G] Focus chain LA [auth H] Focus chain MA [auth H] Focus chain N [auth A] Focus chain O [auth A] Focus chain PA [auth I] Focus chain Q [auth B] Focus chain QA [auth I] Focus chain R [auth B] Focus chain SA [auth J] Focus chain T [auth C] Focus chain UA [auth K] Focus chain V [auth C] Focus chain VA [auth K] Focus chain X [auth D] Focus chain YA [auth L] Focus chain ZA [auth L] Interactions & Density Focus chain BA [auth E] Focus chain CA [auth E] Focus chain EA [auth F] Focus chain FA [auth F] Focus chain HA [auth G] Focus chain IA [auth G] Focus chain LA [auth H] Focus chain MA [auth H] Focus chain N [auth A] Focus chain O [auth A] Focus chain PA [auth I] Focus chain Q [auth B] Focus chain QA [auth I] Focus chain R [auth B] Focus chain SA [auth J] Focus chain T [auth C] Focus chain UA [auth K] Focus chain V [auth C] Focus chain VA [auth K] Focus chain X [auth D] Focus chain YA [auth L] Focus chain ZA [auth L]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain XA [auth L] SDF format, chain U [auth C] SDF format, chain OA [auth I] SDF format, chain KA [auth H] SDF format, chain AA [auth E] MOL2 format, chain Y [auth D] MOL2 format, chain XA [auth L] MOL2 format, chain U [auth C] MOL2 format, chain OA [auth I] MOL2 format, chain KA [auth H] MOL2 format, chain AA [auth E] mmCIF format, chain Y [auth D] mmCIF format, chain XA [auth L] mmCIF format, chain U [auth C] mmCIF format, chain OA [auth I] mmCIF format, chain KA [auth H] mmCIF format, chain AA [auth E]	AA [auth E] KA [auth H] OA [auth I] U [auth C] XA [auth L] AA [auth E], KA [auth H], OA [auth I], U [auth C], XA [auth L], Y [auth D]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth E] Focus chain KA [auth H] Focus chain OA [auth I] Focus chain U [auth C] Focus chain XA [auth L] Focus chain Y [auth D] Interactions & Density Focus chain AA [auth E] Focus chain KA [auth H] Focus chain OA [auth I] Focus chain U [auth C] Focus chain XA [auth L] Focus chain Y [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.243 (Depositor), 0.244 (DCC)
R-Value Work: 0.179 (Depositor), 0.182 (DCC)
R-Value Observed: 0.182 (Depositor)

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 187.787	α = 90
b = 187.787	β = 90
c = 80.858	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data collection
HKL-2000	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHASER	phasing
HKL	data reduction
HKL	data scaling