3GBH | pdb_00003gbh

CRYSTAL STRUCTURE OF A PUTATIVE NAD(P)H:FMN OXIDOREDUCTASE (SE1966) FROM STAPHYLOCOCCUS EPIDERMIDIS ATCC 12228 AT 2.00 A RESOLUTION

PDB DOI: https://doi.org/10.2210/pdb3GBH/pdb

Classification: OXIDOREDUCTASE
Organism(s): Staphylococcus epidermidis ATCC 12228
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2009-02-19 Released: 2009-03-03
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.185 (Depositor), 0.195 (DCC)
R-Value Work:
0.146 (Depositor), 0.158 (DCC)
R-Value Observed:
0.148 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of putative NAD(P)H:FMN oxidoreductase (NP_765521.1) from Staphylococcus epidermidis ATCC 12228 at 2.00 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Macromolecule Content

Total Structure Weight: 101.98 kDa
Atom Count: 7,605
Modeled Residue Count: 847
Deposited Residue Count: 852
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD(P)H-flavin oxidoreductase	A, B, C, D	213	Staphylococcus epidermidis ATCC 12228	Mutation(s): 0 Gene Names: NP_765521.1, SE_1966
UniProt
Find proteins for A0A0H2VHN8 (Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200)) Explore A0A0H2VHN8 Go to UniProtKB: A0A0H2VHN8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A0H2VHN8
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
FMN Query on FMN Download:Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain O [auth C] SDF format, chain H [auth B] SDF format, chain E [auth A] MOL2 format, chain S [auth D] MOL2 format, chain O [auth C] MOL2 format, chain H [auth B] MOL2 format, chain E [auth A] mmCIF format, chain S [auth D] mmCIF format, chain O [auth C] mmCIF format, chain H [auth B] mmCIF format, chain E [auth A]	E [auth A], H [auth B], O [auth C], S [auth D]	FLAVIN MONONUCLEOTIDE C₁₇ H₂₁ N₄ O₉ P FVTCRASFADXXNN-SCRDCRAPSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Focus chain O [auth C] Focus chain S [auth D] Interactions & Density Focus chain E [auth A] Focus chain H [auth B] Focus chain O [auth C] Focus chain S [auth D]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain V [auth D] SDF format, chain L [auth B] MOL2 format, chain V [auth D] MOL2 format, chain L [auth B] mmCIF format, chain V [auth D] mmCIF format, chain L [auth B]	L [auth B], V [auth D]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain L [auth B] Focus chain V [auth D] Interactions & Density Focus chain L [auth B] Focus chain V [auth D]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain U [auth D] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain G [auth A] MOL2 format, chain U [auth D] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain G [auth A] mmCIF format, chain U [auth D] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain G [auth A]	G [auth A] J [auth B] K [auth B] Q [auth C] R [auth C] G [auth A], J [auth B], K [auth B], Q [auth C], R [auth C], U [auth D]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D] Interactions & Density Focus chain G [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain Q [auth C] Focus chain R [auth C] Focus chain U [auth D]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain N [auth B] SDF format, chain M [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] mmCIF format, chain Y [auth D] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B]	M [auth B], N [auth B], W [auth D], X [auth D], Y [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain M [auth B] Focus chain N [auth B] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D] Interactions & Density Focus chain M [auth B] Focus chain N [auth B] Focus chain W [auth D] Focus chain X [auth D] Focus chain Y [auth D]
UNL Query on UNL Download:Ideal Coordinates CCD File	F [auth A], I [auth B], P [auth C], T [auth D]	Unknown ligand BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain I [auth B] Focus chain P [auth C] Focus chain T [auth D] Interactions & Density Focus chain F [auth A] Focus chain I [auth B] Focus chain P [auth C] Focus chain T [auth D]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B, C, D	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.185 (Depositor), 0.195 (DCC)
R-Value Work: 0.146 (Depositor), 0.158 (DCC)
R-Value Observed: 0.148 (Depositor)

Diffraction Data:

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.85	α = 90
b = 86.15	β = 90
c = 160.9	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
SHELXD	phasing
autoSHARP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-03-03

Deposition Author(s):

Joint Center for Structural Genomics (JCSG)

Revision History (Full details and data files)

Version 1.0: 2009-03-03
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Refinement description, Version format compliance
Version 1.2: 2017-10-25
Changes: Author supporting evidence, Refinement description
Version 1.3: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.4: 2023-02-01
Changes: Database references, Derived calculations
Version 1.5: 2024-10-30
Changes: Data collection, Structure summary

3GBH | pdb_00003gbh

CRYSTAL STRUCTURE OF A PUTATIVE NAD(P)H:FMN OXIDOREDUCTASE (SE1966) FROM STAPHYLOCOCCUS EPIDERMIDIS ATCC 12228 AT 2.00 A RESOLUTION

Literature

Crystal structure of putative NAD(P)H:FMN oxidoreductase (NP_765521.1) from Staphylococcus epidermidis ATCC 12228 at 2.00 A resolution

Biological Assembly 1

Biological Assembly 2

Macromolecules

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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