PDB-3gr7: Structure of OYE from Geobacillus kaustophilus, hexagonal crystal form

ID or keywords:

Entry

Database: PDB / ID: 3gr7

Title

Structure of OYE from Geobacillus kaustophilus, hexagonal crystal form

Components

NADPH dehydrogenase

Keywords

OXIDOREDUCTASE / FLAVIN / FMN / BETA-ALPHA-BARREL / Flavoprotein / NADP

Function / homology

Function and homology information

NADPH dehydrogenase / NADPH dehydrogenase activity / response to toxic substance / FMN binding / NADP binding
Similarity search - Function

Biological species

Geobacillus kaustophilus (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.3 Å

Authors

Uhl, M.K. / Gruber, K.

Citation

Journal: ADV.SYNTH.CATAL. / Year: 2011
Title: Old Yellow Enzyme-Catalyzed Dehydrogenation of Saturated Ketones
Authors: Schittmayer, M. / Zach, S. / Winkler, M. / Winkler, A. / Macheroux, P. / Uhl, M.K. / Gruber, K. / Kambourakis, S. / Rozzell, D. / Glieder, A.

History

Deposition	Mar 25, 2009	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Mar 31, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 3, 2014	Group: Database references
Revision 1.3	Nov 1, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3gr7.cif.gz	154.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3gr7.ent.gz	120.1 KB	Display	PDB format
PDBx/mmJSON format	3gr7.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3gr7_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	3gr7_full_validation.pdf.gz	1.1 MB	Display
Data in XML	3gr7_validation.xml.gz	30.3 KB	Display
Data in CIF	3gr7_validation.cif.gz	42.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gr/3gr7 ftp://data.pdbj.org/pub/pdb/validation_reports/gr/3gr7	HTTPS FTP

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Related structure data

Related structure data	3gr8C 1z41S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	3krz-d 1z44-1 3gr8-1 3kru-d 1z42-1 1z48-1 1z41-1 1jof-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: NADPH dehydrogenase

B: NADPH dehydrogenase

hetero molecules

76.7 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: NADPH dehydrogenase

B: NADPH dehydrogenase

hetero molecules

A: NADPH dehydrogenase

B: NADPH dehydrogenase

hetero molecules

defined by author&software
153 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	101.990, 101.990, 260.970
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	179
Space group name H-M	P6₅22

Components on special symmetry positions

ID	Model	Components
1	1	B-363- HOH
2	1	B-486- HOH

#1: Protein	NADPH dehydrogenase / GkOYE / Xenobiotic reductase Mass: 37725.824 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Gene: namA / Plasmid: pEamTA / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a / References: UniProt: Q5KXG9, NADPH dehydrogenase
#2: Chemical	ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₇H₂₁N₄O₉P
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.6 Å³/Da / Density % sol: 52.63 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 50mM Bis-Tris, 50mM ammonium sulfate, 30% v/v pentaerythritole ethoxylate, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54178 Å
Detector	Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 17, 2008
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54178 Å / Relative weight: 1
Reflection	Resolution: 2.3→30 Å / Num. all: 35123 / Num. obs: 35123 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15.8 % / B_iso Wilson estimate: 27.618 Å² / R_sym value: 0.136 / Net I/σ(I): 18.7
Reflection shell	Resolution: 2.3→2.44 Å / Redundancy: 15.8 % / Mean I/σ(I) obs: 4.8 / R_sym value: 0.68 / % possible all: 96.6

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Processing

Software

Name	Version	Classification
PHENIX		refinement
PDB_EXTRACT	3.006	data extraction
MAR345dtb		data collection
XDS		data reduction
XDS		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1z41

1z41

Resolution: 2.3→28.488 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.869 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.223	1748	4.98 %	random
R_work	0.2	-	-	-
all	-	35123	-	-
obs	-	35123	96.04 %	-

Solvent computation

B_sol: 57.939 Å² / k_sol: 0.392 e/Å³

Displacement parameters

B_iso max: 102.87 Å² / B_iso mean: 29.76 Å² / B_iso min: 15.29 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.786 Å²	0 Å²	0 Å²
2-	-	-0.786 Å²	0 Å²
3-	-	-	1.571 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→28.488 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5316	0	82	392	5790

Refine LS restraints

Refine-ID	Type	Dev ideal	Weight
X-RAY DIFFRACTION	f_angle_d	0.876	1
X-RAY DIFFRACTION	f_bond_d	0.003	1
X-RAY DIFFRACTION	f_chiral_restr	0.104	1
X-RAY DIFFRACTION	f_dihedral_angle_d	16.855	1
X-RAY DIFFRACTION	f_plane_restr	0.003	1
X-RAY DIFFRACTION	f_nbd_refined	4.118	1

LS refinement shell

Resolution (Å)	R_factor R_work	Num. reflection R_work	Refine-ID	Total num. of bins used	% reflection obs (%)
2.3-2.312	0.241	434	X-RAY DIFFRACTION	67	82
2.312-2.323	0.256	464	X-RAY DIFFRACTION	67	85
2.323-2.336	0.237	451	X-RAY DIFFRACTION	67	89
2.336-2.348	0.222	463	X-RAY DIFFRACTION	67	87
2.348-2.36	0.248	460	X-RAY DIFFRACTION	67	87
2.36-2.373	0.242	468	X-RAY DIFFRACTION	67	85
2.373-2.386	0.225	471	X-RAY DIFFRACTION	67	88
2.386-2.4	0.233	470	X-RAY DIFFRACTION	67	90
2.4-2.413	0.247	450	X-RAY DIFFRACTION	67	85
2.413-2.427	0.235	477	X-RAY DIFFRACTION	67	87
2.427-2.442	0.231	457	X-RAY DIFFRACTION	67	88
2.442-2.456	0.24	490	X-RAY DIFFRACTION	67	90
2.456-2.471	0.235	487	X-RAY DIFFRACTION	67	92
2.471-2.487	0.225	498	X-RAY DIFFRACTION	67	91
2.487-2.503	0.225	469	X-RAY DIFFRACTION	67	89
2.503-2.519	0.217	472	X-RAY DIFFRACTION	67	91
2.519-2.536	0.228	490	X-RAY DIFFRACTION	67	91
2.536-2.553	0.218	496	X-RAY DIFFRACTION	67	90
2.553-2.57	0.216	484	X-RAY DIFFRACTION	67	92
2.57-2.588	0.21	482	X-RAY DIFFRACTION	67	90
2.588-2.607	0.235	485	X-RAY DIFFRACTION	67	89
2.607-2.626	0.214	474	X-RAY DIFFRACTION	67	89
2.626-2.646	0.225	472	X-RAY DIFFRACTION	67	89
2.646-2.666	0.214	477	X-RAY DIFFRACTION	67	89
2.666-2.687	0.222	489	X-RAY DIFFRACTION	67	89
2.687-2.709	0.209	467	X-RAY DIFFRACTION	67	90
2.709-2.731	0.217	492	X-RAY DIFFRACTION	67	91
2.731-2.754	0.207	510	X-RAY DIFFRACTION	67	92
2.754-2.778	0.209	468	X-RAY DIFFRACTION	67	91
2.778-2.803	0.222	499	X-RAY DIFFRACTION	67	91
2.803-2.829	0.217	486	X-RAY DIFFRACTION	67	90
2.829-2.855	0.21	482	X-RAY DIFFRACTION	67	90
2.855-2.883	0.2	486	X-RAY DIFFRACTION	67	92
2.883-2.912	0.198	517	X-RAY DIFFRACTION	67	92
2.912-2.942	0.215	481	X-RAY DIFFRACTION	67	91
2.942-2.973	0.205	481	X-RAY DIFFRACTION	67	89
2.973-3.006	0.225	515	X-RAY DIFFRACTION	67	93
3.006-3.04	0.198	484	X-RAY DIFFRACTION	67	90
3.04-3.076	0.206	486	X-RAY DIFFRACTION	67	91
3.076-3.113	0.215	496	X-RAY DIFFRACTION	67	90
3.113-3.152	0.222	512	X-RAY DIFFRACTION	67	94
3.152-3.194	0.195	505	X-RAY DIFFRACTION	67	93
3.194-3.238	0.209	496	X-RAY DIFFRACTION	67	93
3.238-3.284	0.188	519	X-RAY DIFFRACTION	67	93
3.284-3.333	0.182	501	X-RAY DIFFRACTION	67	94
3.333-3.385	0.189	517	X-RAY DIFFRACTION	67	94
3.385-3.44	0.192	498	X-RAY DIFFRACTION	67	92
3.44-3.499	0.178	509	X-RAY DIFFRACTION	67	92
3.499-3.563	0.177	490	X-RAY DIFFRACTION	67	93
3.563-3.631	0.172	535	X-RAY DIFFRACTION	67	95
3.631-3.705	0.179	495	X-RAY DIFFRACTION	67	91
3.705-3.786	0.177	515	X-RAY DIFFRACTION	67	93
3.786-3.874	0.174	507	X-RAY DIFFRACTION	67	94
3.874-3.97	0.169	505	X-RAY DIFFRACTION	67	92
3.97-4.077	0.152	533	X-RAY DIFFRACTION	67	94
4.077-4.197	0.169	521	X-RAY DIFFRACTION	67	95
4.197-4.332	0.152	521	X-RAY DIFFRACTION	67	94
4.332-4.486	0.148	518	X-RAY DIFFRACTION	67	93
4.486-4.665	0.173	542	X-RAY DIFFRACTION	67	95
4.665-4.876	0.172	530	X-RAY DIFFRACTION	67	95
4.876-5.132	0.177	526	X-RAY DIFFRACTION	67	94
5.132-5.451	0.197	537	X-RAY DIFFRACTION	67	95
5.451-5.869	0.217	542	X-RAY DIFFRACTION	67	94
5.869-6.453	0.22	561	X-RAY DIFFRACTION	67	96
6.453-7.373	0.219	558	X-RAY DIFFRACTION	67	94
7.373-9.236	0.202	578	X-RAY DIFFRACTION	67	96
9.236-28.49	0.241	624	X-RAY DIFFRACTION	67	95

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