PDB-3wtb: Crystal structure of Gox0525

ID or keywords:

Entry

Database: PDB / ID: 3wtb

Title

Crystal structure of Gox0525

Components

Putative oxidoreductase

Keywords

OXIDOREDUCTASE / Dehydrogenase / reductase

Function / homology

Function and homology information

monocarboxylic acid metabolic process / Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor / lipid metabolic process / oxidoreductase activity
Similarity search - Function

Biological species

Gluconobacter oxydans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Yuan, Y.A. / Lin, J.P.

Citation

Journal: To be Published
Title: Crystal structure of Gox0525
Authors: Yuan, Y.A. / Lin, J.P.

History

Deposition	Apr 9, 2014	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Apr 15, 2015	Provider: repository / Type: Initial release
Revision 1.1	Nov 8, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3wtb.cif.gz	686.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3wtb.ent.gz	572.6 KB	Display	PDB format
PDBx/mmJSON format	3wtb.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3wtb_validation.pdf.gz	470.7 KB	Display	wwPDB validaton report
Full document	3wtb_full_validation.pdf.gz	493.6 KB	Display
Data in XML	3wtb_validation.xml.gz	74.3 KB	Display
Data in CIF	3wtb_validation.cif.gz	103.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/wt/3wtb ftp://data.pdbj.org/pub/pdb/validation_reports/wt/3wtb	HTTPS FTP

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Related structure data

Related structure data	3wtcC 3a28S C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5thk-5 6xex-1 4weo-d 4rf5-1 1zk3-1 3u5t-3 5thk-6 4ure-1 4one-d 6ixm-d Search similar-shape structures by Omokage search (details) 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
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (3) #77 - May 2006 Glucose Oxidase similarity (3) #188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (2)

Deposited unit

A: Putative oxidoreductase

B: Putative oxidoreductase

C: Putative oxidoreductase

D: Putative oxidoreductase

E: Putative oxidoreductase

F: Putative oxidoreductase

G: Putative oxidoreductase

H: Putative oxidoreductase

203 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative oxidoreductase

C: Putative oxidoreductase

G: Putative oxidoreductase

H: Putative oxidoreductase

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

2

B: Putative oxidoreductase

D: Putative oxidoreductase

E: Putative oxidoreductase

F: Putative oxidoreductase

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

Unit cell

Length a, b, c (Å)	58.061, 56.033, 263.992
Angle α, β, γ (deg.)	90.00, 93.20, 90.00
Int Tables number	3
Space group name H-M	P121

Components on special symmetry positions

ID	Model	Components
1	1	G-372- HOH

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	HIS	HIS	ALA	ALA	A	A	0 - 243	3 - 246
2	1	HIS	HIS	ALA	ALA	B	B	0 - 243	3 - 246
1	2	MET	MET	VAL	VAL	A	A	1 - 242	4 - 245
2	2	MET	MET	VAL	VAL	C	C	1 - 242	4 - 245
1	3	MET	MET	VAL	VAL	A	A	1 - 242	4 - 245
2	3	MET	MET	VAL	VAL	D	D	1 - 242	4 - 245
1	4	MET	MET	VAL	VAL	A	A	1 - 242	4 - 245
2	4	MET	MET	VAL	VAL	E	E	1 - 242	4 - 245
1	5	MET	MET	VAL	VAL	A	A	1 - 242	4 - 245
2	5	MET	MET	VAL	VAL	F	F	1 - 242	4 - 245
1	6	MET	MET	VAL	VAL	A	A	1 - 242	4 - 245
2	6	MET	MET	VAL	VAL	G	G	1 - 242	4 - 245
1	7	MET	MET	VAL	VAL	A	A	1 - 242	4 - 245
2	7	MET	MET	VAL	VAL	H	H	1 - 242	4 - 245
1	8	MET	MET	VAL	VAL	B	B	1 - 242	4 - 245
2	8	MET	MET	VAL	VAL	C	C	1 - 242	4 - 245
1	9	MET	MET	VAL	VAL	B	B	1 - 242	4 - 245
2	9	MET	MET	VAL	VAL	D	D	1 - 242	4 - 245
1	10	MET	MET	VAL	VAL	B	B	1 - 242	4 - 245
2	10	MET	MET	VAL	VAL	E	E	1 - 242	4 - 245
1	11	MET	MET	VAL	VAL	B	B	1 - 242	4 - 245
2	11	MET	MET	VAL	VAL	F	F	1 - 242	4 - 245
1	12	MET	MET	VAL	VAL	B	B	1 - 242	4 - 245
2	12	MET	MET	VAL	VAL	G	G	1 - 242	4 - 245
1	13	MET	MET	VAL	VAL	B	B	1 - 242	4 - 245
2	13	MET	MET	VAL	VAL	H	H	1 - 242	4 - 245
1	14	MET	MET	ALA	ALA	C	C	1 - 243	4 - 246
2	14	MET	MET	ALA	ALA	D	D	1 - 243	4 - 246
1	15	MET	MET	ALA	ALA	C	C	1 - 243	4 - 246
2	15	MET	MET	ALA	ALA	E	E	1 - 243	4 - 246
1	16	MET	MET	ALA	ALA	C	C	1 - 243	4 - 246
2	16	MET	MET	ALA	ALA	F	F	1 - 243	4 - 246
1	17	MET	MET	ALA	ALA	C	C	1 - 243	4 - 246
2	17	MET	MET	ALA	ALA	G	G	1 - 243	4 - 246
1	18	MET	MET	ALA	ALA	C	C	1 - 243	4 - 246
2	18	MET	MET	ALA	ALA	H	H	1 - 243	4 - 246
1	19	MET	MET	ALA	ALA	D	D	1 - 243	4 - 246
2	19	MET	MET	ALA	ALA	E	E	1 - 243	4 - 246
1	20	MET	MET	ALA	ALA	D	D	1 - 243	4 - 246
2	20	MET	MET	ALA	ALA	F	F	1 - 243	4 - 246
1	21	MET	MET	ALA	ALA	D	D	1 - 243	4 - 246
2	21	MET	MET	ALA	ALA	G	G	1 - 243	4 - 246
1	22	MET	MET	ALA	ALA	D	D	1 - 243	4 - 246
2	22	MET	MET	ALA	ALA	H	H	1 - 243	4 - 246
1	23	MET	MET	ALA	ALA	E	E	1 - 243	4 - 246
2	23	MET	MET	ALA	ALA	F	F	1 - 243	4 - 246
1	24	MET	MET	ALA	ALA	E	E	1 - 243	4 - 246
2	24	MET	MET	ALA	ALA	G	G	1 - 243	4 - 246
1	25	MET	MET	ALA	ALA	E	E	1 - 243	4 - 246
2	25	MET	MET	ALA	ALA	H	H	1 - 243	4 - 246
1	26	MET	MET	ALA	ALA	F	F	1 - 243	4 - 246
2	26	MET	MET	ALA	ALA	G	G	1 - 243	4 - 246
1	27	MET	MET	ALA	ALA	F	F	1 - 243	4 - 246
2	27	MET	MET	ALA	ALA	H	H	1 - 243	4 - 246
1	28	MET	MET	ALA	ALA	G	G	1 - 243	4 - 246
2	28	MET	MET	ALA	ALA	H	H	1 - 243	4 - 246

NCS ensembles :

#1: Protein	Putative oxidoreductase Mass: 25375.920 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Gluconobacter oxydans (bacteria) / Strain: 621H / Gene: GOX0525 / Production host: Escherichia coli (E. coli) References: UniProt: Q5FTJ3, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 769 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Putative oxidoreductase

Mass: 25375.920 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Gluconobacter oxydans (bacteria) / Strain: 621H / Gene: GOX0525 / Production host:

Escherichia coli (E. coli)
References: UniProt: Q5FTJ3, Oxidoreductases; Acting on the CH-OH group of donors; With NAD+ or NADP+ as acceptor

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 769 / 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: 2.11 Å³/Da / Density % sol: 41.76 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 20, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.075 Å / Relative weight: 1
Reflection	Resolution: 2.2→50 Å / Num. all: 82827 / Num. obs: 80342 / % possible obs: 97 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shell	Resolution: 2.2→2.26 Å / % possible all: 77.2

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
MOLREP		phasing
REFMAC	5.7.0029	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3A28

3a28

Resolution: 2.2→49.73 Å / Cor.coef. F_o:F_c: 0.963 / Cor.coef. F_o:F_c free: 0.951 / SU B: 8.873 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.18555	4232	5 %	RANDOM
R_work	0.1546	-	-	-
all	0.18	82827	-	-
obs	0.15616	80342	97.02 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 30.841 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.42 Å²	0 Å²	-0.27 Å²
2-	-	0.67 Å²	0 Å²
3-	-	-	-1.06 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→49.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	14124	0	0	769	14893

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.019	14326
X-RAY DIFFRACTION	r_bond_other_d	0.011	0.02	14152
X-RAY DIFFRACTION	r_angle_refined_deg	1.72	1.97	19446
X-RAY DIFFRACTION	r_angle_other_deg	1.833	3	32428
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.951	5	1938
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.141	23.985	522
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.387	15	2282
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	18.416	15	88
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	2322
X-RAY DIFFRACTION	r_gen_planes_refined	0.011	0.021	16498
X-RAY DIFFRACTION	r_gen_planes_other	0.008	0.02	3050

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	14031	0.09
1	2	B	14031	0.09
2	1	A	13801	0.09
2	2	C	13801	0.09
3	1	A	14014	0.08
3	2	D	14014	0.08
4	1	A	13753	0.09
4	2	E	13753	0.09
5	1	A	13902	0.1
5	2	F	13902	0.1
6	1	A	13792	0.1
6	2	G	13792	0.1
7	1	A	13784	0.1
7	2	H	13784	0.1
8	1	B	13799	0.09
8	2	C	13799	0.09
9	1	B	13835	0.09
9	2	D	13835	0.09
10	1	B	13714	0.1
10	2	E	13714	0.1
11	1	B	13910	0.09
11	2	F	13910	0.09
12	1	B	13764	0.1
12	2	G	13764	0.1
13	1	B	13936	0.09
13	2	H	13936	0.09
14	1	C	13844	0.09
14	2	D	13844	0.09
15	1	C	13642	0.1
15	2	E	13642	0.1
16	1	C	13835	0.1
16	2	F	13835	0.1
17	1	C	13770	0.1
17	2	G	13770	0.1
18	1	C	13849	0.1
18	2	H	13849	0.1
19	1	D	13814	0.09
19	2	E	13814	0.09
20	1	D	13841	0.1
20	2	F	13841	0.1
21	1	D	13871	0.1
21	2	G	13871	0.1
22	1	D	13903	0.09
22	2	H	13903	0.09
23	1	E	13789	0.1
23	2	F	13789	0.1
24	1	E	13955	0.09
24	2	G	13955	0.09
25	1	E	13662	0.1
25	2	H	13662	0.1
26	1	F	14052	0.09
26	2	G	14052	0.09
27	1	F	13658	0.11
27	2	H	13658	0.11
28	1	G	13751	0.11
28	2	H	13751	0.11

LS refinement shell

Resolution: 2.198→2.255 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.212	237	-
R_work	0.172	4763	-
obs	-	-	77.17 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.2053	0.0099	-0.1265	0.1592	0.0637	0.4381	-0.0099	-0.0034	0.0258	0.0268	-0.0054	-0.0144	0.034	0.0176	0.0154	0.0085	0.002	0.0087	0.0026	0.0101	0.0554	40.558	36.9346	50.4739
2	0.2873	-0.0091	0.1424	0.3613	0.025	0.5096	-0.0116	-0.0183	-0.0091	-0.0692	0.0117	-0.0376	-0.0065	0.0429	-0.0001	0.0142	-0.0002	0.0114	0.0091	0.0089	0.0485	40.2746	55.5096	83.3844
3	0.2572	0.0722	0.0737	0.1819	-0.219	0.6213	0.0121	-0.0008	0.0016	0.0364	-0.0073	0.0087	-0.0225	-0.0633	-0.0047	0.0127	-0.0081	0.0148	0.0219	-0.0026	0.0462	14.4159	52.7773	47.3038
4	0.2454	-0.0477	-0.0262	0.121	-0.2544	0.6083	-0.0163	0.0255	0.0064	-0.0222	0.016	-0.0068	0.06	-0.0534	0.0003	0.0141	-0.0141	0.0071	0.0149	-0.0038	0.047	13.9472	39.6296	82.9021
5	0.4688	-0.1017	-0.3843	0.4135	-0.0989	0.3999	0.0205	-0.0514	0.0206	0.0558	-0.0002	0.0024	-0.046	0.0475	-0.0203	0.0246	-0.011	-0.005	0.012	-0.0096	0.0467	34.142	62.2396	113.0422
6	0.1978	0.1946	0.2128	0.3999	-0.1046	0.7277	0.0148	-0.0171	-0.0037	0.0233	-0.0106	-0.0027	0.0114	-0.0175	-0.0042	0.0075	0.0031	0.0108	0.0086	0.0089	0.0446	15.6002	37.7186	113.6539
7	0.1459	-0.1224	-0.1544	0.3831	-0.1082	0.3655	0.0168	0.023	0.0077	-0.029	-0.0112	-0.0039	-0.004	-0.0311	-0.0056	0.0046	0.0016	0.0061	0.0066	0.0079	0.0446	20.3827	54.782	17.0466
8	0.2861	0.0406	0.2707	0.5507	0.0636	0.464	0.0397	0.0649	0.0144	-0.0635	-0.0186	-0.0167	0.0616	0.0439	-0.0211	0.0298	0.0111	0.0224	0.0174	0.008	0.049	38.8582	30.3316	20.2792

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 243
2	X-RAY DIFFRACTION	2	B	0 - 243
3	X-RAY DIFFRACTION	3	C	1 - 243
4	X-RAY DIFFRACTION	4	D	1 - 243
5	X-RAY DIFFRACTION	5	E	1 - 243
6	X-RAY DIFFRACTION	6	F	1 - 243
7	X-RAY DIFFRACTION	7	G	1 - 243
8	X-RAY DIFFRACTION	8	H	1 - 243

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