PDB-4iqg: Crystal structure of BPRO0239 oxidoreductase from Polaromonas sp....

ID or keywords:

Entry

Database: PDB / ID: 4iqg

Title

Crystal structure of BPRO0239 oxidoreductase from Polaromonas sp. JS666 in NADP bound form

Components

Short-chain dehydrogenase/reductase SDR

Keywords

OXIDOREDUCTASE /

Structural Genomics / NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM / NADP-binding protein / PSI-Biology /

Protein Structure Initiative / NYSGRC / NAD-binding Rossmann fold /

short-chain dehydrogenase/reductase

Function / homology

Function and homology information

oxidoreductase activity /

nucleotide binding
Similarity search - Function

Biological species

Polaromonas sp. JS666 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Niedzialkowska, E. / Majorek, K.A. / Porebski, P.J. / Al Obaidi, N. / Hammonds, J. / Hillerich, B. / Seidel, R. / Bonanno, J.B. / Almo, S.C. / Minor, W. / New York Structural Genomics Research Consortium (NYSGRC)

Citation

Journal: To be Published
Title: Crystal structure of oxidoreductase from Polaromonas sp. in NADP bound form
Authors: Niedzialkowska, E. / Majorek, K.A. / Porebski, P.J. / Al Obaidi, N. / Hammonds, J. / Hillerich, B. / Seidel, R. / Bonanno, J.B. / Almo, S.C. / Minor, W. / New York Structural Genomics ...

History

Deposition	Jan 11, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 30, 2013	Provider: repository / Type: Initial release
Revision 1.1	Nov 15, 2017	Group: Refinement description / Category: software
Revision 1.2	Apr 13, 2022	Group: Database references / Derived calculations / Structure summary Category: audit_author / citation_author ...audit_author / citation_author / database_2 / struct_conn / struct_ref_seq_dif / struct_site Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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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Download

PDBx/mmCIF format	4iqg.cif.gz	375.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4iqg.ent.gz	322.4 KB	Display	PDB format
PDBx/mmJSON format	4iqg.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/iq/4iqg ftp://data.pdbj.org/pub/pdb/validation_reports/iq/4iqg	HTTPS FTP

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Related structure data

Similar structure data	6t77-1 1q7c-1 2pd6-d 6t5x-1 2uvd-2 3wtc-1 4dry-d 3gk3-d 4u0j-1 1q7b-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: NYSGRC-014123

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (2) #77 - May 2006 Glucose Oxidase similarity (2) #90 - Jun 2007 Fatty Acid Synthase similarity (2)

Deposited unit

C: Short-chain dehydrogenase/reductase SDR

A: Short-chain dehydrogenase/reductase SDR

B: Short-chain dehydrogenase/reductase SDR

D: Short-chain dehydrogenase/reductase SDR

hetero molecules

119 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	68.142, 97.710, 70.665
Angle α, β, γ (deg.)	90.00, 97.32, 90.00
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	C
2	1	A
1	2	C
2	2	B
1	3	C
2	3	D
1	4	A
2	4	B
1	5	A
2	5	D
1	6	B
2	6	D

NCS domain segments:

Dom-ID	Ens-ID	Auth asym-ID	Auth seq-ID
1	1	C	2 - 248
2	1	A	2 - 248
1	2	C	2 - 248
2	2	B	2 - 248
1	3	C	2 - 247
2	3	D	2 - 247
1	4	A	2 - 248
2	4	B	2 - 248
1	5	A	1 - 248
2	5	D	1 - 248
1	6	B	2 - 247
2	6	D	2 - 247

NCS ensembles :

ID
1
2
3
4
5
6

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Protein , 1 types, 4 molecules CABD

#1: Protein	Short-chain dehydrogenase/reductase SDR Mass: 28729.428 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Polaromonas sp. JS666 (bacteria) / Strain: JS666 / Gene: Bpro_0239 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q12GY8

#1: Protein

Short-chain dehydrogenase/reductase SDR

Mass: 28729.428 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Polaromonas sp. JS666 (bacteria) / Strain: JS666 / Gene: Bpro_0239 / Plasmid: pSGC-His / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q12GY8

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Non-polymers , 5 types, 583 molecules

#2: Chemical	ChemComp-FMT / FORMIC ACID / Formic acid Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH₂O₂
#3: Chemical	ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₈N₇O₁₇P₃
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 568 / 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: 2.03 Å³/Da / Density % sol: 39.42 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 0.15 M sodium formate, 20% PEG 3350, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 10, 2012 / Details: beryllium lens
Radiation	Monochromator: C(111) diamond laue monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 1.85→50 Å / Num. all: 78447 / Num. obs: 78447 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / R_merge(I) obs: 0.082
Reflection shell	Resolution: 1.85→1.88 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.683 / % possible all: 100

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Processing

Software

Name	Version	Classification
HKL-3000		phasing
MOLREP		phasing
REFMAC	5.7.0029	refinement
Coot		model building
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.85→40.11 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.964 / SU B: 4.812 / SU ML: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.17304	3936	5 %	RANDOM
R_work	0.14845	-	-	-
all	0.14971	74288	-	-
obs	0.14971	74288	99.86 %	-

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: 30.652 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.41 Å²	0 Å²	1.02 Å²
2-	-	-1.29 Å²	0 Å²
3-	-	-	-0.24 Å²

Refinement step

Cycle: LAST / Resolution: 1.85→40.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7048	0	232	568	7848

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.019	7454
X-RAY DIFFRACTION	r_bond_other_d	0.009	0.02	7224
X-RAY DIFFRACTION	r_angle_refined_deg	1.88	2.001	10156
X-RAY DIFFRACTION	r_angle_other_deg	1.522	3	16450
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.981	5	1006
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.904	23.206	287
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.033	15	1097
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.153	15	72
X-RAY DIFFRACTION	r_chiral_restr	0.111	0.2	1214
X-RAY DIFFRACTION	r_gen_planes_refined	0.01	0.02	8657
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	1701

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	C	13471	0.08
1	2	A	13471	0.08
2	1	C	14473	0.06
2	2	B	14473	0.06
3	1	C	14199	0.07
3	2	D	14199	0.07
4	1	A	13458	0.08
4	2	B	13458	0.08
5	1	A	13640	0.08
5	2	D	13640	0.08
6	1	B	14327	0.07
6	2	D	14327	0.07

LS refinement shell

Resolution: 1.85→1.898 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.259	274	-
R_work	0.216	5494	-
obs	-	-	99.98 %

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	4.5689	0.7029	-0.6247	4.5283	0.7037	2.1765	0.0815	0.0112	0.2433	-0.382	-0.01	-0.473	-0.2123	0.0821	-0.0715	0.1842	-0.0146	0.1383	0.2059	0.0387	0.1471	61.639	31.425	38.438
2	4.8254	3.5432	0.8613	7.4339	0.7539	5.231	0.0183	0.3073	0.3926	-0.4683	-0.0304	-0.3997	-0.6767	0.0116	0.0122	0.4373	-0.032	0.2162	0.3051	0.0654	0.2211	61.629	35.098	30.896
3	19.8534	7.7265	6.1526	3.8444	3.2654	6.4526	-0.1208	0.2641	0.3003	-0.543	0.1344	-0.1446	-0.095	0.0317	-0.0136	0.4967	-0.0383	0.2086	0.338	0.0143	0.1774	61.876	20.907	27.449
4	1.3461	0.2116	0.0879	1.1089	-0.0148	0.8192	0.0052	0.2434	0.1345	-0.3184	0.0383	-0.1209	-0.0556	0.0342	-0.0436	0.1296	-0.0042	0.0253	0.233	0.026	0.054	49.243	20.402	40.674
5	2.7785	-1.1895	-0.2884	2.7562	-0.285	0.6684	0.0105	-0.0712	0.2791	-0.09	0.0666	-0.1343	-0.177	-0.0061	-0.0771	0.07	0.0056	0.0111	0.201	-0.0013	0.0715	53.194	30.384	52.072
6	3.0996	1.2644	-0.1403	2.8065	0.9028	1.2419	0.1167	-0.3441	0.2363	0.2874	-0.1415	-0.0681	-0.0948	0.0159	0.0248	0.0831	-0.0384	-0.0573	0.2582	-0.0352	0.1361	62.928	32.7	77.589
7	1.0325	0.549	0.0043	1.3477	-0.0452	0.817	0.0694	-0.1874	0.0496	0.1519	-0.0981	-0.1612	0.0149	0.0779	0.0287	0.0216	-0.0116	-0.0291	0.2095	-0.0146	0.0761	50.051	22.254	72.311
8	2.8562	-1.0844	0.3526	3.139	0.032	1.4437	0.0494	-0.0615	-0.1577	-0.162	0.0188	-0.2983	0.1642	0.1481	-0.0682	0.0323	0.0026	0.0046	0.2035	0.0052	0.0804	59.186	20.406	60.603
9	5.0778	0.0749	-0.0233	3.9117	-0.5214	2.549	-0.012	0.4512	-0.399	-0.4326	-0.0738	0.3718	0.3326	-0.0134	0.0858	0.2092	0.0233	-0.0991	0.2835	-0.0911	0.1216	22.109	-3.511	39.347
10	14.3579	2.5849	-2.9791	1.187	0.6226	4.2548	-0.1535	0.7724	0.0726	-0.4327	0.1986	0.2319	-0.0515	0.1087	-0.045	0.4245	-0.0156	-0.2298	0.485	0.0141	0.1766	22.662	7.95	29.747
11	1.7234	0.4575	-0.2796	1.0312	-0.0119	0.8879	0.0034	0.2899	-0.0431	-0.327	0.0033	0.0229	0.051	-0.031	-0.0067	0.1486	0.0127	-0.0382	0.2368	0.0106	0.0276	35.192	10.72	41.745
12	11.0697	-3.2102	2.1382	1.537	2.6374	17.9618	0.171	-0.0661	-0.1096	-0.045	0.1582	-0.029	0.1142	0.633	-0.3292	0.5705	0.0782	0.0497	0.3899	-0.0699	0.5479	45.937	-6.659	46.332
13	2.4805	-1.2897	0.084	2.953	0.1921	0.3041	0.0075	-0.1371	-0.1183	-0.0213	0.0126	0.0178	0.105	0.0146	-0.02	0.0646	0.0051	-0.0258	0.2027	0.0071	0.0264	31.272	3.267	54.74
14	2.6549	0.1042	-0.2912	1.8803	-0.7308	2.037	0.0271	-0.2721	-0.1925	0.2212	-0.0448	0.2002	0.1371	-0.0466	0.0178	0.0688	-0.0441	0.0205	0.2489	-0.0017	0.0948	21.467	4.778	80.101
15	1.1716	0.4154	-0.1994	1.6574	-0.0123	1.084	0.0768	-0.1772	0.1069	0.1311	-0.0653	0.1537	-0.0111	-0.0118	-0.0114	0.0236	-0.0176	-0.0038	0.212	-0.0224	0.0509	34.512	14.458	73.109
16	2.7604	-1.461	-0.4718	3.5543	0.1266	1.9904	0.0592	-0.0004	0.2848	-0.2135	-0.0332	0.1979	-0.1245	-0.1571	-0.0261	0.0336	-0.0021	-0.0318	0.2067	-0.0116	0.0886	24.88	14.433	61.32

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 34
2	X-RAY DIFFRACTION	2	A	35 - 62
3	X-RAY DIFFRACTION	3	A	63 - 79
4	X-RAY DIFFRACTION	4	A	80 - 192
5	X-RAY DIFFRACTION	5	A	211 - 248
6	X-RAY DIFFRACTION	6	B	2 - 80
7	X-RAY DIFFRACTION	7	B	81 - 202
8	X-RAY DIFFRACTION	8	B	203 - 248
9	X-RAY DIFFRACTION	9	C	2 - 58
10	X-RAY DIFFRACTION	10	C	59 - 80
11	X-RAY DIFFRACTION	11	C	81 - 192
12	X-RAY DIFFRACTION	12	C	193 - 210
13	X-RAY DIFFRACTION	13	C	211 - 248
14	X-RAY DIFFRACTION	14	D	1 - 80
15	X-RAY DIFFRACTION	15	D	81 - 202
16	X-RAY DIFFRACTION	16	D	203 - 248

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