PDB-5tqv: Crystal structure of NADP-dependent carbonyl reductase from Burkh...

ID or keywords:

Entry

Database: PDB / ID: 5tqv

Title

Crystal structure of NADP-dependent carbonyl reductase from Burkholderia multivorans

Components

NADPH-dependent carbonyl reductase

Keywords

OXIDOREDUCTASE / SSGCID / SDR / short-chain dehydrogenase reductase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

carbonyl reductase (NADPH) / carbonyl reductase (NADPH) activity / nucleotide binding
Similarity search - Function

Biological species

Burkholderia multivorans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.65 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: TO BE PUBLISHED
Title: Crystal structure of NADP-dependent carbonyl reductase from Burkholderia multivorans
Authors: Mayclin, S.J. / Abendroth, J. / Lorimer, D. / Edwards, T.E.

History

Deposition	Oct 24, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 9, 2016	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software / Item: _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Oct 4, 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5tqv.cif.gz	190.8 KB	Display	PDBx/mmCIF format
PDB format	pdb5tqv.ent.gz	150 KB	Display	PDB format
PDBx/mmJSON format	5tqv.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	5tqv_validation.pdf.gz	420.3 KB	Display	wwPDB validaton report
Full document	5tqv_full_validation.pdf.gz	420.8 KB	Display
Data in XML	5tqv_validation.xml.gz	21.1 KB	Display
Data in CIF	5tqv_validation.cif.gz	31.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tq/5tqv ftp://data.pdbj.org/pub/pdb/validation_reports/tq/5tqv	HTTPS FTP

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Related structure data

Related structure data	5idqS S: Starting model for refinement
Similar structure data	5idw-d 5u1p-1 4dyv-2 7bys-1 3nr1-d 6hc6-1 3iib-d 2ehd-d 5n2i-2 2p30-2 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: SSGCID-BumuA.00010.e

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1)

Deposited unit

A: NADPH-dependent carbonyl reductase

B: NADPH-dependent carbonyl reductase

50.2 kDa, 2 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)	58.710, 79.250, 86.830
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	NADPH-dependent carbonyl reductase Mass: 25108.457 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia multivorans (strain ATCC 17616 / 249) (bacteria) Strain: ATCC 17616 / 249 / Gene: cbr, BMULJ_02877 / Plasmid: BumuA.00010.e.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3KHT8, carbonyl reductase (NADPH)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

NADPH-dependent carbonyl reductase

Mass: 25108.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Burkholderia multivorans (strain ATCC 17616 / 249) (bacteria)
Strain: ATCC 17616 / 249 / Gene: cbr, BMULJ_02877 / Plasmid: BumuA.00010.e.B1 / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3KHT8, carbonyl reductase (NADPH)

#2: 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: 2.06 Å³/Da / Density % sol: 39 % / Mosaicity: 0.122 °
Crystal grow	Temperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: MORPHEUS A6: 10% w/v PEG8000, 20% v/v ethylene glycol, 30mM MgCl2, 30mM CaCl2, 100mM MOPS/HEPES-NA pH 7.5; protein conc 23.4mg/mL, direct cryo, puck gdy5-4, source plate 274121a6

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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: RAYONIX MX-300 / Detector: CCD / Date: Jul 5, 2016

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 1.65→50 Å / Num. obs: 49378 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6.07 % / B_iso Wilson estimate: 20.71 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.055 / Net I/σ(I): 17.98

Reflection shell

Resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	CC_1/2	Diffraction-ID	% possible all
1.65-1.69	0.577	3.06	0.889	1	99.9
1.69-1.74	0.429	4.07	0.935	1	100
1.74-1.79	0.35	4.96	0.949	1	100
1.79-1.84	0.262	6.37	0.976	1	100
1.84-1.91	0.209	7.89	0.982	1	100
1.91-1.97	0.17	9.81	0.986	1	99.8
1.97-2.05	0.127	12.44	0.992	1	100
2.05-2.13	0.106	14.62	0.994	1	99.9
2.13-2.22	0.082	18.08	0.996	1	100
2.22-2.33	0.076	19.99	0.996	1	99.9
2.33-2.46	0.062	23.91	0.998	1	100
2.46-2.61	0.059	25.29	0.997	1	99.8
2.61-2.79	0.051	28.63	0.998	1	99.9
2.79-3.01	0.045	32.51	0.998	1	100
3.01-3.3	0.04	35.76	0.998	1	99.8
3.3-3.69	0.038	38.47	0.998	1	99.8
3.69-4.26	0.036	40.56	0.999	1	99.6
4.26-5.22	0.034	41.89	0.999	1	99.9
5.22-7.38	0.035	40.44	0.998	1	99.3
7.38-50	0.035	38.65	0.997	1	95.3

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
MOLREP		phasing
PHENIX	(dev_2499)	refinement
PDB_EXTRACT	3.2	data extraction
Coot		model building
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5idq

5idq

Resolution: 1.65→27.527 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.2

	R_factor	Num. reflection	% reflection
R_free	0.2004	1917	3.88 %
R_work	0.1665	-	-
obs	0.1678	49360	99.84 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso max: 93.38 Å² / B_iso mean: 30.2892 Å² / B_iso min: 12.96 Å²

Refinement step

Cycle: final / Resolution: 1.65→27.527 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3299	0	0	404	3703
B_iso mean	-	-	-	39.42	-
Num. residues	-	-	-	-	442

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	3436
X-RAY DIFFRACTION	f_angle_d	0.763	4698
X-RAY DIFFRACTION	f_chiral_restr	0.052	553
X-RAY DIFFRACTION	f_plane_restr	0.005	611
X-RAY DIFFRACTION	f_dihedral_angle_d	16.329	2066

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.6499-1.6912	0.2927	126	0.2386	3331	3457	100
1.6912-1.7369	0.2652	130	0.2207	3364	3494	100
1.7369-1.788	0.2782	126	0.208	3357	3483	100
1.788-1.8457	0.2401	151	0.1946	3341	3492	100
1.8457-1.9116	0.2321	125	0.184	3351	3476	100
1.9116-1.9882	0.2404	155	0.1809	3346	3501	100
1.9882-2.0786	0.2051	143	0.1732	3347	3490	100
2.0786-2.1882	0.2173	139	0.1711	3390	3529	100
2.1882-2.3252	0.231	149	0.1707	3343	3492	100
2.3252-2.5046	0.1872	150	0.16	3376	3526	100
2.5046-2.7564	0.2218	117	0.1699	3425	3542	100
2.7564-3.1548	0.1968	146	0.1643	3413	3559	100
3.1548-3.9728	0.168	127	0.1519	3477	3604	100
3.9728-27.5311	0.1688	133	0.1516	3582	3715	99

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	4.5993	-1.3622	-0.9498	4.5464	-2.3806	4.5392	-0.0888	0.0396	-0.0454	0.1535	0.2417	0.4621	-0.1305	-0.3967	-0.0918	0.1347	-0.0124	-0.0234	0.1748	0.0332	0.2608	-38.1234	-11.0723	16.2544
2	2.0937	0.1416	-1.6987	5.733	-0.6412	2.2019	0.2304	-0.1333	-0.2109	0.8068	-0.1039	-0.2645	-0.0043	0.0011	-0.1528	0.3243	-0.0506	-0.0975	0.2215	0.047	0.1702	-27.2525	-13.4879	23.2681
3	2.2076	0.4482	0.3674	2.096	-1.4049	1.1491	0.1297	0.0649	-0.3454	-0.0511	-0.1194	0.3656	0.3148	-0.0921	-0.0065	0.1946	0.0078	-0.0461	0.1896	-0.0073	0.191	-28.3511	-11.6931	13.3057
4	1.3367	1.1462	0.5895	4.5273	0.894	0.8433	0.0621	-0.0481	-0.0627	0.0867	-0.0086	-0.2803	0.0359	0.0138	-0.0534	0.1603	0.0086	0.0049	0.1774	0.0086	0.1527	-20.1887	-0.0006	17.9455
5	1.9664	1.7091	0.4774	4.7986	1.5828	1.8061	-0.0802	0.3629	0.1274	-0.3041	0.1507	0.1808	-0.0288	0.0934	-0.0375	0.1375	0.014	-0.0279	0.1796	0.0123	0.1126	-24.3037	4.2677	6.428
6	2.654	0.5392	0.8598	3.4112	0.3692	1.2158	0.0085	0.1784	-0.0082	-0.2017	0.0318	0.0572	0.0114	-0.0345	-0.0228	0.1556	-0.0122	-0.0069	0.1648	0.0193	0.093	-25.2698	1.4401	8.9724
7	2.3695	0.8561	0.4712	2.5767	0.0318	1.2593	-0.0976	0.5296	-0.0568	-0.6688	0.1042	0.185	0.0577	0.1036	-0.0063	0.3143	-0.0134	-0.0698	0.2952	-0.0072	0.1454	-30.7596	-3.3885	0.192
8	5.2278	0.9325	-2.3537	2.3286	0.6883	4.9733	0.0924	-0.0678	0.7281	0.007	-0.0307	-0.3197	-0.0647	0.2944	-0.0317	0.1346	-0.0011	0.0209	0.2316	0.0155	0.3935	8.4728	17.7421	14.1802
9	6.3808	0.7248	-2.4053	1.778	-0.0801	4.3702	0.2181	-0.9759	0.5457	0.0652	0.0186	-0.2654	0.0516	0.6843	-0.2471	0.2458	-0.0403	-0.0599	0.3364	-0.0691	0.298	2.8879	17.696	25.1905
10	2.9597	0.3667	-0.332	2.992	-0.1451	1.2018	0.0513	0.2703	0.1082	-0.1199	-0.007	-0.3245	-0.067	0.03	-0.0388	0.1104	0.002	0.0228	0.1719	0.0033	0.1676	-7.7793	8.3902	12.6649
11	5.9125	-0.0822	-0.6928	2.3656	-0.5225	3.4191	-0.0454	0.5652	0.0402	-0.1489	0.0573	-0.1439	0.044	0.0187	-0.0064	0.1985	-0.0121	0.0666	0.2767	0.0647	0.1983	1.4905	13.7199	3.6964
12	2.4972	1.3776	-0.0536	2.2548	1.0551	0.8003	-0.2102	0.5803	0.294	-0.5588	0.1515	0.1695	0.0323	0.0811	0.034	0.277	-0.0133	0.0542	0.453	0.1063	0.2001	-5.9392	14.2206	-1.4952

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 43 )	A	1 - 43
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 44 through 65 )	A	44 - 65
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 66 through 81 )	A	66 - 81
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 82 through 121 )	A	82 - 121
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 122 through 143 )	A	122 - 143
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 144 through 189 )	A	144 - 189
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 190 through 225 )	A	190 - 225
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 34 )	B	1 - 34
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 35 through 66 )	B	35 - 66
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 67 through 163 )	B	67 - 163
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 164 through 205 )	B	164 - 205
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 206 through 225 )	B	206 - 225

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