PDB-2pzj: Crystal structure of the Bordetella bronchiseptica enzyme WbmF in...

ID or keywords:

Entry

Database: PDB / ID: 2pzj

Title

Crystal structure of the Bordetella bronchiseptica enzyme WbmF in complex with NAD+

Components

Putative nucleotide sugar epimerase/ dehydratase

Keywords

SUGAR BINDING PROTEIN /

BORDETELLA BRONCHISEPTICA /

SHORT-CHAIN DEHYDROGENASE/REDUCTASE /

O ANTIGEN

Function / homology

Function and homology information

glutamine metabolic process /

transferase activity /

nucleotide binding
Similarity search - Function

Biological species

Bordetella bronchiseptica (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Harmer, N.J. / King, J.D. / Palmer, C.M. / Maskell, D. / Blundell, T.L.

Citation

Journal: J.Mol.Biol. / Year: 2007
Title: Predicting protein function from structure--the roles of short-chain dehydrogenase/reductase enzymes in Bordetella O-antigen biosynthesis.
Authors: King, J.D. / Harmer, N.J. / Preston, A. / Palmer, C.M. / Rejzek, M. / Field, R.A. / Blundell, T.L. / Maskell, D.J.

History

Deposition	May 18, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 2, 2007	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Derived calculations / Version format compliance
Revision 1.2	Aug 30, 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_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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	2pzj.cif.gz	86.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2pzj.ent.gz	63.4 KB	Display	PDB format
PDBx/mmJSON format	2pzj.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/pz/2pzj ftp://data.pdbj.org/pub/pdb/validation_reports/pz/2pzj	HTTPS FTP

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Related structure data

Related structure data	2pzkC 2pzlC 2pzmC 2q1sC 2q1tC 2q1uC 2q1wC 1bxkS 1keuS 1r6dS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	6nwz-d 2q1s-1 5jxz-d 2w9z-d 5w57-d 1q5m-d 2q1u-d 1yni-2 1xoq-d 1lrl-1 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: Putative nucleotide sugar epimerase/ dehydratase

hetero molecules

42.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative nucleotide sugar epimerase/ dehydratase

hetero molecules

A: Putative nucleotide sugar epimerase/ dehydratase

hetero molecules

defined by author&software
84.5 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	82.884, 77.875, 59.226
Angle α, β, γ (deg.)	90.00, 108.17, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-384- HOH

Details

The second part of the (dimeric) biological assembly is generated by the two fold axis: 0, y, 0, followed by a translation of 0, 0, 1.

#1: Protein	Putative nucleotide sugar epimerase/ dehydratase Mass: 41594.832 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bordetella bronchiseptica (bacteria) / Gene: BbLPS1.16, wbmF / Plasmid: pET15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: O87989
#2: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Comment: NAD*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.18 Å³/Da / Density % sol: 43.63 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 0.1 M bicine, 16 % (w/w) PEG 8000, pH 9, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.977 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: May 18, 2006
Radiation	Monochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.977 Å / Relative weight: 1
Reflection	Resolution: 1.9→50 Å / Num. all: 28232 / Num. obs: 27275 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 5 / Redundancy: 4.6 % / B_iso Wilson estimate: 24.88 Å² / R_merge(I) obs: 0.039 / Net I/σ(I): 32.1
Reflection shell	Resolution: 1.9→1.93 Å / Redundancy: 3 % / R_merge(I) obs: 0.223 / Mean I/σ(I) obs: 5.89 / Num. unique all: 1061 / % possible all: 77.4

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
ADSC	Quantum	data collection
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entries 1BXK, 1KEU, 1R6D

1bxk

1keu

1r6d

Resolution: 1.9→38.38 Å / Cor.coef. F_o:F_c: 0.966 / Cor.coef. F_o:F_c free: 0.942 / SU B: 6.517 / SU ML: 0.101 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20428	1352	5 %	RANDOM
R_work	0.16086	-	-	-
all	0.163	28232	-	-
obs	0.16305	25919	96.48 %	-

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: 23.931 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.31 Å²	0 Å²	-0.73 Å²
2-	-	1.12 Å²	0 Å²
3-	-	-	-1.89 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→38.38 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2519	0	44	192	2755

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	2644
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	1717
X-RAY DIFFRACTION	r_angle_refined_deg	1.458	1.969	3610
X-RAY DIFFRACTION	r_angle_other_deg	1.003	3	4202
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.084	5	335
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.072	24.196	112
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.511	15	413
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.746	15	13
X-RAY DIFFRACTION	r_chiral_restr	0.087	0.2	413
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2944
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	518
X-RAY DIFFRACTION	r_nbd_refined	0.21	0.2	519
X-RAY DIFFRACTION	r_nbd_other	0.196	0.2	1792
X-RAY DIFFRACTION	r_nbtor_refined	0.175	0.2	1281
X-RAY DIFFRACTION	r_nbtor_other	0.086	0.2	1287
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.174	0.2	181
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.087	0.2	1
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.231	0.2	11
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.257	0.2	45
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.153	0.2	12
X-RAY DIFFRACTION	r_mcbond_it	0.651	1.5	1784
X-RAY DIFFRACTION	r_mcbond_other	0.176	1.5	674
X-RAY DIFFRACTION	r_mcangle_it	0.913	2	2653
X-RAY DIFFRACTION	r_scbond_it	1.629	3	1100
X-RAY DIFFRACTION	r_scangle_it	2.324	4.5	953

LS refinement shell

Resolution: 1.899→1.948 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.292	80	-
R_work	0.226	1514	-
obs	-	-	77.6 %

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	4.2969	0.8056	1.2869	60.4337	19.8178	6.7428	-0.6095	0.8341	0.4982	-1.9538	0.574	-0.0337	-0.8276	-0.4206	0.0354	0.1765	-0.1126	0.001	0.1429	0.0224	-0.1064	30.4906	18.5212	-4.8893
2	4.1445	-0.2956	-0.8189	1.3087	1.1569	3.9718	-0.1497	0.6341	-0.1106	-0.4253	0.0651	0.1086	0.2452	-0.428	0.0845	0.0434	-0.1484	-0.0154	-0.0403	-0.0216	-0.165	22.389	13.304	2.7836
3	4.4813	1.8351	-1.3118	1.7408	0.5112	1.4952	-0.3274	0.4311	-0.2587	-0.4627	0.1696	0.14	0.6426	-0.4936	0.1578	0.0905	-0.1725	0.0164	-0.094	-0.032	-0.0763	19.7289	5.0111	10.6749
4	2.5998	0.3162	-1.6704	0.8462	-0.4705	3.5093	-0.2082	0.2293	-0.2896	-0.2716	0.0873	0.0463	0.5651	-0.248	0.1209	-0.0139	-0.0841	0.0356	-0.1725	-0.0303	-0.1373	27.5682	8.2876	15.0263
5	3.2382	0.9162	-0.9176	3.0492	-0.1779	6.023	-0.081	0.1023	0.1889	-0.2117	0.0985	-0.182	0.0761	0.2757	-0.0175	-0.1247	-0.0827	0.0113	-0.1381	0.0022	-0.1856	35.3584	18.2763	9.6728
6	9.875	4.7283	-20.8457	7.8262	-9.301	44.0876	-0.1812	0.9136	0.0811	0.0705	0.2963	0.7019	-0.1923	-1.1579	-0.1152	0.026	0.0184	-0.034	-0.0049	-0.0182	0.0919	28.3382	29.6752	28.3461
7	2.0487	0.8276	-0.4172	1.6989	-0.7509	4.0528	-0.0644	-0.0096	0.2142	-0.0539	0.0673	0.0573	-0.0339	-0.0365	-0.003	-0.16	-0.0287	0.0147	-0.231	0.0025	-0.1808	32.0349	21.0899	19.5757
8	2.1222	-0.2093	-0.2039	2.1142	-1.2381	2.8311	-0.0464	-0.0079	-0.0444	0.0009	-0.0121	0.374	0.1096	-0.3947	0.0585	-0.1376	-0.1259	-0.0454	0.0508	0.0057	-0.0522	7.0481	14.4256	17.9512
9	7.605	5.3906	7.4812	17.8467	18.9333	20.6058	0.431	-0.6019	-0.5197	1.9216	-0.25	0.9543	1.0478	-1.1832	-0.1809	0.0571	-0.1845	-0.0088	0.3409	0.0491	0.2959	-5.8556	18.4906	18.8366
10	32.1584	2.3959	-17.3714	5.648	0.7107	16.3789	-0.6079	-0.9469	-0.9695	0.6931	-0.1945	0.2048	1.0423	0.0718	0.8025	0.0652	-0.0147	0.0223	0.1415	-0.026	0.1256	4.3436	30.0105	23.508
11	7.6935	-1.9896	-1.6267	4.9436	-2.839	2.743	0.1781	0.2958	0.3436	-0.6104	-0.0334	0.2827	-0.3977	-0.7455	-0.1447	-0.1387	-0.0465	-0.0941	0.0539	0.0592	-0.0552	12.6421	25.2698	9.2441
12	3.3583	-0.2726	0.822	2.0429	0.0032	2.3555	-0.0933	0.4559	0.3293	-0.2484	0.1036	0.0978	-0.1598	-0.1516	-0.0104	-0.0957	-0.0612	-0.0228	-0.1095	0.0564	-0.1322	26.489	26.2451	7.2802
13	41.8719	32.6832	-34.2605	29.7864	-27.8827	28.6802	0.5178	-0.0927	0.4509	0.4785	-0.6803	-0.3701	-0.9257	-0.184	0.1625	-0.0128	0.0092	-0.0552	0.0534	0.0143	0.1527	8.3875	33.4978	15.2083
14	5.8076	0.1039	-1.5297	5.071	4.6938	4.8	0.2598	0.26	0.4233	0.0366	-0.1645	0.5847	-0.042	-0.7721	-0.0953	-0.0414	-0.0752	-0.0991	0.2349	0.075	0.1924	-2.5591	26.904	12.2937
15	37.3444	15.2122	11.4071	49.5632	23.3071	11.5139	-0.171	0.6276	0.8434	-1.0692	-0.0091	1.1486	-0.7318	-0.7673	0.1801	0.1499	-0.0512	-0.0125	0.2946	0.0749	0.3433	-7.5711	28.5949	19.1299
16	4.5476	2.2784	4.9822	15.0742	10.4208	16.7479	-0.1042	0.2055	-0.7558	0.422	0.1492	0.1923	-0.1114	-0.0446	-0.045	0.0323	0.1017	0.0697	-0.0794	-0.0232	0.0198	3.741	39.5544	27.0045
17	9.347	-3.3256	-7.0973	5.2894	0.8787	6.0493	-0.3042	0.0436	0.749	0.0304	-0.0296	0.2259	-0.6985	-0.7194	0.3338	0.0784	-0.0058	-0.1268	0.014	0.0309	0.0163	22.9809	35.9264	10.5824
18	22.824	6.7182	-3.9397	4.051	-2.1598	3.2412	0.0619	0.7322	1.5724	-0.1762	0.1141	0.4923	-0.2707	-0.276	-0.176	0.012	-0.0428	-0.0893	0.0131	0.1008	0.0152	16.9818	30.9656	4.6173
19	3.3073	-0.8461	1.2266	5.4704	-5.13	9.7931	-0.1204	0.2588	-0.4019	-0.2716	0.1512	0.3863	0.4201	-0.8426	-0.0308	-0.0912	-0.1656	-0.074	0.1513	-0.0415	0.0591	2.9086	10.2081	11.4504
20	12.3276	11.339	-8.6083	27.7916	-4.5486	6.6651	0.0607	-0.6669	-0.611	2.0001	-0.1607	1.1757	0.1298	-1.4904	0.1	0.135	-0.2078	0.084	0.353	0.1864	0.2904	4.1061	6.3246	30.6155

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	8 - 12	28 - 32
2	X-RAY DIFFRACTION	2	A	A	13 - 38	33 - 58
3	X-RAY DIFFRACTION	3	A	A	39 - 52	59 - 72
4	X-RAY DIFFRACTION	4	A	A	53 - 117	73 - 137
5	X-RAY DIFFRACTION	5	A	A	118 - 148	138 - 168
6	X-RAY DIFFRACTION	6	A	A	149 - 157	169 - 177
7	X-RAY DIFFRACTION	7	A	A	158 - 189	178 - 209
8	X-RAY DIFFRACTION	8	A	A	190 - 223	210 - 243
9	X-RAY DIFFRACTION	9	A	A	224 - 229	244 - 249
10	X-RAY DIFFRACTION	10	A	A	230 - 238	250 - 258
11	X-RAY DIFFRACTION	11	A	A	239 - 244	259 - 264
12	X-RAY DIFFRACTION	12	A	A	245 - 268	265 - 288
13	X-RAY DIFFRACTION	13	A	A	269 - 273	289 - 293
14	X-RAY DIFFRACTION	14	A	A	274 - 286	294 - 306
15	X-RAY DIFFRACTION	15	A	A	287 - 292	307 - 312
16	X-RAY DIFFRACTION	16	A	A	293 - 300	313 - 320
17	X-RAY DIFFRACTION	17	A	A	301 - 312	321 - 332
18	X-RAY DIFFRACTION	18	A	A	313 - 327	333 - 347
19	X-RAY DIFFRACTION	19	A	A	328 - 350	348 - 370
20	X-RAY DIFFRACTION	20	A	A	351 - 355	371 - 375

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