PDB-3ojc: Crystal structure of a putative Asp/Glu Racemase from Yersinia pestis

ID or keywords:

Entry

Database: PDB / ID: 3ojc

Title

Crystal structure of a putative Asp/Glu Racemase from Yersinia pestis

Components

Putative aspartate/glutamate racemase

Keywords

ISOMERASE / Structural Genomics / CSGID / Center for Structural Genomics of Infectious Diseases / alpha beta / 3-layer(aba) sandwich / Rossmann fold / Asp/Glu/Hydantoin racemase family

Function / homology

Function and homology information

aspartate racemase / amino-acid racemase activity / metal ion binding
Similarity search - Function

Biological species

Yersinia pestis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.75 Å

Authors

Anderson, S.M. / Wawrzak, Z. / Kudritska, M. / Kwon, K. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: Crystal structure of a putative Asp/Glu Racemase from Yersinia pestis
Authors: Anderson, S.M. / Wawrzak, Z. / Kudritska, M. / Kwon, K. / Anderson, W.F. / Savchenko, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Aug 21, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 15, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 12, 2014	Group: Structure summary
Revision 1.3	Nov 8, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3ojc.cif.gz	205.6 KB	Display	PDBx/mmCIF format
PDB format	pdb3ojc.ent.gz	175.7 KB	Display	PDB format
PDBx/mmJSON format	3ojc.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3ojc_validation.pdf.gz	470.1 KB	Display	wwPDB validaton report
Full document	3ojc_full_validation.pdf.gz	483.3 KB	Display
Data in XML	3ojc_validation.xml.gz	44.2 KB	Display
Data in CIF	3ojc_validation.cif.gz	63.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/oj/3ojc ftp://data.pdbj.org/pub/pdb/validation_reports/oj/3ojc	HTTPS FTP

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Related structure data

Similar structure data	1kar-d 3f73-1 5vlb-3 1k75-d 6eja-d 3hk2-2 6ej9-d 1kah-d 4g09-1 1ev1-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
Other databases	TargetDB: IDP04122

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Putative aspartate/glutamate racemase

B: Putative aspartate/glutamate racemase

C: Putative aspartate/glutamate racemase

D: Putative aspartate/glutamate racemase

hetero molecules

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

1

Idetical with deposited unit
defined by author

2

A: Putative aspartate/glutamate racemase

C: Putative aspartate/glutamate racemase

hetero molecules

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

3

B: Putative aspartate/glutamate racemase

D: Putative aspartate/glutamate racemase

hetero molecules

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

Unit cell

Length a, b, c (Å)	66.52, 95.41, 142.62
Angle α, β, γ (deg.)	90.0, 90.0, 90.0
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Putative aspartate/glutamate racemase Mass: 25618.457 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Strain: CO92 / Gene: racX, YPO2758, YP_2405 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q74SZ5, UniProt: A0A2S9PI63*PLUS
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-HEZ / HEXANE-1,6-DIOL Mass: 118.174 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C₆H₁₄O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 743 / 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: 2.21 Å³/Da / Density % sol: 44.3 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 200mM calcium acetate, 20% PEG 3350, 2% 1,6-hexanediol, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction

Mean temperature: 110 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 2, 2010 / 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: 1.75→50 Å / Num. all: 92148 / Num. obs: 92056 / % possible obs: 99.9 % / Observed criterion σ(F): 1.7 / Observed criterion σ(I): 3 / Redundancy: 7.3 % / B_iso Wilson estimate: 18.7 Å² / R_merge(I) obs: 0.083 / Χ²: 1.002 / Net I/σ(I): 9.3

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Χ²	% possible all
1.75-1.81	6.4	0.598	3	9040	0.977	99.9
1.81-1.89	7.4	0.456	4.8	9119	1.016	100
1.89-1.97	7.4	0.33	6.3	9137	1.029	100
1.97-2.07	7.4	0.221	9.4	9139	0.997	100
2.07-2.2	7.5	0.151	13.8	9113	1.007	100
2.2-2.38	7.4	0.121	16.3	9209	0.99	100
2.38-2.61	7.4	0.088	23	9154	1.003	100
2.61-2.99	7.4	0.07	26.6	9254	1.004	100
2.99-3.77	7.3	0.066	24.7	9300	1	99.9
3.77-50	6.9	0.045	32.4	9591	0.989	99.1

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHENIX	1.6.2_432	refinement
PDB_EXTRACT	3.1	data extraction
BLU-MAX		data collection
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.75→38.77 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.19 / σ(F): 1.44 / σ(I): 3 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2015	4595	5 %	random
R_work	0.1699	-	-	-
all	0.172	92150	-	-
obs	0.1715	91929	99.76 %	-

Solvent computation

Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 66.687 Å² / k_sol: 0.41 e/Å³

Displacement parameters

B_iso max: 159.73 Å² / B_iso mean: 26.783 Å² / B_iso min: 6.51 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.5222 Å²	0 Å²	-0 Å²
2-	-	5.7664 Å²	0 Å²
3-	-	-	-3.2443 Å²

Refinement step

Cycle: LAST / Resolution: 1.75→38.77 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7072	0	164	743	7979

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	7417
X-RAY DIFFRACTION	f_angle_d	1.039	10000
X-RAY DIFFRACTION	f_chiral_restr	0.077	1163
X-RAY DIFFRACTION	f_plane_restr	0.004	1267
X-RAY DIFFRACTION	f_dihedral_angle_d	13.04	2776

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	Num. reflection obs	% reflection obs (%)
1.7499-1.8125	0.248	448	0.2197	8511	8959	8959	99
1.8125-1.8851	0.2424	456	0.1902	8657	9113	9113	100
1.8851-1.9708	0.2326	456	0.1805	8669	9125	9125	99.9
1.9708-2.0747	0.2011	458	0.1588	8699	9157	9157	100
2.0747-2.2047	0.1915	456	0.1503	8663	9119	9119	100
2.2047-2.3749	0.1929	460	0.1557	8734	9194	9194	99.9
2.3749-2.6139	0.1914	457	0.1568	8697	9154	9154	100
2.6139-2.992	0.1914	464	0.167	8798	9262	9262	100
2.992-3.7691	0.1908	464	0.1665	8836	9300	9300	99.9
3.7691-38.7759	0.2045	476	0.1796	9070	9546	9546	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	1.4034	0.2764	0.4226	1.597	-0.3639	0.7923	-0.0012	0.0225	-0.0332	-0.0419	0.003	-0.0409	0.0785	-0.0165	0.0019	0.0973	-0.0102	-0.0038	0.0971	0.0066	0.0645	43.5157	57.9204	87.9183
2	2.031	0.1902	-1.8758	0.7268	0.499	3.6256	0.0683	-0.2338	0.2707	0.1636	0.101	0.2997	-0.1216	0.1645	-0.1606	0.1509	0.0301	0.0504	0.1539	-0.0035	0.2138	30.48	69.7438	94.325
3	1.0697	1.0107	-0.4696	2.2262	-0.7901	1.0748	0.0809	0.0643	0.078	0.1961	-0.0518	0.2358	-0.069	-0.0598	-0.0287	0.093	-0.0012	0.0075	0.1015	-0.0142	0.1132	29.1137	53.6687	91.1481
4	1.668	0.977	-1.0332	1.3054	0.3994	1.9911	0.0572	-0.4025	0.3011	0.1783	-0.1641	0.2754	-0.0091	0.0329	0.0822	0.1356	-0.0276	0.0342	0.1033	-0.0426	0.1662	32.6013	49.9524	109.1829
5	1.5483	0.1111	-0.2044	1.5523	0.4749	1.4556	-0.032	-0.1009	-0.1527	0.0841	-0.0469	-0.0224	0.227	0.1597	0.059	0.1258	-0.0024	0.0137	0.0694	-0.0103	0.1169	36.7482	43.1538	100.7637
6	1.0418	-0.7046	-0.1797	0.7926	0.2393	1.4374	-0.0304	-0.0024	-0.0918	0.0978	-0.0069	0.1146	0.1187	-0.1757	0.0468	0.1171	-0.0192	-0.0022	0.1113	-0.0029	0.1138	46.3456	66.3719	123.9581
7	1.8569	-0.4968	-0.3232	1.7457	0.5398	0.2731	-0.1123	-0.4578	-0.2331	0.4994	0.069	0.164	0.2602	0.1568	0.0522	0.2406	-0.0063	0.0323	0.1979	0.0273	0.1404	48.1883	64.5488	136.2967
8	0.9421	-0.6802	0.0325	0.9066	0.5073	1.0256	-0.1437	-0.0989	0.0059	0.2008	0.1598	-0.0588	0.1444	0.0781	-0.0043	0.0987	0.0124	-0.0232	0.075	-0.0219	0.0377	45.891	73.0877	136.2121
9	1.2807	0.1051	-0.4681	1.6555	0.0767	1.1182	-0.0698	0.0016	0.0223	0.1311	0.0446	0.1349	0.0398	-0.0319	0.0323	0.0839	-0.0065	0.0016	0.0943	-0.0284	0.0712	25.8494	66.9023	131.759
10	1.868	0.8302	-0.7873	1.2904	-0.2384	0.7324	-0.1167	0.1263	0.008	-0.0846	0.0355	0.0785	0.0976	-0.1085	0.0725	0.0976	-0.021	0.0023	0.0962	-0.0268	0.0755	27.3857	68.9557	123.8179
11	1.1176	0.3137	-0.1858	1.4184	-0.3061	0.9864	-0.0167	-0.0557	-0.0184	-0.0013	-0.0197	-0.1062	-0.1285	0.1336	0.0297	0.0748	0.0063	-0.003	0.103	0.0101	0.0918	50.2722	65.6873	87.5473
12	1.1937	0.1205	-0.6009	0.9803	0.0012	1.1258	-0.0841	0.229	0.0342	-0.1052	0.0562	-0.0416	-0.0149	0.0518	0.0166	0.0979	-0.0005	0.0022	0.1459	0.0269	0.0964	53.4403	71.7122	76.4687
13	1.0788	-0.5877	-0.6883	0.9547	0.0489	0.8905	-0.0436	0.0525	0.1455	-0.0733	0.0376	-0.0489	-0.0599	0.1292	-0.0085	0.1088	-0.0161	0.0041	0.1616	0.0277	0.1699	72.1631	72.5612	80.1928
14	2.7911	-0.6448	-0.6995	0.6051	-0.0729	2.4023	-0.1583	-0.3639	-0.6832	0.1486	0.0715	0.1427	0.6958	-0.1483	0.1101	0.2279	0.0055	0.0202	0.1682	0.0746	0.2701	73.8461	55.815	83.2379
15	1.3365	-0.9466	-0.456	1.3485	0.57	0.707	-0.1054	-0.3251	-0.0692	0.1848	0.0914	-0.0023	0.0687	0.1724	0.0145	0.1441	0.0024	-0.0147	0.2209	0.0386	0.1262	67.0279	68.6659	90.3661
16	1.1122	-0.784	0.4135	1.3154	0.1348	0.388	-0.0309	-0.1033	-0.1525	0.1549	0.062	0.0118	0.1023	-0.0528	-0.0298	0.1206	-0.0182	-0.0177	0.1065	0.006	0.0741	54.5899	58.1467	126.0305
17	1.6016	-0.9077	-0.2188	0.8753	0.0793	1.0346	0.0298	0.2886	0.408	-0.1117	-0.0107	-0.399	-0.2099	-0.1512	0.0042	0.102	-0.0333	0.0131	0.1503	0.0068	0.2335	67.1335	70.4846	119.3419
18	2.4233	-1.3894	0.1446	2.27	0.2723	2.8328	0.026	-0.081	-0.099	-0.1102	0.0069	-0.2244	0.2356	0.3179	-0.0281	0.0611	0.0295	-0.0136	0.0676	0.0015	0.0542	68.4454	55.8146	123.4575
19	2.145	-0.6756	-0.1287	0.8508	0.1305	6.3911	0.1741	0.572	-0.0004	-0.1886	-0.137	-0.1046	0.7975	0.0823	-0.032	0.2671	0.0607	0.0191	0.1809	-0.009	0.1271	64.9421	47.7784	105.6799
20	1.5586	-0.4635	-0.5177	0.4795	-0.7713	5.4559	-0.103	-0.0907	-0.444	0.1097	0.0848	0.0436	1.2642	0.1024	0.0376	0.3444	0.0031	-0.0146	0.098	0.0332	0.1884	61.5577	46.5228	123.197

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 1:48)	A	1 - 48
2	X-RAY DIFFRACTION	2	(chain A and resid 49:75)	A	49 - 75
3	X-RAY DIFFRACTION	3	(chain A and resid 76:120)	A	76 - 120
4	X-RAY DIFFRACTION	4	(chain A and resid 121:179)	A	121 - 179
5	X-RAY DIFFRACTION	5	(chain A and resid 180:231)	A	180 - 231
6	X-RAY DIFFRACTION	6	(chain B and resid 1:28)	B	1 - 28
7	X-RAY DIFFRACTION	7	(chain B and resid 29:63)	B	29 - 63
8	X-RAY DIFFRACTION	8	(chain B and resid 64:107)	B	64 - 107
9	X-RAY DIFFRACTION	9	(chain B and resid 108:180)	B	108 - 180
10	X-RAY DIFFRACTION	10	(chain B and resid 181:231)	B	181 - 231
11	X-RAY DIFFRACTION	11	(chain C and resid 1:53)	C	1 - 53
12	X-RAY DIFFRACTION	12	(chain C and resid 54:112)	C	54 - 112
13	X-RAY DIFFRACTION	13	(chain C and resid 113:154)	C	113 - 154
14	X-RAY DIFFRACTION	14	(chain C and resid 155:187)	C	155 - 187
15	X-RAY DIFFRACTION	15	(chain C and resid 188:231)	C	188 - 231
16	X-RAY DIFFRACTION	16	(chain D and resid 1:48)	D	1 - 48
17	X-RAY DIFFRACTION	17	(chain D and resid 49:75)	D	49 - 75
18	X-RAY DIFFRACTION	18	(chain D and resid 76:117)	D	76 - 117
19	X-RAY DIFFRACTION	19	(chain D and resid 118:209)	D	118 - 209
20	X-RAY DIFFRACTION	20	(chain D and resid 210:231)	D	210 - 231

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