PDB-4jd7: Crystal structure of pput_1285, a putative hydroxyproline epimera...

ID or keywords:

Entry

Database: PDB / ID: 4jd7

Title

Crystal structure of pput_1285, a putative hydroxyproline epimerase from Pseudomonas putida f1 (target EFI-506500), open form, space group P212121, bound sulfate

Components

Proline racemase

Keywords

ISOMERASE / PUTATIVE HYDROXYPROLINE EPIMERASE / enzyme function initiative / EFI / Structural Genomics

Function / homology

4-hydroxyproline epimerase / 4-hydroxyproline epimerase activity / Proline racemase family / Proline racemase / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta / 4-hydroxyproline 2-epimerase

Function and homology information

Biological species

Pseudomonas putida (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.5 Å

Authors

Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. ...

Citation

Journal: To be Published
Title: Crystal structure of pput_1285, a putative hydroxyproline epimerase from Pseudomonas putida f1 (target EFI-506500), open form, space group P212121, bound sulfate
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, J. / Stead, ...

History

Deposition	Feb 24, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 6, 2013	Provider: repository / Type: Initial release
Revision 1.1	Sep 20, 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

-
Download

PDBx/mmCIF format	4jd7.cif.gz	369.8 KB	Display	PDBx/mmCIF format
PDB format	pdb4jd7.ent.gz	308.1 KB	Display	PDB format
PDBx/mmJSON format	4jd7.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4jd7_validation.pdf.gz	455.6 KB	Display	wwPDB validaton report
Full document	4jd7_full_validation.pdf.gz	459 KB	Display
Data in XML	4jd7_validation.xml.gz	31.9 KB	Display
Data in CIF	4jd7_validation.cif.gz	49.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/jd/4jd7 ftp://data.pdbj.org/pub/pdb/validation_reports/jd/4jd7	HTTPS FTP

-
Related structure data

Related structure data	2azpS S: Starting model for refinement
Similar structure data	4qiu-d 4jci-d 5lsm-4 4juu-d 4qis-d 4q4k-d 1j9z-2 5lsm-5 4zy5-d 3l7r-d 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	TargetTrack: EFI-506500

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Proline racemase

D: Proline racemase

hetero molecules

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

1

A: Proline racemase

hetero molecules

D: Proline racemase

hetero molecules

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

Unit cell

Length a, b, c (Å)	64.844, 96.804, 109.214
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Proline racemase Mass: 36170.559 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: F1 / ATCC 700007 / Gene: Pput_1285 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5VZY6
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 752 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.37 Å³/Da / Density % sol: 48.08 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: Protein (15 mM Hepes pH 8.0, 150 mM NaCl, 5% glycerol, 10 mM PYRROLE-2-CARBOXYLATE); Reservoir (0.1 M NaAcetate pH 4.6, 1.5 M LiSO4); Soak 2 minutes in (2.0 M LiSO4 with 20% reservoir), ...Details: Protein (15 mM Hepes pH 8.0, 150 mM NaCl, 5% glycerol, 10 mM PYRROLE-2-CARBOXYLATE); Reservoir (0.1 M NaAcetate pH 4.6, 1.5 M LiSO4); Soak 2 minutes in (2.0 M LiSO4 with 20% reservoir), VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal

Density Matthews: 2.37 Å³/Da / Density % sol: 48.08 %

Crystal grow

Temperature: 298 K / Method: vapor diffusion, sitting drop
Details: Protein (15 mM Hepes pH 8.0, 150 mM NaCl, 5% glycerol, 10 mM PYRROLE-2-CARBOXYLATE); Reservoir (0.1 M NaAcetate pH 4.6, 1.5 M LiSO4); Soak 2 minutes in (2.0 M LiSO4 with 20% reservoir), ...

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 31-ID / Wavelength: 0.9793 Å

Detector

Type: RAYONIX MX225HE / Detector: CCD / Date: Feb 14, 2013 / Details: MIRRORS

Radiation

Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9793 Å / Relative weight: 1

Reflection

Resolution: 1.5→72.443 Å / Num. all: 109888 / Num. obs: 109888 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / R_merge(I) obs: 0.067 / R_sym value: 0.067 / Net I/σ(I): 18

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured all	Num. unique all	R_sym value	% possible all
1.5-1.58	7.1	0.707	1.1	111979	15778	0.707	98.9
1.58-1.68	7.2	0.481	1.6	108058	14976	0.481	99.2
1.68-1.79	7.3	0.308	2.5	103665	14142	0.308	99.4
1.79-1.94	7.4	0.187	4.1	97416	13174	0.187	99.6
1.94-2.12	7.4	0.109	7	90375	12210	0.109	99.7
2.12-2.37	7.4	0.077	9.8	81945	11078	0.077	99.9
2.37-2.74	7.4	0.055	12.7	72560	9840	0.055	99.9
2.74-3.35	7.3	0.039	15.5	61598	8394	0.039	100
3.35-4.74	7.2	0.029	19.1	47567	6566	0.029	99.9
4.74-109.214	6.8	0.026	20	25457	3730	0.026	98.7

-
Processing

Software

Name	Version	Classification
SCALA	3.3.20	data scaling
PHENIX	1.8.1_1168	refinement
PDB_EXTRACT	3.11	data extraction
MOSFLM		data reduction
AMoRE		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 2AZP

2azp

Resolution: 1.5→72.443 Å / Occupancy max: 1 / Occupancy min: 0.32 / FOM work R set: 0.8938 / SU ML: 0.12 / σ(F): 0 / σ(I): 0 / Phase error: 17.37 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1755	5491	5 %	RANDOM
R_work	0.1594	-	-	-
obs	0.1603	109793	99.37 %	-
all	-	109793	-	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 76.55 Å² / B_iso mean: 21.8322 Å² / B_iso min: 6.24 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→72.443 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4810	0	70	752	5632

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	5043
X-RAY DIFFRACTION	f_angle_d	1.325	6875
X-RAY DIFFRACTION	f_chiral_restr	0.084	727
X-RAY DIFFRACTION	f_plane_restr	0.007	910
X-RAY DIFFRACTION	f_dihedral_angle_d	12.651	1781

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.5-1.517	0.2543	183	0.2263	3392	3575	98
1.517-1.5349	0.2481	193	0.22	3420	3613	99
1.5349-1.5536	0.2614	184	0.2078	3421	3605	99
1.5536-1.5733	0.2544	158	0.2095	3432	3590	99
1.5733-1.594	0.2216	174	0.2027	3396	3570	99
1.594-1.6158	0.217	200	0.1913	3451	3651	99
1.6158-1.6389	0.2307	164	0.1772	3421	3585	99
1.6389-1.6634	0.1797	187	0.1788	3472	3659	99
1.6634-1.6894	0.1949	156	0.1733	3422	3578	99
1.6894-1.7171	0.2062	197	0.1658	3451	3648	99
1.7171-1.7467	0.1816	173	0.1696	3408	3581	99
1.7467-1.7784	0.1966	180	0.1544	3469	3649	99
1.7784-1.8127	0.1789	182	0.1559	3460	3642	99
1.8127-1.8497	0.1699	159	0.1543	3462	3621	99
1.8497-1.8899	0.1707	211	0.1589	3427	3638	99
1.8899-1.9338	0.1921	177	0.1652	3458	3635	100
1.9338-1.9822	0.187	182	0.1529	3484	3666	100
1.9822-2.0358	0.1783	189	0.1434	3462	3651	100
2.0358-2.0957	0.1412	170	0.1394	3507	3677	100
2.0957-2.1634	0.1647	170	0.139	3477	3647	100
2.1634-2.2407	0.1838	180	0.1483	3498	3678	100
2.2407-2.3304	0.1647	195	0.1429	3463	3658	100
2.3304-2.4365	0.1658	190	0.1388	3509	3699	100
2.4365-2.5649	0.1755	174	0.1483	3523	3697	100
2.5649-2.7256	0.1862	185	0.1532	3499	3684	100
2.7256-2.9361	0.1602	202	0.1675	3528	3730	100
2.9361-3.2316	0.179	217	0.158	3533	3750	100
3.2316-3.6992	0.1501	188	0.1513	3540	3728	100
3.6992-4.6605	0.1314	186	0.1368	3616	3802	100
4.6605-72.5273	0.2011	185	0.1937	3701	3886	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	1.5271	0.055	-0.215	1.1612	0.1775	1.6296	0.0039	0.3108	0.2108	-0.3088	-0.0303	-0.1941	-0.1493	0.1118	0.0166	0.1189	-0.0015	0.0341	0.146	0.0419	0.1396	25.501	47.3542	9.7095
2	1.2	-0.7281	-0.1775	0.9268	0.0051	1.0085	-0.1217	-0.0441	0.1103	0.0954	-0.0238	-0.5395	-0.1591	0.2319	0.0392	0.0719	-0.033	-0.0143	0.1264	0.0576	0.2557	31.7035	50.6687	18.5116
3	0.9023	0.2646	0.0593	2.0803	-0.3208	1.1208	0.0158	0.1255	-0.0958	-0.1607	-0.0464	-0.7532	0.0856	0.2185	0.0054	0.0862	0.0193	0.0614	0.1404	0.0153	0.2534	33.8827	36.7929	13.2592
4	0.1272	-0.2367	-0.0496	0.84	-0.7255	1.4068	-0.036	0.1431	0.2752	-0.0935	-0.3078	-0.1802	0.1657	0.3368	0.2122	0.129	0.0175	0.0132	0.1591	0.0283	0.2298	35.5796	27.3122	17.3161
5	1.1043	-0.2094	-0.8307	1.1694	0.4868	2.1412	-0.0975	-0.2599	0.1274	0.3208	0.0082	-0.0768	0.1333	0.0443	0.1037	0.18	0.0175	-0.0314	0.2178	-0.0644	0.1286	32.9357	28.5361	46.6118
6	0.9623	-0.3643	-0.2568	1.1451	-0.241	1.4717	0.0036	-0.1681	0.0367	0.1318	-0.0007	0.1227	-0.1286	-0.1428	-0.0021	0.202	0.0218	0.0025	0.1505	-0.0343	0.1552	23.3473	32.9451	41.5503
7	0.7577	0.074	0.1739	0.9244	0.9431	1.6512	0.0173	-0.1092	0.126	0.0652	0.012	-0.0411	-0.0865	0.1272	-0.04	0.1531	0.0145	-0.0127	0.1157	-0.011	0.1107	28.4727	29.1643	38.2872
8	1.4083	-0.5047	0.5674	1.131	-0.2349	1.2175	-0.0201	0.0822	0.0582	0.0546	0.0381	-0.1842	0.0025	0.2014	-0.031	0.1046	0.0106	-0.005	0.1082	-0.018	0.1116	31.4198	23.7692	29.3405
9	0.8008	0.0335	-0.1234	1.5213	0.3208	1.0629	0.0279	0.0747	0.1306	-0.1516	-0.0188	-0.1193	-0.1343	0.0014	0.0065	0.0872	0.0005	0.0067	0.1094	0.0256	0.0939	19.7779	51.5141	13.3792
10	1.6969	0.1508	-0.172	1.5494	0.2901	1.6342	0.0198	0.2993	0.1658	-0.3443	0.0565	-0.034	-0.1665	0.132	0.0081	0.1323	-0.0163	0.0294	0.1385	-0.0007	0.0825	26.1459	53.6108	-44.5068
11	1.1944	-0.6387	-0.0028	1.9564	0.1555	0.9186	-0.0389	0.0195	0.1309	-0.0119	0.0919	-0.3211	-0.0312	0.1553	-0.0421	0.0869	-0.0177	0.0098	0.126	-0.0256	0.1215	33.135	53.0951	-37.7435
12	0.1375	-0.3577	0.0456	0.8835	-0.4426	0.7633	0.018	0.0736	-0.0392	-0.1096	-0.0089	-0.0612	0.0477	0.0122	-0.0248	0.1154	0.0093	0.0082	0.1192	-0.0428	0.1034	33.3003	36.3691	-41.7801
13	0.5742	-0.2901	0.312	1.4252	0.1105	1.2079	-0.063	-0.5044	0.1439	0.4797	0.1192	0.0684	-0.1115	-0.1678	-0.0343	0.2668	0.0573	0.0283	0.2798	-0.0363	0.1233	30.9185	36.076	-12.2607
14	3.7207	0.977	1.0814	1.8327	0.2881	2.3938	-0.1842	-0.297	0.6698	0.3904	0.1336	0.3425	-0.5755	-0.2911	0.0147	0.3167	0.116	0.0455	0.3039	-0.0735	0.2162	22.3023	44.08	-13.3115
15	1.5062	-0.6567	0.1596	1.9831	0.3898	1.6667	-0.0613	-0.2387	0.0876	0.3333	0.1629	-0.0825	-0.1066	0.1257	-0.0829	0.2117	0.0371	0.0031	0.1871	-0.0347	0.1374	30.7846	36.3415	-16.8648
16	1.4427	-0.6114	0.2843	0.965	-0.4654	0.3687	-0.0638	-0.1247	-0.0318	0.1461	0.0678	0.0412	-0.0586	0.0173	-0.0029	0.1339	0.0183	0.0067	0.0966	-0.0123	0.0973	28.0208	32.1547	-23.5264
17	2.4079	-1.0491	0.6192	1.2	-0.3144	1.0036	0.0001	0.1451	-0.2566	0.0325	0.0214	0.0261	0.003	0.089	-0.0241	0.1104	0.0026	0.0047	0.0852	-0.0201	0.104	35.8446	27.8013	-29.7993
18	0.6815	0.1548	0.0494	1.722	0.5357	1.3658	0.0051	0.086	0.0658	-0.2139	0.0178	-0.0232	-0.1582	0.0271	-0.0418	0.0869	-0.0002	0.0058	0.1124	-0.005	0.078	19.6113	58.1246	-41.0971

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	CHAIN A AND (RESID -5:30 )	A
2	X-RAY DIFFRACTION	2	CHAIN A AND (RESID 31:59 )	A
3	X-RAY DIFFRACTION	3	CHAIN A AND (RESID 60:114 )	A
4	X-RAY DIFFRACTION	4	CHAIN A AND (RESID 115:136 )	A
5	X-RAY DIFFRACTION	5	CHAIN A AND (RESID 137:159 )	A
6	X-RAY DIFFRACTION	6	CHAIN A AND (RESID 160:195 )	A
7	X-RAY DIFFRACTION	7	CHAIN A AND (RESID 196:225 )	A
8	X-RAY DIFFRACTION	8	CHAIN A AND (RESID 226:287 )	A
9	X-RAY DIFFRACTION	9	CHAIN A AND (RESID 288:308 )	A
10	X-RAY DIFFRACTION	10	CHAIN D AND (RESID -3:30 )	D
11	X-RAY DIFFRACTION	11	CHAIN D AND (RESID 31:88 )	D
12	X-RAY DIFFRACTION	12	CHAIN D AND (RESID 89:136 )	D
13	X-RAY DIFFRACTION	13	CHAIN D AND (RESID 137:175 )	D
14	X-RAY DIFFRACTION	14	CHAIN D AND (RESID 176:195 )	D
15	X-RAY DIFFRACTION	15	CHAIN D AND (RESID 196:220 )	D
16	X-RAY DIFFRACTION	16	CHAIN D AND (RESID 221:267 )	D
17	X-RAY DIFFRACTION	17	CHAIN D AND (RESID 268:287 )	D
18	X-RAY DIFFRACTION	18	CHAIN D AND (RESID 288:308 )	D

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi