PDB-4k7g: Crystal structure of a 3-hydroxyproline dehydratse from agrobacte...

ID or keywords:

Entry

Database: PDB / ID: 4k7g

Title

Crystal structure of a 3-hydroxyproline dehydratse from agrobacterium vitis, target efi-506470, with bound pyrrole 2-carboxylate, ordered active site

Components

3-hydroxyproline dehydratse

Keywords

ISOMERASE / PROLINE RACEMASE FAMILY / PROPOSED 3-OH PROLINE DEHYDRATASE / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics

Function / homology

Function and homology information

trans-L-3-hydroxyproline dehydratase / trans-L-3-hydroxyproline dehydratase activity / 4-hydroxyproline epimerase activity
Similarity search - Function

Biological species

Agrobacterium vitis S4 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2 Å

Authors

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

Citation

Journal: To be Published
Title: Crystal structure of a 3-hydroxyproline dehydratse from agrobacterium vitis, target efi-506470, with bound pyrrole 2-carboxylate, ordered active site
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Scott Glenn, A. / Chowdhury, S. / Evans, B. / Hammonds, ...

History

Deposition	Apr 17, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	May 1, 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

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Download

PDBx/mmCIF format	4k7g.cif.gz	393.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4k7g.ent.gz	327.1 KB	Display	PDB format
PDBx/mmJSON format	4k7g.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4k7g_validation.pdf.gz	484.5 KB	Display	wwPDB validaton report
Full document	4k7g_full_validation.pdf.gz	486.9 KB	Display
Data in XML	4k7g_validation.xml.gz	33.8 KB	Display
Data in CIF	4k7g_validation.cif.gz	52.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k7/4k7g ftp://data.pdbj.org/pub/pdb/validation_reports/k7/4k7g	HTTPS FTP

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Related structure data

Related structure data	1tm0S S: Starting model for refinement
Similar structure data	5fkt-2 5fkr-d 5jwz-2 5nkk-2 6j7c-1 2pwz-1 4hd4-d 4i1i-d 3l6r-1 6mgj-1 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-506470

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

B: 3-hydroxyproline dehydratse

D: 3-hydroxyproline dehydratse

hetero molecules

78.6 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)	122.584, 122.584, 167.593
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	96
Space group name H-M	P4₃2₁2

#1: Protein	3-hydroxyproline dehydratse Mass: 38954.188 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium vitis S4 (bacteria) / Strain: S4 / Gene: Avi_7022 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B9K4G4
#2: Chemical	ChemComp-CIT / CITRIC ACID Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₆H₈O₇
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Chemical	ChemComp-PYC / PYRROLE-2-CARBOXYLATE Mass: 110.091 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₅H₄NO₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 780 / 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: 4.04 Å³/Da / Density % sol: 69.56 %
Crystal grow	Temperature: 298 K / Method: sitting drop vapor diffusion / pH: 4.6 Details: Protein (10 mM Tris, 20 mM pyrrole 2-carboxylate, TEV Treated, Cleavage Unverified); Reservoir (0.1 M Sodium Acetate Trihydrate, 1 M di-Ammonium Hydrogen citrate (MCSG4 C6)); Cryoprotection ...Details: Protein (10 mM Tris, 20 mM pyrrole 2-carboxylate, TEV Treated, Cleavage Unverified); Reservoir (0.1 M Sodium Acetate Trihydrate, 1 M di-Ammonium Hydrogen citrate (MCSG4 C6)); Cryoprotection (Reservoir+20% glycerol), pH 4.6, sitting drop vapor diffusion, temperature 298K

Crystal

Density Matthews: 4.04 Å³/Da / Density % sol: 69.56 %

Crystal grow

Temperature: 298 K / Method: sitting drop vapor diffusion / pH: 4.6
Details: Protein (10 mM Tris, 20 mM pyrrole 2-carboxylate, TEV Treated, Cleavage Unverified); Reservoir (0.1 M Sodium Acetate Trihydrate, 1 M di-Ammonium Hydrogen citrate (MCSG4 C6)); Cryoprotection ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å
Detector	Type: RAYONIX 225 HE / Detector: CCD / Date: Apr 6, 2012 / 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: 2→33.52 Å / Num. all: 86628 / Num. obs: 86628 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / B_iso Wilson estimate: 19.8 Å² / R_merge(I) obs: 0.17 / R_sym value: 0.17 / Net I/σ(I): 11.6
Reflection shell	Resolution: 2→2.11 Å / Redundancy: 13.2 % / R_merge(I) obs: 0.836 / Mean I/σ(I) obs: 3.3 / Num. unique all: 12481 / R_sym value: 0.836 / % possible all: 100

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1TM0

1tm0

Resolution: 2→32.981 Å / Occupancy max: 1 / Occupancy min: 0.46 / FOM work R set: 0.9164 / SU ML: 0.14 / σ(F): 0 / σ(I): 0 / Phase error: 14.61 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.166	4336	5.01 %	RANDOM
R_work	0.1364	-	-	-
all	0.1379	86532	-	-
obs	0.1379	86532	99.99 %	-

Solvent computation

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

Displacement parameters

B_iso max: 114.66 Å² / B_iso mean: 27.0431 Å² / B_iso min: 7.21 Å²

Refinement step

Cycle: LAST / Resolution: 2→32.981 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5148	0	46	780	5974

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	5305
X-RAY DIFFRACTION	f_angle_d	1.311	7227
X-RAY DIFFRACTION	f_chiral_restr	0.076	833
X-RAY DIFFRACTION	f_plane_restr	0.007	952
X-RAY DIFFRACTION	f_dihedral_angle_d	14.789	1929

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all
2-2.0227	0.229	129	0.1952	2721	2850
2.0227-2.0465	0.2127	136	0.1901	2723	2859
2.0465-2.0715	0.2014	160	0.173	2675	2835
2.0715-2.0977	0.1969	139	0.17	2703	2842
2.0977-2.1253	0.2048	134	0.1593	2696	2830
2.1253-2.1544	0.1854	139	0.1542	2726	2865
2.1544-2.1852	0.1889	160	0.1473	2673	2833
2.1852-2.2178	0.1997	121	0.1451	2720	2841
2.2178-2.2525	0.1898	129	0.1407	2732	2861
2.2525-2.2894	0.1621	144	0.1356	2689	2833
2.2894-2.3288	0.1803	131	0.1307	2735	2866
2.3288-2.3712	0.1582	123	0.127	2718	2841
2.3712-2.4168	0.1665	132	0.1196	2747	2879
2.4168-2.4661	0.1499	136	0.1245	2709	2845
2.4661-2.5197	0.1691	156	0.1256	2699	2855
2.5197-2.5783	0.1733	136	0.1213	2733	2869
2.5783-2.6427	0.1543	138	0.1254	2724	2862
2.6427-2.7141	0.1818	156	0.1274	2726	2882
2.7141-2.794	0.1638	139	0.1354	2755	2894
2.794-2.8841	0.1662	134	0.1356	2735	2869
2.8841-2.9871	0.1651	181	0.1351	2701	2882
2.9871-3.1066	0.1691	158	0.1348	2722	2880
3.1066-3.2479	0.1694	152	0.1333	2736	2888
3.2479-3.419	0.166	150	0.1297	2748	2898
3.419-3.6329	0.1576	141	0.1243	2773	2914
3.6329-3.913	0.1485	145	0.1236	2778	2923
3.913-4.306	0.1404	178	0.1068	2754	2932
4.306-4.9274	0.122	151	0.1009	2817	2968
4.9274-6.2012	0.1614	164	0.1528	2827	2991
6.2012-32.985	0.1864	144	0.1978	3001	3145

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	0.1459	-0.0901	-0.0407	0.1696	-0.1007	0.3139	0.0127	-0.0272	-0.0073	0.0552	-0.0009	0.0221	-0.0113	-0.0092	0.0219	0.093	-0.0107	0.0152	0.0926	0.0178	0.0833	11.549	52.1094	64.3255
2	0.2475	-0.1908	0.0898	0.2623	-0.2042	0.2351	0.0124	0.1154	0.0496	-0.0126	-0.0432	-0.0291	-0.0435	-0.033	-0.0462	0.116	-0.0094	0.0169	0.1352	0.0277	0.106	13.3364	62.9643	48.6518
3	0.062	-0.0385	-0.0627	0.035	0.0307	0.0415	0.0771	0.1017	-0.0236	-0.1446	-0.2455	-0.1355	0.0513	0.0515	-0.0017	0.1389	0.0137	0.0253	0.231	0.0386	0.1363	25.4149	55.9376	41.7584
4	0.0772	0.0624	-0.1055	0.1183	-0.101	0.1093	0.0494	0.0333	0.0304	-0.0102	-0.0366	-0.0652	-0.0325	0.0532	0.0017	0.1194	0.0053	-0.0042	0.1294	0.0265	0.0968	15.6041	61.6648	47.1008
5	0.14	-0.1202	0.0031	0.1117	-0.1135	0.2028	0.1173	0.1577	0.0399	0.0386	-0.0785	0.0031	-0.0873	-0.1829	0.0381	0.148	0.0429	0.0194	0.1025	0.0471	0.0971	6.6111	67.6646	47.5353
6	0.0705	-0.1055	0.0112	0.2056	0.148	0.1169	0.0074	0.0031	0.0419	-0.0435	-0.0168	0.0051	0.0435	0.0172	0	0.0972	-0.0012	0.0059	0.1004	0.0304	0.1251	19.6472	39.675	59.3882
7	0.0644	0.0829	0.0351	0.1779	-0.0287	0.1876	-0.0209	-0.2752	0.0832	0.1407	0.0074	0.1628	0.0414	-0.0663	-0.0011	0.1649	-0.0075	0.0358	0.1456	-0.0109	0.2537	6.8978	32.3366	61.8414
8	0.3278	-0.1867	-0.1245	0.1643	0.0953	0.0891	0.0781	0.1004	-0.2183	-0.0627	-0.0942	0.2847	0.0816	0.0484	-0.0276	0.1731	-0.0143	-0.0507	0.0698	-0.0397	0.2776	12.4352	20.9955	53.3197
9	0.4626	0.0238	-0.1859	0.0424	0.0132	0.1724	0.022	-0.188	-0.4217	0.0354	0.0635	0.2798	-0.0425	0.0153	-0.032	0.2303	-0.0162	-0.0263	0.0503	-0.0084	0.2524	21.1654	14.8979	62.3099
10	0.2918	-0.0347	-0.0101	0.1609	-0	0.1968	0.3684	0.2994	-0.083	-0.3507	-0.2872	0.0372	0.1072	0.1424	0.0635	0.3687	0.1587	0.0582	0.2401	-0.0347	0.1127	35.2422	22.3188	39.1145
11	0.4191	0.0391	0.2393	0.011	0.0062	0.2316	0.2058	0.3304	0.3242	-0.205	-0.2222	-0.0904	0.0582	0.1232	-0.068	0.3071	0.1169	0.0402	0.2649	0.0384	0.0778	31.7539	32.348	38.6326
12	0.0248	0.0146	-0.0335	0.4268	-0.2021	0.13	0.2962	0.2152	-0.0433	-0.3499	-0.3397	-0.2118	0.1107	0.0779	-0.1262	0.3357	0.1443	-0.0543	0.216	-0.1119	0.0921	30.7232	18.7341	43
13	0.037	0.0203	-0.0323	0.0567	0.0262	0.0421	0.107	0.1353	-0.071	-0.1348	-0.1142	-0.0206	0.1137	0.0029	-0.0084	0.2173	0.0521	0.0156	0.1398	-0.0086	0.1154	31.2037	27.3312	49.7393
14	0.0821	-0.0509	0.0188	0.0759	-0.0298	0.0189	0.0629	0.1281	0.1026	-0.0905	-0.0665	-0.0654	0.0801	0.207	0.003	0.2187	0.0792	0.012	0.1081	-0.0198	0.1306	37.0562	16.8664	51.5103
15	0.0299	-0.0467	0.0192	0.0577	-0.0511	0.0313	0.1199	0.1715	-0.2303	-0.0798	-0.033	0.0904	-0.0226	0.0308	-0.0052	0.2536	0.2076	-0.0396	-0.2466	-0.2244	0.1958	30.5788	9.8743	51.7659
16	0.0848	0.006	0.064	0.1831	0.0838	0.0667	0.0445	0.065	-0.0896	-0.139	-0.045	0.0585	0.1608	-0.0067	0	0.1162	0.0119	-0.0121	0.117	-0.0039	0.1307	11.245	37.4512	51.6197

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'B' and (resid 5 through 117 )	B
2	X-RAY DIFFRACTION	2	chain 'B' and (resid 118 through 187 )	B
3	X-RAY DIFFRACTION	3	chain 'B' and (resid 188 through 208 )	B
4	X-RAY DIFFRACTION	4	chain 'B' and (resid 209 through 256 )	B
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 257 through 311 )	B
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 312 through 342 )	B
7	X-RAY DIFFRACTION	7	chain 'D' and (resid -9 through 24 )	D
8	X-RAY DIFFRACTION	8	chain 'D' and (resid 25 through 117 )	D
9	X-RAY DIFFRACTION	9	chain 'D' and (resid 118 through 142 )	D
10	X-RAY DIFFRACTION	10	chain 'D' and (resid 143 through 187 )	D
11	X-RAY DIFFRACTION	11	chain 'D' and (resid 188 through 208 )	D
12	X-RAY DIFFRACTION	12	chain 'D' and (resid 209 through 236 )	D
13	X-RAY DIFFRACTION	13	chain 'D' and (resid 237 through 256 )	D
14	X-RAY DIFFRACTION	14	chain 'D' and (resid 257 through 287 )	D
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 288 through 311 )	D
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 312 through 342 )	D

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