PDB-4lb0: Crystal structure of a hydroxyproline epimerase from agrobacteriu...

ID or keywords:

Entry

Database: PDB / ID: 4lb0

Title

Crystal structure of a hydroxyproline epimerase from agrobacterium vitis, target efi-506420, with bound trans-4-oh-l-proline

Components

Uncharacterized protein

Keywords

ISOMERASE / PROLINE RACEMASE FAMILY / PROPOSED 3-OH and 4-OH PROLINE EPIMERASE / ENZYME FUNCTION INITIATIVE / EFI / Structural Genomics

Function / homology

Function and homology information

4-hydroxyproline epimerase / 4-hydroxyproline epimerase activity
Similarity search - Function

Biological species

Agrobacterium vitis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.7 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. / Glenn, A.S. ...

Citation

Journal: To be Published
Title: Crystal structure of a hydroxyproline epimerase from agrobacterium vitis, target efi-506420, with bound trans-4-oh-l-proline
Authors: Vetting, M.W. / Toro, R. / Bhosle, R. / Al Obaidi, N.F. / Morisco, L.L. / Wasserman, S.R. / Sojitra, S. / Stead, M. / Washington, E. / Glenn, A.S. / Chowdhury, S. / Evans, B. / Hammonds, J. ...

History

Deposition	Jun 20, 2013	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 17, 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	4lb0.cif.gz	394.7 KB	Display	PDBx/mmCIF format
PDB format	pdb4lb0.ent.gz	330 KB	Display	PDB format
PDBx/mmJSON format	4lb0.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4lb0_validation.pdf.gz	463.6 KB	Display	wwPDB validaton report
Full document	4lb0_full_validation.pdf.gz	465.2 KB	Display
Data in XML	4lb0_validation.xml.gz	32.2 KB	Display
Data in CIF	4lb0_validation.cif.gz	49.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/lb/4lb0 ftp://data.pdbj.org/pub/pdb/validation_reports/lb/4lb0	HTTPS FTP

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Related structure data

Related structure data	4k8lS S: Starting model for refinement
Similar structure data	6j7c-1 1og0-3 4kc1-1 4k7g-d 5zi2-d 4q2h-d 5g0y-d 6bm7-1 6mgj-1 1xql-d 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-506420

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uncharacterized protein

B: Uncharacterized protein

hetero molecules

74.9 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)	178.014, 178.014, 49.735
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	94
Space group name H-M	P4₂2₁2

Components on special symmetry positions

ID	Model	Components
1	1	B-584- HOH
2	1	B-624- HOH

#1: Protein	Uncharacterized protein Mass: 37302.648 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Agrobacterium vitis (bacteria) / Strain: S4 / Gene: Avi_0518 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B9JQV3
#2: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-HYP / 4-HYDROXYPROLINE / HYDROXYPROLINE Type: L-peptide linking / Mass: 131.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₅H₉NO₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 699 / 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: 2.64 Å³/Da / Density % sol: 53.42 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein (15 mM Bis-Tris, 500 mM NaCl, 10% glycerol, 5 mM DTT, 200 mM 4-OH PROLINE, TEV Treated, Cleavage Unverified); Reservoir (0.1 M NaAcetate, 25% Peg4000, 8% 2-propanol (MCSG4 H2)); ...Details: Protein (15 mM Bis-Tris, 500 mM NaCl, 10% glycerol, 5 mM DTT, 200 mM 4-OH PROLINE, TEV Treated, Cleavage Unverified); Reservoir (0.1 M NaAcetate, 25% Peg4000, 8% 2-propanol (MCSG4 H2)); Cryoprotection (Reservoir+20% isopropanaol) , pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal

Density Matthews: 2.64 Å³/Da / Density % sol: 53.42 %

Crystal grow

Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein (15 mM Bis-Tris, 500 mM NaCl, 10% glycerol, 5 mM DTT, 200 mM 4-OH PROLINE, TEV Treated, Cleavage Unverified); Reservoir (0.1 M NaAcetate, 25% Peg4000, 8% 2-propanol (MCSG4 H2)); ...

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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 MX225HE / Detector: CCD / Date: Jun 12, 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: 1.7→125.875 Å / Num. all: 88126 / Num. obs: 88126 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.4 % / R_merge(I) obs: 0.078 / R_sym value: 0.078 / Net I/σ(I): 18.3

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
1.7-1.79	7.9	0.745	1	99779	12695	0.745	99.9
1.79-1.9	8.5	0.488	1.6	102322	12030	0.488	100
1.9-2.03	8.9	0.317	2.3	100829	11312	0.317	99.9
2.03-2.19	9.6	0.204	3.5	101693	10565	0.204	99.9
2.19-2.4	10.2	0.153	4.7	99394	9738	0.153	99.9
2.4-2.69	11.5	0.104	7.1	102340	8863	0.104	100
2.69-3.1	13.1	0.075	9.5	103365	7903	0.075	100
3.1-3.8	13.8	0.054	12.1	92721	6704	0.054	100
3.8-5.38	13.9	0.035	18.4	73165	5270	0.035	100
5.38-178.014	13	0.032	21.2	39677	3046	0.032	98.7

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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 4K8L

4k8l

Resolution: 1.7→33.165 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.8796 / SU ML: 0.17 / σ(F): 1.34 / σ(I): 0 / Phase error: 18.7 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1919	4395	5.02 %	RANDOM
R_work	0.1576	-	-	-
obs	0.1594	87548	99.31 %	-
all	-	87548	-	-

Solvent computation

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

Displacement parameters

B_iso max: 107.96 Å² / B_iso mean: 28.1106 Å² / B_iso min: 9.26 Å²

Refinement step

Cycle: LAST / Resolution: 1.7→33.165 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5173	0	17	699	5889

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.01	5318
X-RAY DIFFRACTION	f_angle_d	1.32	7228
X-RAY DIFFRACTION	f_chiral_restr	0.081	833
X-RAY DIFFRACTION	f_plane_restr	0.008	948
X-RAY DIFFRACTION	f_dihedral_angle_d	13.522	1930

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 (%)
1.7-1.7193	0.2729	149	0.2291	2724	2873	100
1.7193-1.7395	0.2861	147	0.2142	2719	2866	100
1.7395-1.7608	0.2319	126	0.2051	2802	2928	100
1.7608-1.783	0.2282	143	0.1953	2768	2911	100
1.783-1.8065	0.2209	129	0.1903	2718	2847	100
1.8065-1.8313	0.2526	161	0.1841	2778	2939	100
1.8313-1.8574	0.246	158	0.1821	2723	2881	100
1.8574-1.8851	0.2508	133	0.2122	2754	2887	100
1.8851-1.9146	0.3745	144	0.3108	2667	2811	96
1.9146-1.946	0.3826	141	0.3178	2646	2787	97
1.946-1.9795	0.2133	135	0.1842	2775	2910	100
1.9795-2.0155	0.1879	137	0.1621	2758	2895	100
2.0155-2.0543	0.2359	137	0.1717	2784	2921	100
2.0543-2.0962	0.2698	150	0.2191	2705	2855	99
2.0962-2.1418	0.1898	148	0.1507	2751	2899	100
2.1418-2.1916	0.2014	135	0.1478	2811	2946	100
2.1916-2.2464	0.2487	154	0.1924	2662	2816	97
2.2464-2.3071	0.2359	142	0.2061	2657	2799	96
2.3071-2.375	0.197	163	0.1379	2801	2964	100
2.375-2.4516	0.1564	141	0.131	2746	2887	100
2.4516-2.5392	0.1762	149	0.1289	2797	2946	100
2.5392-2.6408	0.1636	154	0.1227	2811	2965	100
2.6408-2.761	0.16	169	0.1348	2786	2955	100
2.761-2.9064	0.1734	120	0.1316	2810	2930	100
2.9064-3.0884	0.1565	146	0.1389	2824	2970	100
3.0884-3.3267	0.1472	169	0.1368	2808	2977	100
3.3267-3.6611	0.1874	166	0.1372	2800	2966	100
3.6611-4.1899	0.1496	151	0.1373	2849	3000	99
4.1899-5.2755	0.1357	154	0.117	2892	3046	100
5.2755-33.1709	0.1918	144	0.1636	3027	3171	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	2.09	0.767	0.3529	0.9695	-0.2319	1.3705	0.1002	-0.2896	0.3402	0.5351	-0.1416	0.3054	-0.2669	-0.071	-0.0166	0.4034	-0.0582	0.1056	0.1705	-0.0317	0.2089	47.568	28.6797	31.0582
2	1.1161	0.0722	-0.0411	2.3958	-0.085	1.4042	0.2237	-0.1918	0.1279	0.3013	-0.1343	0.0993	-0.2288	0.0144	-0.0651	0.2809	-0.0527	0.0683	0.1611	-0.013	0.1361	50.1795	26.5089	30.5473
3	1.6975	0.159	-0.6818	2.1681	-0.9896	2.6396	0.1981	0.0885	0.2397	0.2885	0.0397	0.3363	-0.4179	-0.3181	-0.147	0.2137	0.0163	0.0885	0.1525	0.0404	0.194	49.405	33.3	19.3099
4	6.463	-0.6544	1.0729	4.1993	0.8702	3.4212	0.2917	0.3927	0.0158	0.1771	-0.1331	0.9202	-0.2991	-0.7981	-0.0097	0.1845	0.0324	0.0895	0.3145	0.0989	0.3519	47.2959	36.0038	10.0271
5	1.8964	0.5522	-0.1972	4.3825	0.0854	2.4086	-0.0331	-0.0169	-0.4346	0.0281	-0.1404	-0.6518	0.3461	0.3295	0.1282	0.1595	0.0146	0.0655	0.1805	0.0657	0.2591	68.9435	15.0112	13.6542
6	6.0869	2.0366	2.8884	4.4224	0.8592	5.6648	0.0812	-0.3885	-0.6712	0.3298	-0.1528	-0.5973	0.2604	0.0467	-0.0663	0.2008	0.0136	0.0243	0.1579	0.087	0.2682	63.0494	7.826	19.6868
7	1.489	0.5668	-0.6103	2.9863	0.8193	2.2207	-0.0596	0.0806	-0.1553	-0.0814	-0.0563	-0.3977	-0.0816	0.3095	0.0875	0.1639	-0.049	0.0352	0.1798	0.0606	0.1618	64.4113	19.9654	15.2593
8	1.553	1.1688	-0.8614	2.4381	-0.8779	1.0751	-0.1	0.1465	-0.0595	-0.13	0.0728	-0.1282	0.0383	-0.0217	0.0285	0.1533	-0.0261	0.0347	0.1476	0.0169	0.1202	60.9684	23.6473	8.7267
9	2.9319	2.3215	-1.6493	1.6298	-1.211	1.9676	0.049	0.2439	-0.037	0.2127	0.0241	0.0249	-0.1929	-0.1691	-0.0334	0.207	0.0111	0.0294	0.1042	0.0508	0.1763	51.4779	28.4834	16.193
10	1.7722	-0.7918	-0.3474	7.1934	2.4884	3.2362	0.1518	-0.8013	-0.0901	1.0725	-0.2053	-0.3607	-0.0597	-0.1302	0.032	0.3541	-0.0658	-0.024	0.3548	0.0206	0.188	48.0957	10.559	34.3206
11	1.9145	0.1594	0.3993	1.4394	0.534	1.1828	-0.028	0.2499	0.2805	-0.3022	-0.0048	0.1758	-0.3318	0.0022	-0.0527	0.2137	0.032	-0.0066	0.1325	0.0667	0.154	25.5807	12.5862	20.7692
12	2.6908	-0.3958	-0.1217	1.0929	-0.1012	1.5176	-0.1134	0.113	0.1164	-0.1217	0.0928	0.1375	-0.0431	-0.0487	0.0216	0.19	0.0126	-0.0398	0.1242	0.0469	0.1563	27.2535	9.7118	21.0134
13	1.4257	-0.881	-0.343	1.6692	0.4159	1.6944	-0.0575	-0.1933	0.0209	0.159	0.0582	0.0216	-0.1314	-0.0332	0.0074	0.1323	0.0198	-0.0012	0.1262	0.0338	0.1299	23.503	8.8173	36.6387
14	3.6928	-0.5272	-0.2363	0.8096	0.0143	0.7546	-0.0539	0.0192	-0.4353	0.0291	0.0122	-0.0088	0.146	0.1099	0.0454	0.1435	0.026	-0.0089	0.1181	0.0543	0.2152	38.2307	-14.4181	30.0945
15	7.487	2.9144	3.4909	5.653	3.8359	7.6947	-0.1255	0.4782	-0.2901	-0.4393	0.0595	-0.2773	-0.1469	0.2732	-0.041	0.1278	0.0502	0.0268	0.0997	0.0208	0.1471	44.6217	-8.2895	23.6925
16	3.5408	-0.5446	0.99	1.9429	-0.4999	1.5293	-0.023	-0.1631	-0.3141	0.0965	0.0141	-0.0243	0.0015	0.0326	-0.023	0.1168	0.0122	0.0028	0.0858	0.0598	0.1633	33.7811	-8.8593	30.5769
17	1.4416	-0.1196	-0.0609	1.4762	0.0484	0.9196	-0.034	-0.2729	-0.2321	0.2366	0.0641	0.0659	0.0488	0.0076	0.0108	0.1287	0.0348	0.0051	0.1365	0.0939	0.149	32.4455	-6.7797	38.4348
18	2.4245	1.9457	-0.2247	4.2583	-0.807	2.7482	0.1337	-0.0803	-0.0638	0.4257	-0.0133	0.0093	-0.2109	0.0861	-0.1194	0.0049	0.0763	0.0387	0.1254	0.0193	0.1147	27.9515	4.1572	35.2544
19	4.824	-4.2342	1.251	6.3942	-2.1722	2.218	-0.2683	1.2562	-0.0291	-0.7656	0.1118	0.0713	-0.1259	-0.0037	0.1435	0.3821	-0.1226	-0.035	0.3922	0.0831	0.1914	41.179	11.5952	12.5858

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 44 )	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 45 through 79 )	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 80 through 125 )	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 126 through 145 )	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 146 through 190 )	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 191 through 211 )	A
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 212 through 244 )	A
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 245 through 298 )	A
9	X-RAY DIFFRACTION	9	chain 'A' and (resid 299 through 321 )	A
10	X-RAY DIFFRACTION	10	chain 'A' and (resid 322 through 344 )	A
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 0 through 44 )	B
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 45 through 79 )	B
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 80 through 145 )	B
14	X-RAY DIFFRACTION	14	chain 'B' and (resid 146 through 190 )	B
15	X-RAY DIFFRACTION	15	chain 'B' and (resid 191 through 211 )	B
16	X-RAY DIFFRACTION	16	chain 'B' and (resid 212 through 244 )	B
17	X-RAY DIFFRACTION	17	chain 'B' and (resid 245 through 298 )	B
18	X-RAY DIFFRACTION	18	chain 'B' and (resid 299 through 320 )	B
19	X-RAY DIFFRACTION	19	chain 'B' and (resid 321 through 346 )	B

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