PDB-4xda: Vibrio cholerae O395 Ribokinase complexed with Ribose, ADP and So...

ID or keywords:

Entry

Database: PDB / ID: 4xda

Title

Vibrio cholerae O395 Ribokinase complexed with Ribose, ADP and Sodium ion.

Components

Ribokinase

Keywords

TRANSFERASE / ribokinase / ribose / kinase

Function / homology

Function and homology information

ribokinase / ribokinase activity / D-ribose catabolic process / ATP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function

Biological species

Vibrio cholerae serotype O1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 1.75 Å

Authors

Paul, R. / Patra, M.D. / Sen, U.

Funding support

India, 1items

Citation

Journal: Adv.Exp.Med.Biol. / Year: 2015
Title: Crystal Structure of Apo and Ligand Bound Vibrio cholerae Ribokinase (Vc-RK): Role of Monovalent Cation Induced Activation and Structural Flexibility in Sugar Phosphorylation
Authors: Paul, R. / Patra, M.D. / Sen, U.

History

Deposition	Dec 19, 2014	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Mar 4, 2015	Provider: repository / Type: Initial release
Revision 2.0	Jul 29, 2020	Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / entity_src_gen / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_keywords / struct_site / struct_site_gen Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.name / _chem_comp.type / _citation.journal_id_CSD / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_keywords.text Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1	Mar 20, 2024	Group: Data collection / Database references / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4xda.cif.gz	478.2 KB	Display	PDBx/mmCIF format
PDB format	pdb4xda.ent.gz	390.7 KB	Display	PDB format
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Validation report

Summary document	4xda_validation.pdf.gz	2 MB	Display	wwPDB validaton report
Full document	4xda_full_validation.pdf.gz	2.1 MB	Display
Data in XML	4xda_validation.xml.gz	58.5 KB	Display
Data in CIF	4xda_validation.cif.gz	85.5 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/xd/4xda ftp://data.pdbj.org/pub/pdb/validation_reports/xd/4xda	HTTPS FTP

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Related structure data

Related structure data	4x8fC 4xckC C: citing same article (ref.)
Similar structure data	4xck-2 4xck-1 3b1q-1 3b1q-2 1gqt-2 1v1a-d 1rk2-2 1rk2-1 3i3y-1 7agh-2 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Ribokinase

B: Ribokinase

C: Ribokinase

D: Ribokinase

hetero molecules

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

1

A: Ribokinase

B: Ribokinase

hetero molecules

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

2

C: Ribokinase

D: Ribokinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	59.420, 70.700, 79.880
Angle α, β, γ (deg.)	106.29, 97.65, 98.68
Int Tables number	1
Space group name H-M	P1

#1: Protein

Ribokinase

Mass: 32392.740 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Vibrio cholerae serotype O1 (strain ATCC 39541 / Classical Ogawa 395 / O395) (bacteria)
Strain: ATCC 39541 / Classical Ogawa 395 / O395 / Gene: rbsK, VC0395_0007, VC395_A0124 / Plasmid: pET-28 A(+) / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21 -DE3
References: UniProt: A5F1B7, UniProt: A0A0H2UL04*PLUS, ribokinase

#2: Sugar

ChemComp-RIB / alpha-D-ribofuranose / alpha-D-ribose / D-ribose / ribose

Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₅H₁₀O₅

#3: Chemical

ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE

Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM

#4: Chemical

ChemComp-NA / SODIUM ION

Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na

#5: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 1168 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 2.44 Å³/Da / Density % sol: 49.51 % Description: rectangular parallelepiped, THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS.
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 Details: PEG 6000, MES buffer 0.1mM was used as precipitant. Crystal grown in 7 days. PH range: 6

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Data collection

Diffraction	Mean temperature: 100 K / Ambient temp details: 1 degree oscillation
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.973 Å
Detector	Type: MAR CCD 130 mm / Detector: CCD / Date: Feb 12, 2012
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.973 Å / Relative weight: 1
Reflection	Resolution: 1.75→27.42 Å / Num. obs: 117286 / % possible obs: 96.2 % / Redundancy: 4 % / R_sym value: 0.094 / Net I/σ(I): 8.4
Reflection shell	Resolution: 1.75→1.84 Å / Redundancy: 3.9 % / R_merge(I) obs: 0.617 / Mean I/σ(I) obs: 2.3 / % possible all: 94.3

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: 1.8_1069)	refinement
MOSFLM		data reduction
SCALA		data scaling
PHASER		phasing

Refinement

Resolution: 1.75→27.42 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 25.34 / Stereochemistry target values: ML
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2249	5882	5.02 %	Random selection
R_work	0.1865	-	-	-
obs	0.1885	117278	95.92 %	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 1.75→27.42 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	9000	0	169	1168	10337

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.011	9350
X-RAY DIFFRACTION	f_angle_d	1.278	12759
X-RAY DIFFRACTION	f_dihedral_angle_d	15.494	3397
X-RAY DIFFRACTION	f_chiral_restr	0.16	1528
X-RAY DIFFRACTION	f_plane_restr	0.005	1653

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.75-1.7699	0.2855	201	0.2553	3613	X-RAY DIFFRACTION	93
1.7699-1.7907	0.2844	204	0.251	3597	X-RAY DIFFRACTION	94
1.7907-1.8125	0.3161	194	0.2496	3688	X-RAY DIFFRACTION	93
1.8125-1.8355	0.2893	184	0.2397	3564	X-RAY DIFFRACTION	94
1.8355-1.8596	0.2649	167	0.2242	3758	X-RAY DIFFRACTION	94
1.8596-1.8851	0.2518	192	0.2149	3582	X-RAY DIFFRACTION	94
1.8851-1.912	0.2827	189	0.2086	3684	X-RAY DIFFRACTION	95
1.912-1.9406	0.2504	180	0.216	3662	X-RAY DIFFRACTION	95
1.9406-1.9709	0.2427	186	0.2007	3740	X-RAY DIFFRACTION	95
1.9709-2.0032	0.251	192	0.2073	3638	X-RAY DIFFRACTION	95
2.0032-2.0377	0.2551	234	0.2054	3696	X-RAY DIFFRACTION	95
2.0377-2.0747	0.2675	175	0.2048	3691	X-RAY DIFFRACTION	96
2.0747-2.1146	0.2671	198	0.2002	3732	X-RAY DIFFRACTION	96
2.1146-2.1578	0.2468	186	0.1937	3724	X-RAY DIFFRACTION	96
2.1578-2.2047	0.2338	196	0.194	3731	X-RAY DIFFRACTION	96
2.2047-2.2559	0.2391	186	0.1899	3687	X-RAY DIFFRACTION	96
2.2559-2.3123	0.2478	198	0.1919	3740	X-RAY DIFFRACTION	96
2.3123-2.3748	0.2506	176	0.1871	3744	X-RAY DIFFRACTION	96
2.3748-2.4447	0.2243	188	0.1919	3770	X-RAY DIFFRACTION	97
2.4447-2.5235	0.2407	220	0.1943	3704	X-RAY DIFFRACTION	97
2.5235-2.6136	0.2586	207	0.1896	3725	X-RAY DIFFRACTION	97
2.6136-2.7182	0.2375	196	0.1896	3784	X-RAY DIFFRACTION	97
2.7182-2.8418	0.2556	192	0.1916	3746	X-RAY DIFFRACTION	97
2.8418-2.9914	0.2211	200	0.184	3756	X-RAY DIFFRACTION	97
2.9914-3.1786	0.221	228	0.1823	3718	X-RAY DIFFRACTION	97
3.1786-3.4236	0.2082	200	0.1813	3766	X-RAY DIFFRACTION	97
3.4236-3.7674	0.2085	181	0.1749	3814	X-RAY DIFFRACTION	98
3.7674-4.3107	0.1705	191	0.1551	3792	X-RAY DIFFRACTION	98
4.3107-5.4242	0.1838	233	0.1586	3772	X-RAY DIFFRACTION	98
5.4242-27.476	0.1941	208	0.1805	3778	X-RAY DIFFRACTION	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	0.0417	-0.0013	-0.0508	0.088	-0.0622	0.0702	0.0291	0.1466	0.0175	-0.0273	0.0272	-0.0089	-0.0086	-0.0303	-0	0.1307	-0.0255	-0.0107	0.177	0.0018	0.1169	-8.2191	-12.9429	0.5141
2	0.0813	-0.0211	-0.0644	0.0998	0.0213	0.0617	0.0036	0.0658	0.0133	0.0485	0.0001	-0.0181	-0.033	0.006	0	0.1457	-0.0131	-0.0164	0.1368	0.0106	0.1274	-0.6974	-7.5666	11.9404
3	0.2364	-0.1494	-0.123	0.1439	0.0351	0.0886	0.0465	0.2335	0.135	-0.0912	0.0219	0.0415	-0.2343	-0.0577	0.0576	0.2194	-0.0428	0.0318	0.1239	0.0073	0.1571	-3.6563	0.9612	8.1819
4	0.0104	0.0023	-0.0062	0.0009	0.0031	0.0024	0.0416	0.0696	0.0958	-0.0172	0.0819	0.0019	-0.2038	0.0488	0	0.3116	-0.0217	0.0321	0.151	0.0273	0.2651	-2.2658	11.5718	10.1404
5	0.0743	0.0971	-0.0228	0.15	-0.03	0.0105	0.15	0.3927	0.2012	0.042	-0.0265	0.1404	-0.1691	-0.2071	0.0064	0.2362	0.0845	0.0022	0.2913	0.1062	0.2581	-6.6716	9.2433	-4.868
6	0.341	0.2743	0.2266	0.2134	0.1783	0.1687	0.0716	0.3317	0.1514	-0.001	0.112	-0.001	-0.3631	-0.11	0.105	0.4025	0.0336	0.0255	0.3807	0.1915	0.2884	0.8904	10.8219	-12.5165
7	0.0233	0.0048	-0.0205	0.025	0.0393	0.0516	0.086	0.3035	0.0643	0.0237	0.0358	0.0071	-0.0775	-0.0355	0.0011	0.1555	-0.0228	-0.0156	0.2246	0.0197	0.158	8.5284	-5.9681	-5.8003
8	0.2379	0.0089	-0.092	0.241	0.1895	0.1339	-0.0096	0.0792	0.0345	0.0159	0.0288	-0	-0.02	-0.0149	0.0007	0.1124	0.0038	-0.0283	0.172	0.0024	0.1473	-21.8133	-25.6911	7.5074
9	0.5924	0.1023	-0.1747	0.2215	-0.0525	0.1778	-0.056	0.2028	0.0309	-0.0535	0.0296	0.0814	0.0166	-0.0763	0.0006	0.0987	-0.0176	-0.0348	0.1887	-0.0183	0.1167	-38.3055	-33.8531	1.495
10	0.1507	-0.001	0.0734	0.0038	-0.0095	0.1488	-0.1835	-0.1428	-0.06	0.0955	-0.0005	0.2385	-0.0352	0.2149	-0.0816	0.2342	0.0499	0.0386	0.0959	0.0199	0.2041	-2.5487	-32.6583	-28.5711
11	0.1982	0.1129	-0.0642	0.1523	0.0841	0.2166	-0.2548	-0.1294	-0.1941	-0.0279	0.1649	-0.0296	-0.0821	0.3142	-0.0654	0.2456	0.1762	0.1808	-0.1369	-0.0033	0.2918	-1.7805	-46.4252	-33.2369
12	0.0023	-0.0016	0.0045	0.0036	0.002	-0.0047	-0.1154	0.0715	-0.0356	-0.0507	-0.0685	0.0237	0.1462	-0.0955	-0.0001	0.3636	-0.0454	0.1475	0.1787	-0.0256	0.3381	-13.2206	-54.4392	-40.8675
13	0.0198	-0.0031	-0.0093	0.0011	-0.007	0.0111	-0.1235	0.0434	-0.1293	-0.0145	0.1517	0.1998	-0.0066	-0.2104	-0	0.2787	-0.0314	0.0301	0.1863	0.0031	0.3649	-22.2293	-42.7983	-34.9589
14	0.0507	-0.0097	-0.0775	0.08	0.1548	0.3149	-0.189	-0.0702	-0.1528	0.0552	0.0487	0.2473	-0.0239	-0.2136	-0.0521	0.0035	0.1031	0.1351	0.0604	-0.0193	0.3483	-28.1962	-45.0787	-26.0913
15	0.045	0.0479	0.0169	0.0417	-0.009	0.2035	-0.1944	-0.1609	-0.1333	0.143	0.0586	0.1964	-0.0577	0.0329	-0.1825	0.2973	0.1246	0.1653	0.1357	0.053	0.2809	-11.3646	-45.0241	-16.4642
16	0.0093	0.0425	-0.0367	0.2828	0.0079	0.1583	0.0064	-0.0372	0.0028	-0.0399	0.0003	0.0333	0.1255	0.0835	0	0.1678	0.0128	-0.0251	0.1631	0.016	0.1596	10.8879	-20.2623	-35.6309
17	0.2196	0.0447	-0.1723	0.3735	-0.3412	0.3897	0.0519	-0.0299	-0.0455	0.0508	-0.021	0.0301	-0.108	0.0911	0.0001	0.1128	-0.0224	-0.0242	0.1505	-0.0193	0.1256	13.0674	-0.9557	-39.9087

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 39 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 40 through 99 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 100 through 139 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 140 through 159 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 160 through 199 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 200 through 239 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 240 through 306 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 1 through 119 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 120 through 306 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 1 through 39 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 40 through 139 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 140 through 159 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 160 through 199 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 200 through 239 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 240 through 306 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 1 through 119 )
17	X-RAY DIFFRACTION	17	chain 'D' and (resid 120 through 306 )

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