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- PDB-4xck: Vibrio cholerae O395 Ribokinase complexed with ADP, Ribose and Ce... -

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Basic information

Entry
Database: PDB / ID: 4xck
TitleVibrio cholerae O395 Ribokinase complexed with ADP, Ribose and Cesium ion.
ComponentsRibokinase
KeywordsTRANSFERASE / kinase / phosphotransfer / sugar binding protein
Function / homology
Function and homology information


ribokinase / ribokinase activity / D-ribose catabolic process / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Ribokinase / Ribokinase/fructokinase / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / alpha-D-ribofuranose / Ribokinase / Ribokinase
Similarity search - Component
Biological speciesVibrio cholerae serotype O1 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsPaul, R. / Patra, M.D. / Sen, U.
Funding support India, 1items
OrganizationGrant numberCountry
DEPARTMENT OF ATOMIC ENERGY, DEPARTMENT OF BIOTECHNOLOGY India
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.
#1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2014
Title: Crystallization and preliminary X-ray analysis of a ribokinase from Vibrio cholerae O395.
Authors: Paul, R. / Patra, M.D. / Banerjee, R. / Sen, U.
History
DepositionDec 18, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: chem_comp / entity ...chem_comp / entity / entity_src_gen / pdbx_entity_nonpoly / pdbx_prerelease_seq / pdbx_struct_oper_list / reflns_shell
Item: _chem_comp.type / _entity.pdbx_description ..._chem_comp.type / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _reflns_shell.Rmerge_I_obs
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_validate_close_contact / struct_conn / 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 / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_validate_close_contact.auth_atom_id_2 / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribokinase
B: Ribokinase
C: Ribokinase
D: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,53915
Polymers129,5714
Non-polymers2,96811
Water4,468248
1
A: Ribokinase
B: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4838
Polymers64,7852
Non-polymers1,6986
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-120 kcal/mol
Surface area22080 Å2
MethodPISA
2
C: Ribokinase
D: Ribokinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0567
Polymers64,7852
Non-polymers1,2705
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-118 kcal/mol
Surface area22350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.304, 69.553, 78.316
Angle α, β, γ (deg.)106.99, 98.77, 96.46
Int Tables number1
Space group name H-MP1

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Components

#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 / 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 / Ribose


Type: D-saccharide, alpha linking / Mass: 150.130 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H10O5
IdentifierTypeProgram
DRibfaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-ribofuranoseCOMMON NAMEGMML 1.0
a-D-RibfIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RibSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cs
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 248 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.53 % / Description: rectangular parallelepiped.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: PEG 6000, 0.1M MES BUFFER, pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.37→30 Å / Num. obs: 47045 / % possible obs: 93.8 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 5.1
Reflection shellResolution: 2.37→2.41 Å / Redundancy: 2.11 % / Mean I/σ(I) obs: 1.5 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RK2

1rk2


Resolution: 2.37→26.643 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2507 2243 5.05 %Random selection
Rwork0.1882 ---
obs0.1914 44384 93.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.37→26.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9000 0 159 248 9407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0139370
X-RAY DIFFRACTIONf_angle_d1.27812772
X-RAY DIFFRACTIONf_dihedral_angle_d16.1453403
X-RAY DIFFRACTIONf_chiral_restr0.1251527
X-RAY DIFFRACTIONf_plane_restr0.0051660
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.37-2.42150.31281250.27212605X-RAY DIFFRACTION93
2.4215-2.47780.32891400.25732673X-RAY DIFFRACTION93
2.4778-2.53970.33491490.25362592X-RAY DIFFRACTION94
2.5397-2.60840.33371390.23542633X-RAY DIFFRACTION94
2.6084-2.6850.29881430.23492647X-RAY DIFFRACTION94
2.685-2.77160.34611270.22842648X-RAY DIFFRACTION94
2.7716-2.87060.30641530.2252610X-RAY DIFFRACTION94
2.8706-2.98540.28951300.21272644X-RAY DIFFRACTION94
2.9854-3.1210.28271320.21422681X-RAY DIFFRACTION94
3.121-3.28530.28241480.20842643X-RAY DIFFRACTION94
3.2853-3.49070.2961480.19762603X-RAY DIFFRACTION94
3.4907-3.75950.23741450.17922630X-RAY DIFFRACTION94
3.7595-4.13660.22191370.15912614X-RAY DIFFRACTION93
4.1366-4.73230.18831470.13842617X-RAY DIFFRACTION94
4.7323-5.95120.2091360.16492665X-RAY DIFFRACTION94
5.9512-26.64490.20351440.15992636X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
11.08820.37-0.20380.93150.55230.47320.0155-0.02860.05960.00150.0206-0.0229-0.02140.0191-0.03630.2881-0.0102-0.00720.36060.00920.3062-22.1218-25.94916.6821
21.305-0.0629-0.02490.9131-0.13131.0609-0.01340.2922-0.0096-0.11380.00110.09710.0429-0.19990.01360.2811-0.0258-0.0130.4127-0.00050.2938-39.1421-33.39490.7729
32.04781.2464-0.78822.56070.51081.1137-0.02630.3178-0.0274-0.00580.20570.0180.06550.0619-0.15930.27450.0064-0.0210.32930.04710.2815-5.1803-10.86791.3517
41.30610.1944-0.37770.947-0.15021.30010.00190.06120.15940.06320.07120.0461-0.16770.0058-0.03860.3405-0.00120.00660.31280.01140.3158-2.2052-0.50898.847
51.579-0.2069-0.55220.9787-0.1142.15340.01730.64660.31810.05220.12620.2071-0.6434-0.361-0.09540.53770.07650.01260.54560.1430.4571-3.198211.6389-8.9767
61.12560.214-0.56110.8045-0.24051.31810.01440.23130.0817-0.12530.01860.0211-0.1172-0.1508-0.01660.3341-0.00840.00790.43160.0250.31438.1981-2.9821-8.2822
71.91460.8751-0.10250.40930.07021.58140.0392-0.00330.0184-0.0695-0.0201-0.0503-0.1145-0.0010.01490.38710.04050.05630.33060.04970.3738-5.4497-35.3328-29.8039
81.16360.7889-0.05821.0392-0.10750.9533-0.17790.0302-0.2653-0.09710.096-0.07310.16340.0970.05320.38850.00780.05850.32880.01080.3919-4.4908-45.5084-33.4316
91.82230.6997-0.26521.4028-0.53691.4746-0.10850.3608-0.0173-0.23370.10050.27650.0675-0.56360.05280.4646-0.0125-0.04130.49150.00650.586-25.9696-42.9031-33.3021
101.96070.1486-0.54880.9846-0.4211.1266-0.031-0.0755-0.05910.0055-0.13320.2846-0.1495-0.19710.03660.5175-0.00060.11070.56-0.06090.4949-22.7077-40.5545-19.398
110.82930.0566-0.33310.7426-0.17191.1656-0.1016-0.0366-0.18530.04050.02540.0319-0.01110.03940.07080.42290.04350.07490.33780.02010.4319-12.4571-46.4974-16.7344
120.57050.7985-0.26611.2685-0.10741.0346-0.085-0.0973-0.0287-0.0613-0.0174-0.0030.06960.0150.09740.35220.0147-0.00150.34610.00320.339112.6371-18.8552-34.4439
130.7604-0.2818-0.37730.6162-0.26131.54210.05840.04820.02850.02520.01090.0219-0.11020.0493-0.050.283-0.0270.0010.3255-0.00570.310412.8999-0.301-40.5293
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 122 )
2X-RAY DIFFRACTION2chain 'B' and (resid 123 through 306 )
3X-RAY DIFFRACTION3chain 'A' and (resid 1 through 50 )
4X-RAY DIFFRACTION4chain 'A' and (resid 51 through 171 )
5X-RAY DIFFRACTION5chain 'A' and (resid 172 through 220 )
6X-RAY DIFFRACTION6chain 'A' and (resid 221 through 306 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 27 )
8X-RAY DIFFRACTION8chain 'C' and (resid 28 through 162 )
9X-RAY DIFFRACTION9chain 'C' and (resid 163 through 220 )
10X-RAY DIFFRACTION10chain 'C' and (resid 221 through 249 )
11X-RAY DIFFRACTION11chain 'C' and (resid 250 through 306 )
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 131 )
13X-RAY DIFFRACTION13chain 'D' and (resid 132 through 306 )

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