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- PDB-2vvq: Crystal structure of Mycobacterium tuberculosis ribose-5-phosphat... -

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Basic information

Entry
Database: PDB / ID: 2vvq
TitleCrystal structure of Mycobacterium tuberculosis ribose-5-phosphate isomerase B in complex with the inhibitor 5-deoxy-5-phospho-D- ribonate
ComponentsRIBOSE-5-PHOSPHATE ISOMERASE B
KeywordsISOMERASE / PENTOSE PHOSPHATE PATHWAY / RPIB / RV2465C / CARBOHYDRATE METABOLISM
Function / homology
Function and homology information


D-allose catabolic process / ribose-5-phosphate isomerase / ribose-5-phosphate isomerase activity / pentose-phosphate shunt, non-oxidative branch / carbohydrate metabolic process / extracellular region
Similarity search - Function
Ribose 5-phosphate isomerase B, Actinobacteria-type / Sugar-phosphate isomerase, RpiB/LacA/LacB family / Sugar-phosphate isomerase, RpiB/LacA/LacB superfamily / Ribose/Galactose Isomerase / Ribose 5-phosphate Isomerase B; Chain: A, / Sugar-phosphate isomerase, RpiB/LacA/LacB / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
5-O-phosphono-D-ribonic acid / Ribose-5-phosphate isomerase B / Ribose-5-phosphate isomerase B
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKowalinski, E. / Roos, A.K. / Mariano, S. / Salmon, L. / Mowbray, S.L.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: D-Ribose-5-Phosphate Isomerase B from Escherichia Coli is Also a Functional D-Allose-6-Phosphate Isomerase, While the Mycobacterium Tuberculosis Enzyme is not.
Authors: Roos, A.K. / Mariano, S. / Kowalinski, E. / Salmon, L. / Mowbray, S.L.
History
DepositionJun 10, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RIBOSE-5-PHOSPHATE ISOMERASE B
B: RIBOSE-5-PHOSPHATE ISOMERASE B
C: RIBOSE-5-PHOSPHATE ISOMERASE B
D: RIBOSE-5-PHOSPHATE ISOMERASE B
E: RIBOSE-5-PHOSPHATE ISOMERASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,92012
Polymers86,4985
Non-polymers1,4237
Water9,854547
1
A: RIBOSE-5-PHOSPHATE ISOMERASE B
B: RIBOSE-5-PHOSPHATE ISOMERASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1875
Polymers34,5992
Non-polymers5883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-33.1 kcal/mol
Surface area14620 Å2
MethodPQS
2
C: RIBOSE-5-PHOSPHATE ISOMERASE B
D: RIBOSE-5-PHOSPHATE ISOMERASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1875
Polymers34,5992
Non-polymers5883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5290 Å2
ΔGint-32.2 kcal/mol
Surface area14730 Å2
MethodPQS
3
E: RIBOSE-5-PHOSPHATE ISOMERASE B
hetero molecules

E: RIBOSE-5-PHOSPHATE ISOMERASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0914
Polymers34,5992
Non-polymers4922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5190 Å2
ΔGint-36.7 kcal/mol
Surface area14550 Å2
MethodPQS
Unit cell
Length a, b, c (Å)136.369, 102.119, 69.604
Angle α, β, γ (deg.)90.00, 96.18, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2042-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.39359, 0.91323, 0.10533), (0.9122, 0.37379, 0.16787), (0.11393, 0.16216, -0.98017)22.03996, -16.93469, 19.20143
2given(-0.35413, -0.92553, 0.13407), (-0.92331, 0.32324, -0.20741), (0.14863, -0.19724, -0.96902)38.73606, 34.63326, 50.30714
3given(-0.68949, -0.64804, -0.32349), (0.63732, -0.75502, 0.15413), (-0.34413, -0.0999, 0.93359)49.16639, 4.88663, 38.24229
4given(-0.75853, 0.54709, -0.35401), (-0.55088, -0.82856, -0.10009), (-0.34808, 0.11909, 0.92987)80.79425, 5.48696, 30.44961

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Components

#1: Protein
RIBOSE-5-PHOSPHATE ISOMERASE B / RIBOSE-5-PHOSPHATE ISOMERASE / PHOSPHORIBOISOMERASE B


Mass: 17299.514 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PCRT7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q79FD7, UniProt: P9WKD7*PLUS, ribose-5-phosphate isomerase
#2: Chemical
ChemComp-R10 / 5-O-phosphono-D-ribonic acid


Mass: 246.109 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H11O9P
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.9 % / Description: NONE
Crystal growDetails: 15% PEG 8000,0.1 M MES PH6, 5% PEG 1000, 0.2 M LISO4

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.94
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 14, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 2→81.65 Å / Num. obs: 62962 / % possible obs: 98.5 % / Observed criterion σ(I): 3 / Redundancy: 2.6 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.7
Reflection shellResolution: 2→2.11 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
REFMAC5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1USL

1usl


Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.015 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.193 3193 5.1 %RANDOM
Rwork0.159 ---
obs0.161 59767 98.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å20 Å2-0.37 Å2
2---0.01 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5915 0 85 547 6547
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0216113
X-RAY DIFFRACTIONr_bond_other_d0.0020.024048
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.9538317
X-RAY DIFFRACTIONr_angle_other_deg1.00839816
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3345778
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.57923.214280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94315921
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3531555
X-RAY DIFFRACTIONr_chiral_restr0.0820.2917
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026941
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021228
X-RAY DIFFRACTIONr_nbd_refined0.2370.21286
X-RAY DIFFRACTIONr_nbd_other0.2020.24267
X-RAY DIFFRACTIONr_nbtor_refined0.1690.22926
X-RAY DIFFRACTIONr_nbtor_other0.0850.23042
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2475
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3270.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.232
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.45824001
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.07736165
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.45422396
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2732152
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.264 206
Rwork0.195 4383

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