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

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Basic information

Entry
Database: PDB / ID: 2vvp
TitleCrystal structure of Mycobacterium tuberculosis ribose-5-phosphate isomerase B in complex with its substrates ribose 5-phosphate and ribulose 5-phosphate
ComponentsRIBOSE-5-PHOSPHATE ISOMERASE B
KeywordsISOMERASE / RPIB / RV2465C / RARE SUGAR / CARBOHYDRATE METABOLISM / PENTOSE PHOSPHATE PATHWAY
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
RIBULOSE-5-PHOSPHATE / 5-O-phosphono-D-ribose / Ribose-5-phosphate isomerase B / Ribose-5-phosphate isomerase B
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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)88,79915
Polymers86,4985
Non-polymers2,30110
Water17,673981
1
A: RIBOSE-5-PHOSPHATE ISOMERASE B
B: RIBOSE-5-PHOSPHATE ISOMERASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,5196
Polymers34,5992
Non-polymers9204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4960 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)35,5196
Polymers34,5992
Non-polymers9204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5220 Å2
ΔGint-37.5 kcal/mol
Surface area14710 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)35,5196
Polymers34,5992
Non-polymers9204
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5290 Å2
ΔGint-37.7 kcal/mol
Surface area14760 Å2
MethodPQS
Unit cell
Length a, b, c (Å)136.832, 103.058, 69.728
Angle α, β, γ (deg.)90.00, 95.51, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2078-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.39722, 0.91359, 0.08703), (0.91281, 0.3835, 0.14038), (0.09487, 0.13521, -0.98626)22.72341, -16.97616, 19.99602
2given(-0.35306, -0.92494, 0.14083), (-0.92395, 0.32101, -0.20804), (0.14722, -0.20357, -0.96793)39.06989, 35.13174, 50.42159
3given(-0.6903, -0.65919, -0.29825), (0.64246, -0.74805, 0.16635), (-0.33276, -0.07678, 0.93988)49.54621, 4.54831, 37.83466
4given(-0.76512, 0.53876, -0.35261), (-0.54707, -0.83273, -0.08527), (-0.33957, 0.12766, 0.93188)81.86645, 5.33485, 30.31059

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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-R52 / 5-O-phosphono-D-ribose


Mass: 230.110 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C5H11O8P
#3: Sugar
ChemComp-5RP / RIBULOSE-5-PHOSPHATE


Type: saccharide / Mass: 230.110 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 981 / 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: 2.83 Å3/Da / Density % sol: 56.5 % / Description: NONE
Crystal growDetails: 20% PEG 3000, 0.1 M TRIS PH 7, 0.2 M CA ACETATE

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: May 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.65→35 Å / Num. obs: 115358 / % possible obs: 99.9 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Biso Wilson estimate: 19.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.3
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3 / % possible all: 99.9

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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: 1.65→34.71 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU B: 1.501 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.187 5805 5 %RANDOM
Rwork0.166 ---
obs0.168 109551 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.95 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å2-0.78 Å2
2---0.45 Å20 Å2
3---0.21 Å2
Refinement stepCycle: LAST / Resolution: 1.65→34.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5929 0 140 981 7050
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0216192
X-RAY DIFFRACTIONr_bond_other_d0.0020.024095
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.9638420
X-RAY DIFFRACTIONr_angle_other_deg1.31139945
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8925782
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.53923.262282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1615926
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6181555
X-RAY DIFFRACTIONr_chiral_restr0.1060.2934
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026987
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021242
X-RAY DIFFRACTIONr_nbd_refined0.2150.21356
X-RAY DIFFRACTIONr_nbd_other0.2090.24598
X-RAY DIFFRACTIONr_nbtor_refined0.1720.23017
X-RAY DIFFRACTIONr_nbtor_other0.0870.23037
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2743
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1230.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3430.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1330.268
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9931.55041
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.0526182
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.97532600
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8434.52238
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: 1.65→1.69 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.294 441
Rwork0.251 8015

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