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

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Basic information

Entry
Database: PDB / ID: 2vvo
TitleCrystal structure of Mycobacterium tuberculosis ribose-5-phosphate isomerase B in complex with alpha d-allose 6-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
6-O-phosphono-alpha-D-allopyranose / Ribose-5-phosphate isomerase B / Ribose-5-phosphate isomerase B
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsRoos, A.K. / Mariano, S. / Kowalinski, E. / 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 1.3Jul 29, 2020Group: Data collection / Derived calculations / Other
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / pdbx_database_status / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_database_status.status_code_sf
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 13, 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

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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)87,79810
Polymers86,4985
Non-polymers1,3015
Water7,566420
1
A: RIBOSE-5-PHOSPHATE ISOMERASE B
B: RIBOSE-5-PHOSPHATE ISOMERASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1194
Polymers34,5992
Non-polymers5202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-35.3 kcal/mol
Surface area14820 Å2
MethodPQS
2
C: RIBOSE-5-PHOSPHATE ISOMERASE B
D: RIBOSE-5-PHOSPHATE ISOMERASE B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1194
Polymers34,5992
Non-polymers5202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4780 Å2
ΔGint-37.5 kcal/mol
Surface area14720 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)35,1194
Polymers34,5992
Non-polymers5202
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area4980 Å2
ΔGint-34.6 kcal/mol
Surface area14480 Å2
MethodPQS
Unit cell
Length a, b, c (Å)152.744, 92.501, 60.967
Angle α, β, γ (deg.)90.00, 98.92, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-2029-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.75208, -0.61603, 0.23425), (-0.61576, -0.7835, -0.08348), (0.23496, -0.08146, -0.96858)7.87969, 12.88402, -25.07828
2given(-0.30924, 0.95055, 0.0289), (0.94278, 0.30245, 0.1403), (0.12462, 0.07063, -0.98969)67.18098, -41.92689, 9.7219
3given(-0.81635, -0.54747, -0.18398), (0.54443, -0.83577, 0.07127), (-0.19279, -0.04199, 0.98034)76.42657, -33.62962, 36.83132
4given(0.34528, 0.93364, -0.09543), (-0.93404, 0.33195, -0.13183), (-0.09141, 0.13465, 0.98667)67.66603, 50.98852, 12.07473

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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: Sugar
ChemComp-A6P / 6-O-phosphono-alpha-D-allopyranose / 6-O-phosphono-alpha-D-allose / 6-O-phosphono-D-allose / 6-O-phosphono-allose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H13O9P
IdentifierTypeProgram
a-D-Allp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 420 / 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: 2.46 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growDetails: 1M TRI-NA CITRATE, 0.1M NA CACODYLATE PH 6.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.94
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 1.85→60.19 Å / Num. obs: 65360 / % possible obs: 91.7 % / Observed criterion σ(I): 2.6 / Redundancy: 4.2 % / Biso Wilson estimate: 23.4 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.8
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2.6 / % possible all: 61.8

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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: 1.85→40 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.332 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 2.6 / ESU R: 0.13 / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.196 3307 5.1 %RANDOM
Rwork0.16 ---
obs0.162 62048 91.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.56 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å20 Å2-0.17 Å2
2---0.39 Å20 Å2
3---0.91 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5897 0 80 420 6397
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0216102
X-RAY DIFFRACTIONr_bond_other_d0.0010.024047
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.9568309
X-RAY DIFFRACTIONr_angle_other_deg1.00239822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0435775
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.27423.214280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.14815920
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0161555
X-RAY DIFFRACTIONr_chiral_restr0.0880.2925
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026908
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021225
X-RAY DIFFRACTIONr_nbd_refined0.2090.21206
X-RAY DIFFRACTIONr_nbd_other0.2050.24175
X-RAY DIFFRACTIONr_nbtor_refined0.1680.22921
X-RAY DIFFRACTIONr_nbtor_other0.0860.22978
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2341
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0820.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3230.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1320.227
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0821.54212
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36126139
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.46332426
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6754.52170
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: 1.85→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.322 146
Rwork0.218 2786

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