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- PDB-2bes: Structure of Mycobacterium tuberculosis Ribose-5-Phosphate Isomer... -

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Basic information

Entry
Database: PDB / ID: 2bes
TitleStructure of Mycobacterium tuberculosis Ribose-5-Phosphate Isomerase, RpiB, Rv2465c, in complex with 4-phospho-D-erythronohydroxamic acid.
ComponentsCARBOHYDRATE-PHOSPHATE ISOMERASE
KeywordsISOMERASE / RIBOSE 5-PHOSPHATE EPIMERASE / PHOSPHOPENTOSISOMERASE / PENTOSE PHOSPHATE PATHWAY / HIGH-ENERGY ENEDIOLATE INTERMEDIATE
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
4-PHOSPHO-D-ERYTHRONOHYDROXAMIC 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: 2.1 Å
AuthorsRoos, A.K. / Ericsson, D.J. / Mowbray, S.L.
Citation
Journal: J.Biol.Chem. / Year: 2005
Title: Competitive Inhibitors of Mycobacterium Tuberculosis Ribose-5-Phosphate Isomerase B Reveal New Information About the Reaction Mechanism.
Authors: Roos, A.K. / Burgos, E. / Ericsson, D.J. / Salmon, L. / Mowbray, S.L.
#1: Journal: J.Mol.Biol. / Year: 2004
Title: Mycobacterium Tuberculosis Ribose-5-Phosphate Isomerase Has a Known Fold, But a Novel Active Site
Authors: Roos, A.K. / Andersson, C.E. / Bergfors, T. / Jacobsson, M. / Karlen, A. / Unge, T. / Jones, T.A. / Mowbray, S.L.
History
DepositionNov 30, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 3, 2004Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Version format compliance
Revision 1.2Jul 5, 2017Group: Refinement description / Category: software
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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)93,53010
Polymers92,3745
Non-polymers1,1555
Water7,026390
1
A: CARBOHYDRATE-PHOSPHATE ISOMERASE
B: CARBOHYDRATE-PHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4124
Polymers36,9502
Non-polymers4622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-35.7 kcal/mol
Surface area14960 Å2
MethodPQS
2
C: CARBOHYDRATE-PHOSPHATE ISOMERASE
D: CARBOHYDRATE-PHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4124
Polymers36,9502
Non-polymers4622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4920 Å2
ΔGint-33.2 kcal/mol
Surface area14870 Å2
MethodPQS
3
E: CARBOHYDRATE-PHOSPHATE ISOMERASE
hetero molecules

E: CARBOHYDRATE-PHOSPHATE ISOMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4124
Polymers36,9502
Non-polymers4622
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area5260 Å2
ΔGint-38.1 kcal/mol
Surface area14860 Å2
MethodPQS
Unit cell
Length a, b, c (Å)136.479, 102.855, 69.545
Angle α, β, γ (deg.)90.00, 95.37, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2022-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.4013, 0.9114, 0.0907), (0.9114, 0.3875, 0.1383), (0.0909, 0.1382, -0.9862)22.7606, 16.9835, 20.0276
2given(-0.3482, -0.9259, 0.1466), (-0.9265, 0.3161, -0.2041), (0.1426, -0.2069, -0.9679)38.7542, 35.2852, 50.5035
3given(-0.6907, 0.6429, -0.3311), (-0.6584, -0.7484, -0.0799), (-0.2991, 0.1628, 0.9402)43.7924, 39.0992, -21.4308
4given(-0.7678, -0.5474, -0.3328), (0.5398, -0.8326, 0.1242), (-0.3451, -0.0843, 0.9348)75.6625, -43.4282, 0.5581

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Components

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


Mass: 18474.803 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PCR T7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21
References: UniProt: Q7D737, UniProt: P9WKD7*PLUS, ribose-5-phosphate isomerase
#2: Chemical
ChemComp-RES / 4-PHOSPHO-D-ERYTHRONOHYDROXAMIC ACID


Mass: 231.098 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10NO8P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 390 / 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: 2.8 Å3/Da / Density % sol: 55.9 %
Crystal growDetails: 1.55 M AMMONIUM PHOSPHATE, 0.1 M HEPES, PH 7.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.009
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 8, 2003 / Details: MIRRORS
RadiationMonochromator: S1(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 2.1→81.65 Å / Num. obs: 55757 / % possible obs: 99.9 % / Observed criterion σ(I): 2.5 / Redundancy: 3.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 5.3
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 2.5 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1USL

1usl


Resolution: 2.1→81.65 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.922 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.164 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2830 5.1 %RANDOM
Rwork0.202 ---
obs0.203 52926 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 19.65 Å2
Baniso -1Baniso -2Baniso -3
1--0.51 Å20 Å2-1.1 Å2
2---0.53 Å20 Å2
3---0.83 Å2
Refinement stepCycle: LAST / Resolution: 2.1→81.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5929 0 70 390 6389
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0216119
X-RAY DIFFRACTIONr_bond_other_d00.025512
X-RAY DIFFRACTIONr_angle_refined_deg1.4411.9458320
X-RAY DIFFRACTIONr_angle_other_deg3.794312748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.7865782
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0580.2914
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.026974
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021232
X-RAY DIFFRACTIONr_nbd_refined0.1620.21326
X-RAY DIFFRACTIONr_nbd_other0.2430.25840
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.1060.22863
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0930.2385
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1120.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2630.272
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0980.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2041.53892
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.38526180
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.43432227
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it0.84.52140
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: 2.1→2.15 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.264 210
Rwork0.255 3900

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