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- PDB-2vvr: Crystal structure of the H99N mutant of ribose-5-phosphate isomer... -

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Basic information

Entry
Database: PDB / ID: 2vvr
TitleCrystal structure of the H99N mutant of ribose-5-phosphate isomerase B from E. coli soaked with ribose 5-phosphate
ComponentsRIBOSE-5-PHOSPHATE ISOMERASE B
KeywordsISOMERASE / RPIB / CARBOHYDRATE METABOLISM / PENTOSE PHOSPHATE PATHWAY
Function / homology
Function and homology information


D-allose 6-phosphate isomerase activity / D-allose catabolic process / ribose-5-phosphate isomerase / ribose-5-phosphate isomerase activity / pentose-phosphate shunt, non-oxidative branch
Similarity search - Function
: / Ribose 5-phosphate isomerase B / 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
Ribose-5-phosphate isomerase B
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRoos, A.K. / 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 11, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 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 / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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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
F: RIBOSE-5-PHOSPHATE ISOMERASE B


Theoretical massNumber of molelcules
Total (without water)96,4226
Polymers96,4226
Non-polymers00
Water6,179343
1
A: RIBOSE-5-PHOSPHATE ISOMERASE B
B: RIBOSE-5-PHOSPHATE ISOMERASE B


Theoretical massNumber of molelcules
Total (without water)32,1412
Polymers32,1412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-25 kcal/mol
Surface area14410 Å2
MethodPQS
2
C: RIBOSE-5-PHOSPHATE ISOMERASE B
D: RIBOSE-5-PHOSPHATE ISOMERASE B


Theoretical massNumber of molelcules
Total (without water)32,1412
Polymers32,1412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-22.7 kcal/mol
Surface area14510 Å2
MethodPQS
3
E: RIBOSE-5-PHOSPHATE ISOMERASE B
F: RIBOSE-5-PHOSPHATE ISOMERASE B


Theoretical massNumber of molelcules
Total (without water)32,1412
Polymers32,1412
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-21.4 kcal/mol
Surface area14540 Å2
MethodPQS
Unit cell
Length a, b, c (Å)89.701, 51.862, 207.209
Angle α, β, γ (deg.)90.00, 115.55, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 16070.268 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PBAD/TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10 / References: UniProt: P37351, ribose-5-phosphate isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, HIS 99 TO ASN ENGINEERED RESIDUE IN CHAIN B, HIS 99 TO ASN ...ENGINEERED RESIDUE IN CHAIN A, HIS 99 TO ASN ENGINEERED RESIDUE IN CHAIN B, HIS 99 TO ASN ENGINEERED RESIDUE IN CHAIN C, HIS 99 TO ASN ENGINEERED RESIDUE IN CHAIN D, HIS 99 TO ASN ENGINEERED RESIDUE IN CHAIN E, HIS 99 TO ASN ENGINEERED RESIDUE IN CHAIN F, HIS 99 TO ASN
Sequence detailsH99N MUTANT

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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: 2.11 Å3/Da / Density % sol: 41.7 % / Description: NONE
Crystal growDetails: 20% PEG 3350, 0.1 M MES PH6

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.94
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 5, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 2.1→40.49 Å / Num. obs: 50635 / % possible obs: 99.9 % / Observed criterion σ(I): 5.8 / Redundancy: 3.6 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.1
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 5.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1NN4

1nn4


Resolution: 2.1→40 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.903 / SU B: 4.579 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.236 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.237 2574 5.1 %RANDOM
Rwork0.188 ---
obs0.19 48057 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: 13.77 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å2-0.19 Å2
2---0.61 Å20 Å2
3---0.87 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6621 0 0 343 6964
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226729
X-RAY DIFFRACTIONr_bond_other_d0.0010.024437
X-RAY DIFFRACTIONr_angle_refined_deg1.1751.9329096
X-RAY DIFFRACTIONr_angle_other_deg0.95310800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5895873
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.44423.939297
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.654151113
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1641545
X-RAY DIFFRACTIONr_chiral_restr0.0680.21029
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027656
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021377
X-RAY DIFFRACTIONr_nbd_refined0.1960.21338
X-RAY DIFFRACTIONr_nbd_other0.1840.24700
X-RAY DIFFRACTIONr_nbtor_refined0.1710.23270
X-RAY DIFFRACTIONr_nbtor_other0.0830.23098
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2303
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1660.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2120.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1530.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.871.55564
X-RAY DIFFRACTIONr_mcbond_other0.1281.51842
X-RAY DIFFRACTIONr_mcangle_it0.99926840
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.78632811
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5714.52256
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
Rfree0.269 176
Rwork0.204 3564

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