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- PDB-3ono: Crystal Structure of Ribose-5-phosphate Isomerase LacAB_rpiB from... -

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Basic information

Entry
Database: PDB / ID: 3ono
TitleCrystal Structure of Ribose-5-phosphate Isomerase LacAB_rpiB from Vibrio parahaemolyticus
ComponentsRibose/Galactose Isomerase
KeywordsISOMERASE / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG / alpha-beta-alpha sandwich / cytosol
Function / homology
Function and homology information


intramolecular oxidoreductase activity, interconverting aldoses and ketoses / carbohydrate metabolic process
Similarity search - Function
Ribose-5-phosphate isomerase, C-terminal / Ribose-5-phosphate isomerase / 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
Putative sugar-phosphate isomerase
Similarity search - Component
Biological speciesVibrio parahaemolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsKim, Y. / Volkart, L. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Ribose-5-phosphate Isomerase LacAB_rpiB from Vibrio parahaemolyticus
Authors: Kim, Y. / Volkart, L. / Abdullah, J. / Joachimiak, A.
History
DepositionAug 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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/Galactose Isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2422
Polymers23,1501
Non-polymers921
Water3,333185
1
A: Ribose/Galactose Isomerase
hetero molecules

A: Ribose/Galactose Isomerase
hetero molecules

A: Ribose/Galactose Isomerase
hetero molecules

A: Ribose/Galactose Isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,9698
Polymers92,6014
Non-polymers3684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z1
crystal symmetry operation10_555-x,-y,z1
crystal symmetry operation15_555y,x,-z1
Buried area11910 Å2
ΔGint-89 kcal/mol
Surface area28190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.924, 62.924, 242.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-397-

HOH

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Components

#1: Protein Ribose/Galactose Isomerase / Putative sugar-phosphate isomerase


Mass: 23150.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus (bacteria) / Strain: RIMD 2210633 / Gene: VPA0080 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic / References: UniProt: Q87K18
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.59 Å3/Da / Density % sol: 52.51 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M postassium formate, 20 % (v/v) PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97896 Å
DetectorType: SBC-3 / Detector: CCD / Date: Jun 1, 2007 / Details: morrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97896 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 25080 / Num. obs: 25080 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 29.1 % / Biso Wilson estimate: 21.74 Å2 / Rsym value: 0.091 / Net I/σ(I): 7.1
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 23.9 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 2153 / Rsym value: 0.492 / % possible all: 86.6

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXSphasing
MLPHAREphasing
RESOLVEmodel building
SOLVEphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-3000data reduction
HKL-3000data scaling
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→30.452 Å / SU ML: 0.2 / Isotropic thermal model: mixed / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.19 1997 8.15 %random
Rwork0.166 ---
all0.168 24510 --
obs0.168 24510 97.31 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.833 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso mean: 30.3 Å2
Baniso -1Baniso -2Baniso -3
1-6.3524 Å20 Å2-0 Å2
2--6.3524 Å20 Å2
3----12.7048 Å2
Refinement stepCycle: LAST / Resolution: 1.75→30.452 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1583 0 6 185 1774
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011772
X-RAY DIFFRACTIONf_angle_d1.3042414
X-RAY DIFFRACTIONf_dihedral_angle_d14.656636
X-RAY DIFFRACTIONf_chiral_restr0.083264
X-RAY DIFFRACTIONf_plane_restr0.007325
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.7505-1.8130.23531940.22882178237297
1.813-1.88560.23991950.2042191238697
1.8856-1.97140.26151950.19062212240797
1.9714-2.07530.21881970.17852212240997
2.0753-2.20530.1881980.16932237243598
2.2053-2.37550.19631970.17022213241097
2.3755-2.61450.19611970.16962238243596
2.6145-2.99250.18542000.17182251245197
2.9925-3.76910.18612070.16472329243699
3.7691-30.45650.16492170.14362452266998
Refinement TLS params.Method: refined / Origin x: 11.2483 Å / Origin y: 3.3129 Å / Origin z: 18.9137 Å
111213212223313233
T0.1599 Å2-0.0577 Å2-0.0279 Å2-0.1699 Å20.025 Å2--0.1466 Å2
L0.3174 °2-0.1391 °2-0.0488 °2-0.5249 °2-0.4071 °2--1.846 °2
S0.0193 Å °0.026 Å °0.0575 Å °0.1266 Å °-0.121 Å °-0.0241 Å °-0.2092 Å °0.3136 Å °0.097 Å °
Refinement TLS groupSelection details: chain A

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