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- PDB-3sdw: Crystal structure of a ribose-5-phosphate isomerase B RpiB from C... -

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Basic information

Entry
Database: PDB / ID: 3sdw
TitleCrystal structure of a ribose-5-phosphate isomerase B RpiB from Coccidioides immitis bound to phosphate
Componentsribose 5-phosphate isomerase
KeywordsISOMERASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / ribose-5-phosphate / RpiB / Valley Fever / Coccidioidomycosis / pathogenic fungus / dust-borne pathogen / nucleotide and co-factor biogenesis / pentose phosphate pathway
Function / homology
Function and homology information


Isomerases; Intramolecular oxidoreductases; Interconverting aldoses and ketoses, and related compounds / isomerase activity / carbohydrate metabolic process
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
PHOSPHATE ION / Putative ribose 5-phosphate isomerase
Similarity search - Component
Biological speciesCoccidioides immitis (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Bmc Struct.Biol. / Year: 2011
Title: Structural characterization of a ribose-5-phosphate isomerase B from the pathogenic fungus Coccidioides immitis.
Authors: Edwards, T.E. / Abramov, A.B. / Smith, E.R. / Baydo, R.O. / Leonard, J.T. / Leibly, D.J. / Thompkins, K.B. / Clifton, M.C. / Gardberg, A.S. / Staker, B.L. / Van Voorhis, W.C. / Myler, P.J. / Stewart, L.J.
History
DepositionJun 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 26, 2011Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: ribose 5-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9645
Polymers19,7091
Non-polymers2554
Water3,117173
1
A: ribose 5-phosphate isomerase
hetero molecules

A: ribose 5-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,92810
Polymers39,4192
Non-polymers5098
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_555-x+1/2,-y+1/2,z1
Buried area5150 Å2
ΔGint-23 kcal/mol
Surface area11950 Å2
MethodPISA
2
A: ribose 5-phosphate isomerase
hetero molecules

A: ribose 5-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,92810
Polymers39,4192
Non-polymers5098
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+1/2,y,-z+1/21
Buried area2140 Å2
ΔGint-19 kcal/mol
Surface area15090 Å2
MethodPISA
3
A: ribose 5-phosphate isomerase
hetero molecules

A: ribose 5-phosphate isomerase
hetero molecules

A: ribose 5-phosphate isomerase
hetero molecules

A: ribose 5-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,85620
Polymers78,8384
Non-polymers1,01816
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y+1/2,-z+1/21
crystal symmetry operation11_555-x+1/2,y,-z+1/21
crystal symmetry operation14_555-x+1/2,-y+1/2,z1
Buried area13430 Å2
ΔGint-94 kcal/mol
Surface area21030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.700, 85.220, 96.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-167-

CL

21A-195-

HOH

31A-335-

HOH

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Components

#1: Protein ribose 5-phosphate isomerase


Mass: 19709.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Coccidioides immitis (fungus) / Strain: RS / Gene: CIMG_07932 / Production host: Escherichia coli (E. coli)
References: UniProt: P0CL19, Isomerases; Intramolecular oxidoreductases; Interconverting aldoses and ketoses, and related compounds
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 2.02 Å3/Da / Density % sol: 39.16 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: CoimA.00584.a.A1 PS00647 at 66 mg/mL with 20 mM ribose-5-phosphate and 12 mM MnCl2 against PACT screen condition A2 0.1 M SPG buffer pH 5.0, 25% PEG 1500 with 20% ethylene glycol as cryo- ...Details: CoimA.00584.a.A1 PS00647 at 66 mg/mL with 20 mM ribose-5-phosphate and 12 mM MnCl2 against PACT screen condition A2 0.1 M SPG buffer pH 5.0, 25% PEG 1500 with 20% ethylene glycol as cryo-protection reagent, crystal tracking ID 222975a2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 24, 2011 / Details: VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 28652 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 19.61 Å2 / Rmerge(I) obs: 0.119 / Net I/σ(I): 12.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
1.8-1.8520.4382.0842492133210798.8
1.85-1.90.3792.294273203299.5
1.9-1.950.3262.834433200999.8
1.95-2.010.2783.614502194699.9
2.01-2.080.224.784613189599.9
2.08-2.150.1776.144925185499.8
2.15-2.230.1627.6755421745100
2.23-2.320.1598.945609165799.8
2.32-2.430.14510.0459041644100
2.43-2.550.14511.235988155599.9
2.55-2.680.15412.1163571500100
2.68-2.850.16314.9668021382100
2.85-3.040.15717.8874871338100
3.04-3.290.13121.4867101209100
3.29-3.60.10526.5562941145100
3.6-4.030.07235.6153731011100
4.03-4.650.07135.844865890100
4.65-5.690.08234.214431766100
5.69-8.050.11732.183629588100
8.050.06747.56188332198.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 36.42 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3 Å31.91 Å
Translation3 Å31.91 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3qd5

3qd5


Resolution: 1.8→30.24 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.947 / WRfactor Rfree: 0.1515 / WRfactor Rwork: 0.1327 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.9265 / SU B: 4.066 / SU ML: 0.058 / SU R Cruickshank DPI: 0.1092 / SU Rfree: 0.1011 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1762 752 5 %RANDOM
Rwork0.1486 ---
obs0.15 14922 99.47 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 37.7 Å2 / Biso mean: 13.1584 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2--0.72 Å20 Å2
3----0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1179 0 14 173 1366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221227
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.9721665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1425163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98124.46847
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.64515207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.876157
X-RAY DIFFRACTIONr_chiral_restr0.0890.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021899
X-RAY DIFFRACTIONr_mcbond_it0.6331.5794
X-RAY DIFFRACTIONr_mcangle_it1.06921277
X-RAY DIFFRACTIONr_scbond_it1.9963433
X-RAY DIFFRACTIONr_scangle_it3.3134.5385
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 53 -
Rwork0.212 1031 -
all-1084 -
obs--98.55 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.22081.1144-0.3122.25050.37961.407-0.0381-0.0103-0.20960.0140.1075-0.27620.08690.2496-0.06940.01350.0212-0.00170.0523-0.02570.078134.44499.378111.9991
20.82050.11880.03150.77480.01840.9681-0.0140.0403-0.0226-0.07390.0311-0.0255-0.00490.0184-0.0170.03340.00480.01450.0257-0.01450.023929.347117.77754.2919
30.85360.1480.30580.91140.73371.10770.0220.0004-0.04350.0474-0.00090.00160.0971-0.0301-0.02110.03950.00560.00360.0132-0.00540.026721.994710.898615.3764
41.36171.1914-1.09271.5291-1.99973.1270.0340.1286-0.1014-0.09430.06560.00370.21920.013-0.09960.04750.0035-0.0350.0522-0.0330.047113.223313.2024-4.5419
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 43
2X-RAY DIFFRACTION2A44 - 98
3X-RAY DIFFRACTION3A99 - 140
4X-RAY DIFFRACTION4A141 - 163

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