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- PDB-3sgw: Crystal structure of ribose-5-phosphate isomerase B RpiB from Coc... -

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Basic information

Entry
Database: PDB / ID: 3sgw
TitleCrystal structure of ribose-5-phosphate isomerase B RpiB from Coccidioides immitis semi-covalently bound to malonic acid
Componentsribose 5-phosphate isomerase
KeywordsISOMERASE/ISOMERASE INHIBITOR / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / Valley Fever / Coccidioidomycosis immitis / pathogenic fungus / RpiB / dust-borne pathogen / iodoacetic acid / covalent inhibitor / ribulose-5-phosphate / ribose-5-phosphate / ISOMERASE / ISOMERASE-ISOMERASE INHIBITOR complex
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
MALONIC ACID / Putative ribose 5-phosphate isomerase
Similarity search - Component
Biological speciesCoccidioides immitis (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 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 15, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 26, 2011Group: Database references
Revision 1.3Apr 29, 2015Group: Non-polymer description
Revision 1.4Sep 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_conn / 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_conn.pdbx_leaving_atom_flag / _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)20,0096
Polymers19,7091
Non-polymers2995
Water3,027168
1
A: ribose 5-phosphate isomerase
hetero molecules

A: ribose 5-phosphate isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,01712
Polymers39,4192
Non-polymers59810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation14_555-x+1/2,-y+1/2,z1
Buried area5530 Å2
ΔGint-46 kcal/mol
Surface area11940 Å2
MethodPISA
2
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)80,03424
Polymers78,8384
Non-polymers1,19620
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 area14220 Å2
ΔGint-143 kcal/mol
Surface area20980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.460, 84.420, 96.170
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-186-

HOH

31A-302-

HOH

41A-317-

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 / Plasmid: pAVA0421 / Production host: Escherichia coli (E. coli)
References: UniProt: P0CL19, Isomerases; Intramolecular oxidoreductases; Interconverting aldoses and ketoses, and related compounds
#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O4
#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.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 1.99 Å3/Da / Density % sol: 38.32 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: protein at 66 mg/mL with 20 mM ribose-5-phosphate and 12 mM MnCl2. Reservoir: 25% PEG 1500 and 0.1 M MIB (malonic acid, imidazole, boric acid), with 25% ethylene glycol as cryo-protection ...Details: protein at 66 mg/mL with 20 mM ribose-5-phosphate and 12 mM MnCl2. Reservoir: 25% PEG 1500 and 0.1 M MIB (malonic acid, imidazole, boric acid), with 25% ethylene glycol as cryo-protection reagent, pH 5.0, 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: Jun 10, 2011 / Details: VariMax
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 17530 / Num. obs: 16561 / % possible obs: 94.5 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Biso Wilson estimate: 20.011 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 34.74
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
1.7-1.745.30.2566.6254531281102880.2
1.74-1.790.2387.996839105084.2
1.79-1.840.1899.797078105686.8
1.84-1.90.17310.777205105990.1
1.9-1.960.14212.827273105992.4
1.96-2.030.11116.267314105095.3
2.03-2.110.09219.797557104597.4
2.11-2.190.0825.548780101998.2
2.19-2.290.0730.26927098598.3
2.29-2.40.06333.29903391999.1
2.4-2.530.05837.29944890098.8
2.53-2.690.05340.8969885299.2
2.69-2.870.04849.181070280499.4
2.87-3.10.04591084274999.7
3.1-3.40.03465.851016770299.9
3.4-3.80.02781.83900462799.8
3.8-4.390.02592.488124570100
4.39-5.380.02591.526797478100
5.38-7.60.02783.945358381100
7.60.02199.02285222898.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
StructureStudiodata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3SDW

3sdw


Resolution: 1.7→49.08 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.1573 / WRfactor Rwork: 0.131 / Occupancy max: 1 / Occupancy min: 0.25 / FOM work R set: 0.9104 / SU B: 3.235 / SU ML: 0.05 / SU R Cruickshank DPI: 0.0931 / SU Rfree: 0.092 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1749 832 5 %RANDOM
Rwork0.1421 ---
obs0.1438 16509 94.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 42.3 Å2 / Biso mean: 13.745 Å2 / Biso min: 3.48 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2--0.68 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 1.7→49.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1183 0 17 168 1368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0221240
X-RAY DIFFRACTIONr_angle_refined_deg1.3231.971683
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.15165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78824.37548
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.19915209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.074157
X-RAY DIFFRACTIONr_chiral_restr0.0870.2202
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021917
X-RAY DIFFRACTIONr_mcbond_it0.6411.5797
X-RAY DIFFRACTIONr_mcangle_it1.11921285
X-RAY DIFFRACTIONr_scbond_it2.0243443
X-RAY DIFFRACTIONr_scangle_it3.5354.5394
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.189 55 -
Rwork0.156 968 -
all-1023 -
obs--79.98 %
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)
11.09621.151-0.02832.8630.45321.0874-0.0137-0.0391-0.14660.01410.0675-0.21260.07480.2051-0.0538-0.00090.0336-0.00460.0293-0.01720.050134.25179.385512.0686
20.67140.19690.05260.667100.60170.00820.0427-0.0174-0.03920.0281-0.0273-0.01620.0166-0.03630.02660.00370.01020.0197-0.01360.015229.301517.5794.3904
30.40150.07360.33330.60290.5660.99760.01560.0038-0.03050.04450.01570.00870.0816-0.0068-0.03130.03610.0034-0.00040.0047-0.00110.020321.71210.665115.2827
40.26390.8747-0.78721.3298-1.622.8260.0440.1303-0.0855-0.07440.08120.07160.20820.0119-0.12520.04790.0077-0.05230.0485-0.04180.047512.864412.6784-4.3764
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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