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- PDB-5ifz: Crystal Structure of Ribose-5-phosphate Isomerase from Brucella m... -

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Basic information

Entry
Database: PDB / ID: 5ifz
TitleCrystal Structure of Ribose-5-phosphate Isomerase from Brucella melitensis 16M
ComponentsRibose 5-phosphate isomerase
KeywordsISOMERASE / alpha-beta-alpha / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


ribose-5-phosphate isomerase / ribose-5-phosphate isomerase activity / carbohydrate metabolic process
Similarity search - Function
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
Similarity search - Component
Biological speciesBrucella melitensis bv. 1 str. 16M (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal Structure of Ribose-5-phosphate Isomerase from Brucella melitensis 16M
Authors: Delker, S.L. / Dranow, D.M. / Abendroth, J. / Lorimer, D. / Edwards, T.E.
History
DepositionFeb 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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: Ribose 5-phosphate isomerase


Theoretical massNumber of molelcules
Total (without water)36,4552
Polymers36,4552
Non-polymers00
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1650 Å2
ΔGint-9 kcal/mol
Surface area9180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.570, 51.570, 177.290
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Ribose 5-phosphate isomerase


Mass: 18227.471 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis bv. 1 str. 16M (bacteria)
Strain: 16M / ATCC 23456 / NCTC 10094 / Gene: BMEII0424 / Plasmid: BrmeA.00966.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8YCV4, ribose-5-phosphate isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.09 Å3/Da / Density % sol: 41.23 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: MCSG-1 a5(250341a5): 0.2 M Sodium Chloride, 0.1 M Sodium Acetate: Acetic Acid pH 4.5, 1.26 M Ammomium Sulfate; cryo: 20% GLYCEROL; BrmeA.00966.a.B1.PW37380 at 25.8 mg/ml, puck twt3-5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 3, 2014 / Details: Beryllium Lenses
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.6→44.935 Å / Num. obs: 32358 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 7.81 % / Biso Wilson estimate: 22.89 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Net I/σ(I): 26.12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.6-1.647.970.4823.5199.8
1.64-1.690.44.261100
1.69-1.740.3285.2199.9
1.74-1.790.246.98199.9
1.79-1.850.1759.25199.8
1.85-1.910.13312.33199.6
1.91-1.980.10116.49199.4
1.98-2.070.07421.91199.4
2.07-2.160.06326.2199.6
2.16-2.260.05331.34199.4
2.26-2.390.04635.82198.7
2.39-2.530.04239.16198.6
2.53-2.70.03745.2198.4
2.7-2.920.03449.9198
2.92-3.20.03253.34198.6
3.2-3.580.02959.05198.3
3.58-4.130.02761.49198
4.13-5.060.02661.54196.8
5.06-7.160.02659.13198.3
7.16-44.9350.02651.05166.2

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2313refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3he8

3he8


Resolution: 1.6→44.323 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.34
RfactorNum. reflection% reflection
Rfree0.2115 2112 6.55 %
Rwork0.1807 --
obs0.1827 32247 98.67 %
all-162986 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.81 Å2 / Biso mean: 33.0413 Å2 / Biso min: 14.94 Å2
Refinement stepCycle: final / Resolution: 1.6→44.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1659 0 0 135 1794
Biso mean---40.46 -
Num. residues----235
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051699
X-RAY DIFFRACTIONf_angle_d0.6972313
X-RAY DIFFRACTIONf_chiral_restr0.048293
X-RAY DIFFRACTIONf_plane_restr0.004299
X-RAY DIFFRACTIONf_dihedral_angle_d8.7031031
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.63720.27861480.25419442092100
1.6372-1.67810.28641720.237119582130100
1.6781-1.72350.27951330.231220162149100
1.7235-1.77420.27031260.206120272153100
1.7742-1.83150.20371400.204119642104100
1.8315-1.8970.2421370.19271992212999
1.897-1.97290.21811330.192720052138100
1.9729-2.06270.20621370.18482009214699
2.0627-2.17150.21821420.173219982140100
2.1715-2.30750.20511660.17131980214699
2.3075-2.48560.20621530.17631990214399
2.4856-2.73580.2061160.17242047216398
2.7358-3.13150.20171230.18022057218099
3.1315-3.9450.1981320.16422085221798
3.945-44.33950.20641540.18142063221792
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)
14.23352.9333-0.70856.8204-1.45357.8812-0.02830.36170.3134-0.140.05310.2253-0.5247-0.1986-0.02630.09440.031-0.04080.25530.07150.217549.29271.543930.5362
24.50196.22993.70058.78884.72597.31920.12350.32160.2930.1377-0.12680.273-0.1872-0.26170.01340.17980.0496-0.02260.31770.06680.298848.0415-1.786223.6585
32.2960.02020.6612.84550.23144.28040.0320.4287-0.03-0.2576-0.1155-0.0780.0920.0960.06620.14390.01130.00360.21320.00610.144955.6781-7.952429.3726
46.43223.7035-1.39753.8144-2.99993.1633-0.23930.9607-0.6406-0.90780.1954-0.930.6953-0.03680.02260.5423-0.01330.12170.2629-0.09320.369160.1954-30.222838.9663
54.79392.58111.28185.5355-0.55730.71310.26650.0191-0.82060.1757-0.2158-0.43740.87960.2406-0.00520.55550.050.02720.18490.01960.379360.4995-31.64744.8116
65.71215.46732.09489.48020.86271.0738-0.12030.2645-0.2551-0.45560.03830.29810.68340.07740.06170.5-0.02140.0510.2158-0.05650.30953.9392-30.471335.3062
73.79610.27531.14545.0913.87168.60080.15450.209-0.2477-0.0837-0.1560.27750.4837-0.26940.010.2775-0.0016-0.01110.10490.00160.219850.9902-19.581936.8416
82.9778-4.6438-1.17178.67832.32214.53080.22060.4423-0.73480.0327-0.33510.93450.6124-0.5520.1350.3137-0.07260.00180.1807-0.03370.276748.1824-22.645438.3039
96.86423.4328-2.69585.9885-2.61826.3867-0.22280.1765-0.18210.02650.09580.17440.7218-0.07490.12280.30150.00760.02620.0916-0.00080.180957.4334-21.459245.8545
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 14 through 35 )A14 - 35
2X-RAY DIFFRACTION2chain 'A' and (resid 36 through 67 )A36 - 67
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 142 )A68 - 142
4X-RAY DIFFRACTION4chain 'B' and (resid 14 through 24 )B14 - 24
5X-RAY DIFFRACTION5chain 'B' and (resid 25 through 58 )B25 - 58
6X-RAY DIFFRACTION6chain 'B' and (resid 59 through 81 )B59 - 81
7X-RAY DIFFRACTION7chain 'B' and (resid 82 through 110 )B82 - 110
8X-RAY DIFFRACTION8chain 'B' and (resid 111 through 118 )B111 - 118
9X-RAY DIFFRACTION9chain 'B' and (resid 119 through 141 )B119 - 141

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