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- PDB-5uf2: Crystal Structure of ribose 5 phosphate isomerase A from Neisseri... -

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Basic information

Entry
Database: PDB / ID: 5uf2
TitleCrystal Structure of ribose 5 phosphate isomerase A from Neisseria gonorrhoeae
ComponentsRibose-5-phosphate isomerase A
KeywordsISOMERASE / SSGCID / Neisseria gonorrhoeae / ribose-5-phosphate / rpiA / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


ribose-5-phosphate isomerase / ribose-5-phosphate isomerase activity / pentose-phosphate shunt, non-oxidative branch
Similarity search - Function
Ribose-5-phosphate isomerase, type A, subgroup / Ribose 5-phosphate isomerase, type A / Ribose 5-phosphate isomerase A (phosphoriboisomerase A) / Rossmann fold - #1360 / ACT domain / NagB/RpiA transferase-like / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Ribose-5-phosphate isomerase A
Similarity search - Component
Biological speciesNeisseria gonorrhoeae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of ribose 5 phosphate isomerase A from Neisseria gonorrhoeae
Authors: Mayclin, S.J. / Abendroth, J. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJan 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribose-5-phosphate isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,83313
Polymers24,9471
Non-polymers88612
Water6,792377
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.650, 75.870, 46.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-627-

HOH

21A-756-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ribose-5-phosphate isomerase A / Phosphoriboisomerase A / PRI


Mass: 24947.439 Da / Num. of mol.: 1 / Fragment: NegoA.00944.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria gonorrhoeae (strain NCCP11945) (bacteria)
Strain: NCCP11945 / Gene: rpiA, NGK_0826 / Plasmid: NegoA.00944.a.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B4RL16, ribose-5-phosphate isomerase

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Non-polymers , 5 types, 389 molecules

#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 377 / 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: 2.52 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: MCSG1 F1 (283224f1): 100mM Bis-Tris:HCl pH6.5, 20% (w/v) PEG 5000 MME: protein conc. 18.44mg/mL, cryoprotectant 20% ethylene glycol, puck kgc9-3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 10, 2016
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.4→50 Å / Num. obs: 49825 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 5.69 % / Biso Wilson estimate: 10.52 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.075 / Net I/σ(I): 14.67
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsCC1/2Diffraction-ID% possible all
1.4-1.445.6260.513.240.8561100
1.44-1.485.6390.4253.930.879199.9
1.48-1.525.6490.325.140.915199.9
1.52-1.575.6820.2596.310.941199.8
1.57-1.625.6580.2237.370.95199.8
1.62-1.675.6710.1818.660.97199.7
1.67-1.745.6970.14710.560.979199.2
1.74-1.815.7030.12712.10.984199.4
1.81-1.895.70.10414.480.99199.4
1.89-1.985.6960.08816.820.992199.7
1.98-2.095.70.07819.20.995199.7
2.09-2.215.6760.06821.880.995199.8
2.21-2.375.7140.06423.470.994199.2
2.37-2.565.730.05925.390.996198.5
2.56-2.85.7390.05626.90.996198.4
2.8-3.135.7470.05128.190.997197.7
3.13-3.615.7360.04830.880.997197.1
3.61-4.435.8040.04732.680.997195.7
4.43-6.265.7620.04532.80.998193.7
6.26-505.6970.04533.410.997185.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREPphasing
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1m0s

1m0s


Resolution: 1.4→50 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 14.26
RfactorNum. reflection% reflection
Rfree0.1635 2035 4.08 %
Rwork0.1352 --
obs0.1363 49817 98.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.34 Å2 / Biso mean: 16.1999 Å2 / Biso min: 5.52 Å2
Refinement stepCycle: final / Resolution: 1.4→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1672 0 74 390 2136
Biso mean--28.2 31.32 -
Num. residues----223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051859
X-RAY DIFFRACTIONf_angle_d1.0412516
X-RAY DIFFRACTIONf_chiral_restr0.102297
X-RAY DIFFRACTIONf_plane_restr0.005318
X-RAY DIFFRACTIONf_dihedral_angle_d24.213721
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.43260.22531440.196131633307100
1.4326-1.46840.1951490.165331403289100
1.4684-1.50810.16561510.140131573308100
1.5081-1.55250.16551390.13331723311100
1.5525-1.60260.18111130.123731913304100
1.6026-1.65990.16391480.127631643312100
1.6599-1.72630.14451300.12263165329599
1.7263-1.80490.1521280.12743180330899
1.8049-1.90.17711360.12573186332299
1.9-2.01910.15131340.129332013335100
2.0191-2.17490.14941260.124332323358100
2.1749-2.39380.14311390.13153188332799
2.3938-2.740.16621370.1373218335599
2.74-3.45160.15591210.1383219334098
3.4516-34.56260.17581400.14013206334694

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