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- PDB-1lkz: Crystal structure of D-ribose-5-phosphate isomerase (RpiA) from E... -

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Basic information

Entry
Database: PDB / ID: 1lkz
TitleCrystal structure of D-ribose-5-phosphate isomerase (RpiA) from Escherichia coli.
ComponentsRibose 5-phosphate isomerase A
KeywordsISOMERASE / ribose phosphate isomerase / RpiA / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI / Structural Genomics
Function / homology
Function and homology information


D-ribose metabolic process / ribose-5-phosphate isomerase / ribose-5-phosphate isomerase activity / pentose-phosphate shunt, non-oxidative branch / protein homodimerization activity / identical protein binding / cytosol
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
Ribose-5-phosphate isomerase A
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsRangarajan, E.S. / Sivaraman, J. / Matte, A. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Proteins / Year: 2002
Title: Crystal structure of D-ribose-5-phosphate isomerase (RpiA) from Escherichia coli
Authors: Rangarajan, E.S. / Sivaraman, J. / Matte, A. / Cygler, M.
History
DepositionApr 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software

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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
B: Ribose 5-phosphate isomerase A


Theoretical massNumber of molelcules
Total (without water)46,4232
Polymers46,4232
Non-polymers00
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-12 kcal/mol
Surface area17950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.335, 71.809, 193.067
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 23211.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: MC1061 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: P0A7Z0, ribose-5-phosphate isomerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 2.62 Å3/Da / Density % sol: 53.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5
Details: Ammonium sulfate, Isopropanol, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
pH: 8.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
14.7 mg/mlprotein1drop
250 mMTris1droppH8.5
3400 mM1dropNaCl
45 %(v/v)glycerol1drop
51.05 Mtrisodium citrate1reservoir
60.1 MHEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 0.97193 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 17, 2002
RadiationMonochromator: SILICON / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97193 Å / Relative weight: 1
ReflectionResolution: 2.5→45 Å / Num. obs: 29225 / % possible obs: 87.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 42.8 Å2 / Rsym value: 0.055 / Net I/σ(I): 16.9
Reflection shellResolution: 2.5→2.58 Å / Rsym value: 0.322 / % possible all: 73.5
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 45 Å / Num. measured all: 89423 / Rmerge(I) obs: 0.055

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Processing

Software
NameVersionClassification
Adxvdata processing
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2.5→45 Å / Rfactor Rfree error: 0.005 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 2868 10.1 %RANDOM
Rwork0.227 ---
all-29225 --
obs-28384 86.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.7353 Å2 / ksol: 0.368334 e/Å3
Displacement parametersBiso mean: 29.9 Å2
Baniso -1Baniso -2Baniso -3
1-3.1 Å20 Å20 Å2
2---3.57 Å20 Å2
3---0.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.5→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3206 0 0 129 3335
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.111.5
X-RAY DIFFRACTIONc_mcangle_it1.872
X-RAY DIFFRACTIONc_scbond_it2.732
X-RAY DIFFRACTIONc_scangle_it2.592.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.02 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.368 330 8.8 %
Rwork0.317 3440 -
obs--69 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
Refinement
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 45 Å / % reflection Rfree: 10 % / Rfactor obs: 0.227 / Rfactor Rfree: 0.27
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.85
LS refinement shell
*PLUS
Rfactor obs: 0.317

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