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- PDB-3ixq: Structure of ribose 5-phosphate isomerase a from methanocaldococc... -

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Basic information

Entry
Database: PDB / ID: 3ixq
TitleStructure of ribose 5-phosphate isomerase a from methanocaldococcus jannaschii
ComponentsRibose-5-phosphate isomerase A
KeywordsISOMERASE / STRUCTURAL GENOMICS / PENTOSE PHOSPHATE PATHWAY / CARBON FIXATION / NPPSFA / NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL ANALYSES / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI / Carbohydrate metabolism
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 / 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
ACETATE ION / S-1,2-PROPANEDIOL / Ribose-5-phosphate isomerase A
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.78 Å
AuthorsAntonyuk, S.V. / Ellis, M.J. / Strange, R.W. / Hasnain, S.S. / Bessho, Y. / Kuramitsu, S. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: The structure of an archaeal ribose-5-phosphate isomerase from Methanocaldococcus jannaschii (MJ1603).
Authors: Strange, R.W. / Antonyuk, S.V. / Ellis, M.J. / Bessho, Y. / Kuramitsu, S. / Yokoyama, S. / Hasnain, S.S.
History
DepositionSep 4, 2009Deposition site: RCSB / Processing site: PDBJ
SupersessionOct 6, 2009ID: 2PJM
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 A
B: Ribose-5-phosphate isomerase A
C: Ribose-5-phosphate isomerase A
D: Ribose-5-phosphate isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,47720
Polymers99,4394
Non-polymers1,03816
Water15,889882
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11240 Å2
ΔGint-44 kcal/mol
Surface area33210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.856, 100.273, 80.465
Angle α, β, γ (deg.)90.000, 92.540, 90.000
Int Tables number4
Space group name H-MP1211
Detailsfull tetramer is in A.U.

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Components

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


Mass: 24859.838 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: DSM2661 / Gene: rpiA, MJ1603 / Plasmid: PET-21A / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3) / References: UniProt: Q58998, ribose-5-phosphate isomerase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical
ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O2
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 882 / 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: 2.22 Å3/Da / Density % sol: 44.68 % / Mosaicity: 0.448 °
Crystal growTemperature: 298 K / Method: oil batch (tera) / pH: 4.75
Details: 20MM TRIS-HCL PH 8.0, 200MM NACL. 40% V/V 1,2-PROPANEDIOL, 0.1M ACETATE PH 4.5, 0.05M CA ACETATE, oil batch (TERA), temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.074 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 3, 2007 / Details: mirrors
RadiationMonochromator: SAGITALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.074 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. all: 94575 / Num. obs: 94575 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Biso Wilson estimate: 17 Å2 / Rmerge(I) obs: 0.104 / Rsym value: 0.087 / Χ2: 1.022 / Net I/σ(I): 13.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.392 / Mean I/σ(I) obs: 4 / Num. unique all: 8356 / Rsym value: 0.38 / Χ2: 1.182 / % possible all: 98.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KL5

1kl5


Resolution: 1.78→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.944 / WRfactor Rfree: 0.19 / WRfactor Rwork: 0.151 / Occupancy max: 1 / Occupancy min: 0.2 / FOM work R set: 0.899 / SU B: 2.207 / SU ML: 0.071 / SU R Cruickshank DPI: 0.117 / SU Rfree: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.117 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.188 4045 5 %RANDOM
Rwork0.148 ---
all0.15 81022 --
obs0.15 81022 97.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 75.38 Å2 / Biso mean: 17.944 Å2 / Biso min: 4.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.42 Å20 Å20.66 Å2
2---0.6 Å20 Å2
3---0.24 Å2
Refinement stepCycle: LAST / Resolution: 1.78→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7259 0 69 889 8217
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227453
X-RAY DIFFRACTIONr_bond_other_d0.0010.025161
X-RAY DIFFRACTIONr_angle_refined_deg1.4692.00310109
X-RAY DIFFRACTIONr_angle_other_deg1.015312826
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.03851007
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.3925.844308
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.942151491
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1811534
X-RAY DIFFRACTIONr_chiral_restr0.0880.21212
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028200
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021334
X-RAY DIFFRACTIONr_nbd_refined0.2180.21433
X-RAY DIFFRACTIONr_nbd_other0.1910.25692
X-RAY DIFFRACTIONr_nbtor_refined0.1680.23629
X-RAY DIFFRACTIONr_nbtor_other0.0830.23995
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2656
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2860.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2670.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1990.231
X-RAY DIFFRACTIONr_mcbond_it1.1861.56192
X-RAY DIFFRACTIONr_mcbond_other0.2251.51912
X-RAY DIFFRACTIONr_mcangle_it1.3127582
X-RAY DIFFRACTIONr_scbond_it2.34633165
X-RAY DIFFRACTIONr_scangle_it3.2464.52471
LS refinement shellResolution: 1.781→1.827 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 302 -
Rwork0.199 5553 -
all-5855 -
obs--95.37 %

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