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- PDB-1o8b: Structure of Escherichia coli ribose-5-phosphate isomerase, RpiA,... -

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Basic information

Entry
Database: PDB / ID: 1o8b
TitleStructure of Escherichia coli ribose-5-phosphate isomerase, RpiA, complexed with arabinose-5-phosphate.
ComponentsRIBOSE 5-PHOSPHATE ISOMERASE
KeywordsISOMERASE / RIBOSE PHOSPHATE ISOMERASE / RPIA / PSI / PROTEIN STRUCTURE INITIATIVE / MCSG / MIDWEST CENTER FOR 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
5-O-phosphono-beta-D-arabinofuranose / Ribose-5-phosphate isomerase A
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsZhang, R.-g. / Andersson, C.E. / Savchenko, A. / Skarina, T. / Evdokimova, E. / Beasley, S. / Arrowsmith, C.H. / Edwards, A.M. / Joachimiak, A. / Mowbray, S.L. / Midwest Center for Structural Genomics (MCSG)
Citation
Journal: Structure / Year: 2003
Title: Structure of Escherichia Coli Ribose-5-Phosphate Isomerase: A Ubiquitous Enzyme of the Pentose Phosphate Pathway and the Calvin Cycle
Authors: Zhang, R.-G. / Andersson, C.E. / Savchenko, A. / Skarina, T. / Evdokimova, E. / Beasley, S. / Arrowsmith, C.H. / Edwards, A.M. / Joachimiak, A. / Mowbray, S.L.
#1: Journal: J.Bacteriol. / Year: 1993
Title: Escherichia Coli Rpia Gene Encoding Ribose Phosphate Isomerase A
Authors: Hove-Jensen, B. / Maigaard, M.
History
DepositionNov 26, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 24, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 21, 2019Group: Data collection / Database references / Derived calculations
Category: pdbx_database_related / struct_conn
Item: _pdbx_database_related.db_name / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8834
Polymers46,4232
Non-polymers4602
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-13.11 kcal/mol
Surface area16050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.049, 42.400, 60.195
Angle α, β, γ (deg.)90.23, 100.98, 98.98
Int Tables number1
Space group name H-MP1

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Components

#1: Protein RIBOSE 5-PHOSPHATE ISOMERASE / PHOSPHORIBOISOMERASE A / RPIA


Mass: 23211.604 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET15B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0A7Z0, ribose-5-phosphate isomerase
#2: Sugar ChemComp-ABF / 5-O-phosphono-beta-D-arabinofuranose / BETA-D-ARABINOFURANOSE-5'-PHOSPHATE / 5-O-phosphono-beta-D-arabinose / 5-O-phosphono-D-arabinose / 5-O-phosphono-arabinose


Type: D-saccharide, beta linking / Mass: 230.110 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C5H11O8P
IdentifierTypeProgram
b-D-Araf5PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.3 Å3/Da / Density % sol: 46 %
Crystal growpH: 8.5
Details: CRYSTALS WERE GROWN FROM A SOLUTION CONTAINING 3.5 MG/ML PROTEIN, 30-35 % PEG 4000 10 MM ARABINOSE-5-PHOSPHATE, 0.05M TRIS-HCL PH 8.4, 0.1 M MGCL2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 13, 2002 / Details: GE(220),HORIZONTAL FOCUSING MULTILAYER
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.25→40 Å / Num. obs: 90067 / % possible obs: 81.8 % / Redundancy: 4.3 % / Rsym value: 0.095 / Net I/σ(I): 12.4
Reflection shellResolution: 1.25→1.32 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.1 / Rsym value: 0.76 / % possible all: 40.1

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Processing

Software
NameVersionClassification
REFMAC5refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KS2

1ks2


Resolution: 1.25→40 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.934 / SU B: 1.076 / SU ML: 0.046 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.06 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ELECTRON DENSITY COULD NOT BE OBSERVED FOR RESIDUES 1-22, 32-46, 56-67, 98 AND 219 IN MOLECULE A AND RESIDUES 1,18-21, 98 AND 219 IN MOLECULE B. THESE RESIDUES WERE OMITTED AND ARE NOT PRESENT IN THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.24 4498 4.9 %RANDOM
Rwork0.224 ---
obs0.224 86708 81.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 10.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.54 Å2-0.68 Å20.25 Å2
2---0.48 Å2-0.3 Å2
3---0.89 Å2
Refinement stepCycle: LAST / Resolution: 1.25→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2771 0 28 159 2958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222828
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg
X-RAY DIFFRACTIONr_angle_other_deg1.8631.9813829
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1080.2460
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022041
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.220.31223
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1160.5260
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.322
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5070.51
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7751.51861
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.14722982
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.2363967
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1224.5847
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.25→1.28 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.293 136
Rwork0.304 2767
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)
113.661212.8122-3.369314.4295-8.07746.6576-0.87820.7406-0.7833-0.7150.4396-0.81070.6265-0.07820.43860.1241-0.02290.07540.1251-0.07660.10883.2535-4.3999-7.1036
231.6244-0.3751-8.30843.7495-0.02294.3765-1.12481.032-2.1034-0.04550.4302-0.1840.4329-0.21020.69460.1102-0.04650.09420.126-0.12470.229210.1763-3.2891-7.8715
33.44111.0103-1.90151.4398-0.34532.7794-0.14750.30770.0789-0.24110.14630.10250.046-0.03140.00120.0477-0.0225-0.03530.06970.00450.0320.85732.686-2.9094
41.30970.1935-0.13860.9522-0.24351.0099-0.02610.0896-0.0615-0.02580.05460.16840.0769-0.0883-0.02850.01810.0015-0.00630.01290.00640.054-1.63431.98898.1974
55.69363.8307-2.74685.893-2.96266.02270.181-0.22430.05270.3466-0.2783-0.20560.02520.16640.09730.1067-0.0292-0.01560.0489-0.01580.012125.845628.351331.5816
61.49780.26040.56242.3325-0.52241.95610.1062-0.2402-0.13760.416-0.0848-0.1350.14330.0463-0.02140.1257-0.0094-0.01730.06180.00050.048220.523615.877629.3018
70.69190.23480.13021.01070.2390.95830.0280.01920.10740.0115-0.00910.0084-0.06170.0437-0.01890.00930.00650.01010.0168-0.00020.037814.5421.043813.0985
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 31
2X-RAY DIFFRACTION2A47 - 55
3X-RAY DIFFRACTION3A68 - 97
4X-RAY DIFFRACTION4A99 - 218
5X-RAY DIFFRACTION5B2 - 17
6X-RAY DIFFRACTION6B22 - 97
7X-RAY DIFFRACTION7B99 - 218

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