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- PDB-1lk7: Structure of D-Ribose-5-Phosphate Isomerase from in complex with ... -

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Basic information

Entry
Database: PDB / ID: 1lk7
TitleStructure of D-Ribose-5-Phosphate Isomerase from in complex with phospho-erythronic acid
ComponentsD-Ribose-5-Phosphate Isomerase
KeywordsISOMERASE / alpha/beta structure
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
D-4-PHOSPHOERYTHRONIC ACID / Ribose-5-phosphate isomerase A
Similarity search - Component
Biological speciesPyrococcus horikoshii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsIshikawa, K. / Matsui, I. / Payan, F. / Cambillau, C. / Ishida, H. / Kawarabayasi, Y. / Kikuchi, H. / Roussel, A.
CitationJournal: STRUCTURE / Year: 2002
Title: A Hyperthermostable D-Ribose-5-Phosphate Isomerase from Pyrococcus horikoshii Characterization and Three-Dimensional Structure
Authors: Ishikawa, K. / Matsui, I. / Payan, F. / Cambillau, C. / Ishida, H. / Kawarabayasi, Y. / Kikuchi, H. / Roussel, A.
History
DepositionApr 24, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

Downloads & links

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Assembly

Deposited unit
A: D-Ribose-5-Phosphate Isomerase
B: D-Ribose-5-Phosphate Isomerase
C: D-Ribose-5-Phosphate Isomerase
D: D-Ribose-5-Phosphate Isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,02220
Polymers100,7574
Non-polymers1,26516
Water7,296405
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13140 Å2
ΔGint-162 kcal/mol
Surface area32460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.689, 114.923, 119.578
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is the tetramer in the asymetric unit

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Components

#1: Protein
D-Ribose-5-Phosphate Isomerase


Mass: 25189.211 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii (archaea) / Plasmid: PET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O50083, ribose-5-phosphate isomerase
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-DER / D-4-PHOSPHOERYTHRONIC ACID


Mass: 216.083 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H9O8P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.51 Å3/Da / Density % sol: 51.03 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1M acetate buffer, 2.0M NaCl, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
115 mg/mlprotein1drop
250 mMTris-HCl1droppH8.0
3150 mM1dropNaCl
40.1 Msodium acetate1reservoirpH4.6
52.0 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9326 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9326 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / Num. all: 70244 / Num. obs: 67418 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2→2.03 Å / % possible all: 99.2
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 96.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.05
Reflection shell
*PLUS
% possible obs: 96.2 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 1.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNSrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LK5

1lk5


Resolution: 2→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: The structure was refined also with REFMAC
RfactorNum. reflectionSelection details
Rfree0.24739 3307 RANDOM
Rwork0.20229 --
all0.2045 70244 -
obs0.2045 62962 -
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7024 0 64 405 7493
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.013
X-RAY DIFFRACTIONr_angle_refined_deg1.538
LS refinement shellResolution: 2→2.051 Å
RfactorNum. reflection
Rfree0.303 238
Rwork0.25 -
obs-4631
Refinement
*PLUS
Num. reflection obs: 65509 / Num. reflection Rfree: 3322 / % reflection Rfree: 5 % / Rfactor Rfree: 0.27 / Rfactor Rwork: 0.239
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_deg1.32
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg25.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.74
LS refinement shell
*PLUS
Rfactor Rwork: 0.25

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