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- PDB-1jdi: CRYSTAL STRUCTURE OF L-RIBULOSE-5-PHOSPHATE 4-EPIMERASE -

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Basic information

Entry
Database: PDB / ID: 1jdi
TitleCRYSTAL STRUCTURE OF L-RIBULOSE-5-PHOSPHATE 4-EPIMERASE
ComponentsL-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
KeywordsISOMERASE / epimerase / ribulose / aldolase
Function / homology
Function and homology information


L-ribulose-5-phosphate 4-epimerase / L-ribulose-phosphate 4-epimerase activity / L-arabinose catabolic process to xylulose 5-phosphate / L-lyxose metabolic process / pentose catabolic process / aldehyde-lyase activity / protein-containing complex / zinc ion binding / identical protein binding / cytosol
Similarity search - Function
L-ribulose-5-phosphate 4-epimerase / L-ribulose-5-phosphate 4-epimerase AraD / L-fuculose-1-phosphate Aldolase / Class II aldolase/adducin N-terminal domain / Class II aldolase/adducin N-terminal / Class II Aldolase and Adducin N-terminal domain / Class II Aldolase and Adducin N-terminal domain / Class II aldolase/adducin N-terminal domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L-ribulose-5-phosphate 4-epimerase AraD
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLuo, Y. / Samuel, J. / Mosimann, S.C. / Lee, J.E. / Tanner, M.E. / Strynadka, N.C.J.
CitationJournal: Biochemistry / Year: 2001
Title: The structure of L-ribulose-5-phosphate 4-epimerase: an aldolase-like platform for epimerization.
Authors: Luo, Y. / Samuel, J. / Mosimann, S.C. / Lee, J.E. / Tanner, M.E. / Strynadka, N.C.
History
DepositionJun 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Aug 16, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_conn.ptnr2_symmetry / _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:
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Assembly

Deposited unit
A: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
B: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
C: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
D: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
E: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
F: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,58412
Polymers153,1916
Non-polymers3926
Water7,800433
1
A: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules

A: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules

A: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules

A: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3898
Polymers102,1284
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area10670 Å2
ΔGint-206 kcal/mol
Surface area32940 Å2
MethodPISA, PQS
2
B: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules

B: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules

B: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules

B: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3898
Polymers102,1284
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area10480 Å2
ΔGint-212 kcal/mol
Surface area33060 Å2
MethodPISA, PQS
3
C: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules

C: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules

C: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules

C: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3898
Polymers102,1284
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area10470 Å2
ΔGint-207 kcal/mol
Surface area32980 Å2
MethodPISA, PQS
4
D: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules

D: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules

D: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules

D: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3898
Polymers102,1284
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area10580 Å2
ΔGint-203 kcal/mol
Surface area32880 Å2
MethodPISA
5
E: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules

E: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules

E: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules

E: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3898
Polymers102,1284
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area10580 Å2
ΔGint-203 kcal/mol
Surface area33030 Å2
MethodPISA, PQS
6
F: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules

F: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules

F: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules

F: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,3898
Polymers102,1284
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area10560 Å2
ΔGint-202 kcal/mol
Surface area33160 Å2
MethodPISA, PQS
7
D: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules

D: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules

D: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules

D: L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE
hetero molecules


  • defined by software
  • 102 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)102,3898
Polymers102,1284
Non-polymers2624
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z1
crystal symmetry operation4_455y-1/2,-x+1/2,z1
MethodPQS
Unit cell
Length a, b, c (Å)105.900, 105.900, 274.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
DetailsTetramer generated by crystallographic 4-fold symmetry

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Components

#1: Protein
L-RIBULOSE 5 PHOSPHATE 4-EPIMERASE


Mass: 25531.893 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: AraD / Plasmid: pRE1 / Production host: Escherichia coli (E. coli) / Strain (production host): Y1090
References: UniProt: P08203, L-ribulose-5-phosphate 4-epimerase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 2.57 Å3/Da / Density % sol: 51.7 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 4.0 M sodium formate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
24.0 Msodium formate1reservoir
30.1 %n-octyl-beta-D-glucoside1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.97 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Jul 25, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 62146 / Num. obs: 58293 / % possible obs: 93.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 37.8 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 19.4
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 4.1 / Num. unique all: 4187 / Rsym value: 0.201 / % possible all: 68.8
Reflection
*PLUS
Highest resolution: 2.4 Å / Redundancy: 3.64 %
Reflection shell
*PLUS
% possible obs: 68.8 % / Num. unique obs: 4187

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FUA

1fua


Resolution: 2.4→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 3283 6 %RANDOM
Rwork0.208 ---
all0.208 62146 --
obs0.208 58263 93.8 %-
Solvent computationSolvent model: CNS / Bsol: 37.1 Å2 / ksol: 0.399 e/Å3
Displacement parametersBiso mean: 37.7 Å2
Refinement stepCycle: LAST / Resolution: 2.4→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10410 0 6 433 10849
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0067
X-RAY DIFFRACTIONc_angle_deg1.262
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Num. reflection obs: 54929 / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 37.7 Å2

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