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- PDB-1k0w: CRYSTAL STRUCTURE OF L-RIBULOSE-5-PHOSPHATE 4-EPIMERASE -

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Basic information

Entry
Database: PDB / ID: 1k0w
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-lyxose metabolic process / L-arabinose catabolic process to xylulose 5-phosphate / 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: 2.1 Å
AuthorsLuo, Y. / Samuel, J. / Mosimann, S.C. / Lee, J.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.J.
History
DepositionSep 21, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 28, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_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_atom_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 16, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)153,57812
Polymers153,1856
Non-polymers3926
Water11,385632
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)102,3858
Polymers102,1244
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 area10570 Å2
ΔGint-205 kcal/mol
Surface area33280 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)102,3858
Polymers102,1244
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 area10400 Å2
ΔGint-201 kcal/mol
Surface area33000 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)102,3858
Polymers102,1244
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 area10440 Å2
ΔGint-201 kcal/mol
Surface area33080 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)102,3858
Polymers102,1244
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 area10530 Å2
ΔGint-205 kcal/mol
Surface area32850 Å2
MethodPISA, PQS
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)102,3858
Polymers102,1244
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 area10540 Å2
ΔGint-202 kcal/mol
Surface area32840 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)102,3858
Polymers102,1244
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 area10490 Å2
ΔGint-210 kcal/mol
Surface area33070 Å2
MethodPISA, PQS
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

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Components

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


Mass: 25530.908 Da / Num. of mol.: 6 / Mutation: D120N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / 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.: 632 / 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: 4.0M sodium formate, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.97 / Wavelength: 1 Å
DetectorType: BRANDEIS - B1.2 / Detector: CCD / Date: Jul 5, 2001
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.971
211
ReflectionResolution: 2.1→30 Å / Num. all: 90092 / Num. obs: 84503 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.652 % / Biso Wilson estimate: 24.39 Å2 / Rmerge(I) obs: 0.066 / Rsym value: 0.066 / Net I/σ(I): 23
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.325 / % possible all: 72.1

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JDI

1jdi


Resolution: 2.1→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.251 8140 10 %RANDOM
Rwork0.205 ---
all0.207 91767 --
obs0.205 81151 88.4 %-
Solvent computationSolvent model: CNS / Bsol: 51.4 Å2 / ksol: 0.43 e/Å3
Displacement parametersBiso mean: 24.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.746 Å20 Å20 Å2
2--0.746 Å20 Å2
3----1.491 Å2
Refinement stepCycle: LAST / Resolution: 2.1→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10410 0 6 632 11048
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0061
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.25
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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