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- PDB-1bwz: DIAMINOPIMELATE EPIMERASE FROM HEMOPHILUS INFLUENZAE -

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Basic information

Entry
Database: PDB / ID: 1bwz
TitleDIAMINOPIMELATE EPIMERASE FROM HEMOPHILUS INFLUENZAE
ComponentsPROTEIN (DIAMINOPIMELATE EPIMERASE)
KeywordsISOMERASE / METABOLIC ROLE / STRUCTURAL CLASSIFICATION
Function / homology
Function and homology information


diaminopimelate epimerase / diaminopimelate epimerase activity / lysine biosynthetic process via diaminopimelate / cytosol
Similarity search - Function
Diaminopimelate epimerase, active site / Diaminopimelate epimerase signature. / Diaminopimelate epimerase, DapF / Diaminopimelate epimerase / Diaminopimelate Epimerase; Chain A, domain 1 / Diaminopimelate Epimerase; Chain A, domain 1 / Roll / Alpha Beta
Similarity search - Domain/homology
Diaminopimelate epimerase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.72 Å
AuthorsCirilli, M. / Zheng, R. / Scapin, G. / Blanchard, J.S.
CitationJournal: Biochemistry / Year: 1998
Title: Structural symmetry: the three-dimensional structure of Haemophilus influenzae diaminopimelate epimerase.
Authors: Cirilli, M. / Zheng, R. / Scapin, G. / Blanchard, J.S.
History
DepositionSep 29, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 16, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (DIAMINOPIMELATE EPIMERASE)


Theoretical massNumber of molelcules
Total (without water)30,2961
Polymers30,2961
Non-polymers00
Water52229
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)102.100, 115.400, 66.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PROTEIN (DIAMINOPIMELATE EPIMERASE) / E.C.5.1.1.7 ISOMERASE / DAP EPIMERASE


Mass: 30295.584 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: DAPF / Plasmid: PET 23A(+) / Species (production host): Escherichia coli / Gene (production host): DAPF / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P44859, diaminopimelate epimerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / 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

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Sample preparation

CrystalDensity Matthews: 3.2 Å3/Da / Density % sol: 62 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal
*PLUS
Density % sol: 62 %
Crystal grow
*PLUS
Temperature: 15 ℃ / Method: vapor diffusion, hanging drop / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
225 mMHEPES1droppH7.5
30.05 %1dropNaN3
41 Msodium acetate1reservoir
50.1 Msodium cacodylate1reservoirpH6.8

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.72→23.79 Å / Num. obs: 9691 / % possible obs: 89.4 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rsym value: 0.061 / Net I/σ(I): 11.61
Reflection shellResolution: 2.72→2.83 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 10.89 / Rsym value: 0.061 / % possible all: 51.6
Reflection
*PLUS
Num. measured all: 33313 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
% possible obs: 51.6 % / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 6.2

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Processing

Software
NameVersionClassification
X-GENdata scaling
X-GENdata reduction
X-PLOR3.851refinement
RefinementMethod to determine structure: MIR / Resolution: 2.72→23.79 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.242 -7 %RANDOM
Rwork0.19 ---
obs0.19 9411 86.8 %-
Displacement parametersBiso mean: 37.65 Å2
Refinement stepCycle: LAST / Resolution: 2.72→23.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2117 0 0 29 2146
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.825
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d28.59
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor fileSerial no: 1 / Param file: PARAM19X.PR / Topol file: TOPH19X.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
σ(F): 2 / % reflection Rfree: 7 % / Rfactor obs: 0.19 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.59

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