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- PDB-2q9h: Crystal structure of the C73S mutant of diaminopimelate epimerase -

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Basic information

Entry
Database: PDB / ID: 2q9h
TitleCrystal structure of the C73S mutant of diaminopimelate epimerase
ComponentsDiaminopimelate epimerase
KeywordsISOMERASE / C73S mutant / two structurally equivalent domains / apo form has an open conformation
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
ACETIC ACID / L(+)-TARTARIC ACID / Diaminopimelate epimerase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsPillai, B. / Cherney, M. / Diaper, C.M. / Sutherland, A. / Blanchard, J.S. / Vederas, J.C. / James, M.N.G.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2007
Title: Dynamics of catalysis revealed from the crystal structures of mutants of diaminopimelate epimerase.
Authors: Pillai, B. / Cherney, M. / Diaper, C.M. / Sutherland, A. / Blanchard, J.S. / Vederas, J.C. / James, M.N.G.
History
DepositionJun 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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 / _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 30, 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: Diaminopimelate epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,5344
Polymers30,2631
Non-polymers2703
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.910, 114.047, 66.777
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-464-

HOH

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Components

#1: Protein Diaminopimelate epimerase / DAP epimerase


Mass: 30263.412 Da / Num. of mol.: 1 / Mutation: C73S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: dapF / Production host: Escherichia coli (E. coli) / References: UniProt: P44859, diaminopimelate epimerase
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 3.17 Å3/Da / Density % sol: 61.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.8 M potassium sodium tartrate tetrahydrate, 0.2 M NaCl, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115869 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 21, 2005
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115869 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. all: 17427 / Num. obs: 17427 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.053 / Rsym value: 0.053 / Net I/σ(I): 31
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 5.05 / Rsym value: 0.349 / % possible all: 99.8

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Processing

Software
NameClassification
Blu-Icedata collection
AMoREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1GQZ

1gqz


Resolution: 2.3→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.24 890 RANDOM
Rwork0.199 --
all0.199 17427 -
obs0.199 17427 -
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 18 154 2294
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.41
X-RAY DIFFRACTIONc_bond_d0.006

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