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- PDB-1gqz: Refinement of Haemophilus influenzae Diaminopimelate epimerase at 1.7A -

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Basic information

Entry
Database: PDB / ID: 1gqz
TitleRefinement of Haemophilus influenzae Diaminopimelate epimerase at 1.7A
ComponentsDIAMINOPIMELATE EPIMERASE
KeywordsISOMERASE / PEPTIDOGLYCAN BIOSYNTHESIS
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsRoper, D.I. / Huyton, T. / Turkenburg, J.P.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2004
Title: Refinement of Haemophilus influenzae diaminopimelic acid epimerase (DapF) at 1.75 A resolution suggests a mechanism for stereocontrol during catalysis.
Authors: Lloyd, A.J. / Huyton, T. / Turkenburg, J. / Roper, D.I.
History
DepositionDec 7, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 28, 2018Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DIAMINOPIMELATE EPIMERASE


Theoretical massNumber of molelcules
Total (without water)30,2791
Polymers30,2791
Non-polymers00
Water6,359353
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)99.637, 113.870, 64.481
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 DIAMINOPIMELATE EPIMERASE / / DAP EPIMERASE


Mass: 30279.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HAEMOPHILUS INFLUENZAE (bacteria) / Strain: KW20 / Plasmid: PET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): T7 / References: UniProt: P44859, diaminopimelate epimerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 353 / 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: 2.64 Å3/Da / Density % sol: 53.12 %
Crystal growpH: 6.5 / Details: 0.1M IMIDIZOLE PH 6.5,
Crystal grow
*PLUS
Temperature: 290 K / pH: 6.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11 Msodium acetate1drop
20.1 Mimidazole1droppH6.5
310 mg/mlprotein1drop
425 mMHEPES1reservoirpH8.0
55 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 1.54
DetectorDate: Jul 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.75→56 Å / Num. obs: 37280 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 29.98
Reflection shellResolution: 1.75→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 7.41 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 1.75 Å / Lowest resolution: 56.8 Å / Num. obs: 37359 / % possible obs: 99.18 % / Rmerge(I) obs: 0.039
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 7.41

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1BWZ

1bwz


Resolution: 1.75→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.955 / SU B: 4.788 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.126 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SIDE CHAIN DENSITY FOR THE FOLLOWING RESIDUES WAS POOR AND THEREFORE OCCUPANCIES SET TO ZERO: GLU 28, GLU 55, LYS93,LYS 109, GLU124, LYS ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. SIDE CHAIN DENSITY FOR THE FOLLOWING RESIDUES WAS POOR AND THEREFORE OCCUPANCIES SET TO ZERO: GLU 28, GLU 55, LYS93,LYS 109, GLU124, LYS 134, ARG 142, PHE 271. THE LAST TWO RESIDUES WERE SIMULARLY DISORDED AND MODELED AS ALANINE.
RfactorNum. reflection% reflectionSelection details
Rfree0.196 1850 5 %RANDOM
Rwork0.165 ---
obs0.167 35201 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2083 0 0 353 2436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d
X-RAY DIFFRACTIONr_bond_other_d0.0010.021899
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.9352884
X-RAY DIFFRACTIONr_angle_other_deg0.83734405
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3943273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.50915364
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.2323
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022428
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02421
X-RAY DIFFRACTIONr_nbd_refined0.230.3337
X-RAY DIFFRACTIONr_nbd_other0.2060.31820
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.5269
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.040.38
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2190.325
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1290.523
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3091.51354
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.18622173
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.2843771
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.2014.5711
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.79 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.228 138
Rwork0.173 2544
Refinement
*PLUS
Num. reflection obs: 37280
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.02
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.9

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