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- PDB-2otn: Crystal structure of the catalytically active form of diaminopime... -

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Basic information

Entry
Database: PDB / ID: 2otn
TitleCrystal structure of the catalytically active form of diaminopimelate epimerase from Bacillus anthracis
ComponentsDiaminopimelate epimerase
KeywordsISOMERASE / Bacillus anthracis diaminopimelate epimerase / DAP / lysine metabolism / lanthionine
Function / homology
Function and homology information


diaminopimelate epimerase / diaminopimelate epimerase activity / lysine biosynthetic process via diaminopimelate / cytoplasm
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 speciesBacillus anthracis str. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMatho, M.H. / Fukuda, K. / Santelli, E. / Jaroszewski, L. / Liddington, R.C. / Roper, D.
CitationJournal: To be Published
Title: Crystal structure and inhibition of a catalytically active form of diaminopimelate epimerase (DapF)from Bacillus anthracis
Authors: Matho, M.H. / Fukuda, K. / Lloyd, A.J. / Santelli, E. / Jaroszewski, L. / Scott, D.J. / Liddington, R.C. / Roper, D.
History
DepositionFeb 8, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Assembly

Deposited unit
A: Diaminopimelate epimerase
B: Diaminopimelate epimerase


Theoretical massNumber of molelcules
Total (without water)67,6272
Polymers67,6272
Non-polymers00
Water4,324240
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.863, 87.334, 110.453
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Diaminopimelate epimerase /


Mass: 33813.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis str. (bacteria) / Species: Bacillus anthracis / Strain: Ames / Gene: dapF / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(Rosetta) / References: UniProt: Q81XR2, diaminopimelate epimerase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 293 K / pH: 6.6
Details: 0.2 M ammonium formate, 20% PEG 3350, 3% ethylene glycol, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 6.60

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Sep 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 24966 / % possible obs: 98.9 % / Observed criterion σ(I): -4 / Redundancy: 6.7 % / Biso Wilson estimate: 54 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 23.6
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.488 / Mean I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GQZ

1gqz


Resolution: 2.4→36.23 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.929 / SU B: 17.426 / SU ML: 0.212 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.437 / ESU R Free: 0.274 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1234 5 %RANDOM
Rwork0.18 ---
obs0.184 23674 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.879 Å2
Baniso -1Baniso -2Baniso -3
1--1.67 Å20 Å20 Å2
2--0.51 Å20 Å2
3---1.16 Å2
Refinement stepCycle: LAST / Resolution: 2.4→36.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4470 0 0 240 4710
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224553
X-RAY DIFFRACTIONr_bond_other_d0.0010.023034
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.966160
X-RAY DIFFRACTIONr_angle_other_deg1.14537427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7225578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7324.829205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.21515783
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.4021524
X-RAY DIFFRACTIONr_chiral_restr0.0770.2693
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.025102
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02882
X-RAY DIFFRACTIONr_nbd_refined0.1820.2719
X-RAY DIFFRACTIONr_nbd_other0.1980.23102
X-RAY DIFFRACTIONr_nbtor_refined0.170.22098
X-RAY DIFFRACTIONr_nbtor_other0.0860.22638
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2200
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1310.214
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2410.235
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.49723726
X-RAY DIFFRACTIONr_mcbond_other0.87421191
X-RAY DIFFRACTIONr_mcangle_it4.19334629
X-RAY DIFFRACTIONr_scbond_it5.46941924
X-RAY DIFFRACTIONr_scangle_it6.7551531
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.393 83 -
Rwork0.275 1579 -
obs--91.22 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.84182.0978-0.25913.42580.41492.24150.0302-0.19780.17450.028-0.16520.2598-0.1306-0.29950.1349-0.27760.0346-0.0166-0.1633-0.0343-0.12-13.906-0.07222.413
21.95380.021.2452.54230.06885.36320.18990.1912-0.1705-0.2542-0.00490.19840.23820.0665-0.1851-0.17490.0046-0.056-0.1425-0.10530.1168-22.581-14.260.418
36.28240.918-0.05853.21470.30992.5421-0.0504-0.1990.2680.01280.1125-0.26950.05710.3887-0.0621-0.27960.0286-0.0032-0.155-0.0379-0.108913.694-4.01522.455
42.1628-0.4305-4.20781.99211.293712.39670.85030.51910.396-0.3211-0.0769-0.0417-1.4647-0.9725-0.77340.02030.11920.113-0.03070.03130.463721.64514.1870.187
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA-4 - 12516 - 145
2X-RAY DIFFRACTION1AA277 - 287297 - 307
3X-RAY DIFFRACTION2AA126 - 276146 - 296
4X-RAY DIFFRACTION3BB-1 - 12519 - 145
5X-RAY DIFFRACTION3BB277 - 287297 - 307
6X-RAY DIFFRACTION4BB126 - 276146 - 296

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