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- PDB-4onw: Crystal structure of the catalytic domain of DapE protein from V.... -

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Basic information

Entry
Database: PDB / ID: 4onw
TitleCrystal structure of the catalytic domain of DapE protein from V.cholerea
ComponentsSuccinyl-diaminopimelate desuccinylase
KeywordsHYDROLASE / DapE / M20 / aminopeptidase / CSGID / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / Zn binding
Function / homology
Function and homology information


succinyl-diaminopimelate desuccinylase / succinyl-diaminopimelate desuccinylase activity / diaminopimelate biosynthetic process / cobalt ion binding / lysine biosynthetic process via diaminopimelate / zinc ion binding / cytosol
Similarity search - Function
Succinyl-diaminopimelate desuccinylase, proteobacteria / ArgE / dapE / ACY1 / CPG2 / yscS family signature 2. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / : / Bacterial exopeptidase dimerisation domain / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases ...Succinyl-diaminopimelate desuccinylase, proteobacteria / ArgE / dapE / ACY1 / CPG2 / yscS family signature 2. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / : / Bacterial exopeptidase dimerisation domain / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / 1,4-BUTANEDIOL / Succinyl-diaminopimelate desuccinylase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsNocek, B. / Makowska-Grzyska, M. / Jedrzejczak, R. / Gu, M. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Plos One / Year: 2014
Title: The Dimerization Domain in DapE Enzymes Is required for Catalysis.
Authors: Nocek, B. / Starus, A. / Makowska-Grzyska, M. / Gutierrez, B. / Sanchez, S. / Jedrzejczak, R. / Mack, J.C. / Olsen, K.W. / Joachimiak, A. / Holz, R.C.
History
DepositionJan 29, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionApr 23, 2014ID: 3T68
Revision 1.0Apr 23, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Jul 26, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Succinyl-diaminopimelate desuccinylase
B: Succinyl-diaminopimelate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,38515
Polymers57,3532
Non-polymers1,03213
Water9,746541
1
A: Succinyl-diaminopimelate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0736
Polymers28,6771
Non-polymers3965
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Succinyl-diaminopimelate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3129
Polymers28,6771
Non-polymers6368
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.649, 49.649, 232.566
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Succinyl-diaminopimelate desuccinylase / SDAP desuccinylase / N-succinyl-LL-2 / 6-diaminoheptanedioate amidohydrolase


Mass: 28676.559 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria)
Strain: N16961 / Gene: dapE, VC_2152 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9KQ52, succinyl-diaminopimelate desuccinylase

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Non-polymers , 5 types, 554 molecules

#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-BU1 / 1,4-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / 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: 2.89 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 20% (V/V) 1,4-BUTANEDIOL, 0.1M Acetate,, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 14, 2011 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.508
11K, H, -L20.492
ReflectionResolution: 1.65→37.6 Å / Num. all: 77006 / Num. obs: 77006 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 30
Reflection shellResolution: 1.65→1.68 Å / % possible all: 93.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
CCP4model building
MOLREPphasing
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3ISZ

3isz


Resolution: 1.65→37.6 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.96 / SU B: 0.902 / SU ML: 0.033 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.015 / ESU R Free: 0.016 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17137 3829 5.3 %RANDOM
Rwork0.13622 ---
all0.131 72756 --
obs0.13807 68927 94.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.514 Å2
Baniso -1Baniso -2Baniso -3
1-0.52 Å20 Å20 Å2
2--0.52 Å20 Å2
3----1.05 Å2
Refinement stepCycle: LAST / Resolution: 1.65→37.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3956 0 68 541 4565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0194235
X-RAY DIFFRACTIONr_bond_other_d0.0010.024097
X-RAY DIFFRACTIONr_angle_refined_deg2.1131.9695761
X-RAY DIFFRACTIONr_angle_other_deg0.97439452
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1295573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.17924.693179
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87615687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5381525
X-RAY DIFFRACTIONr_chiral_restr0.1240.2671
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214872
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02917
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.187 139 -
Rwork0.156 2762 -
obs--51.5 %

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