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- PDB-4op4: Crystal structure of the catalytic domain of DapE protein from V.... -

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Basic information

Entry
Database: PDB / ID: 4op4
TitleCrystal structure of the catalytic domain of DapE protein from V.cholerea in the Zn bound form
ComponentsSuccinyl-diaminopimelate desuccinylase
KeywordsHYDROLASE / aminopeptidase / M20 / CSGID / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases
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 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase ...Succinyl-diaminopimelate desuccinylase, proteobacteria / ArgE / dapE / ACY1 / CPG2 / yscS family signature 2. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / Peptidase M20, dimerisation domain / Bacterial exopeptidase 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
1,4-BUTANEDIOL / Succinyl-diaminopimelate desuccinylase
Similarity search - Component
Biological speciesVibrio cholerae O1 biovar El Tor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.651 Å
AuthorsNocek, B. / Makowska-Grzyska, M. / Jedrzejczak, R. / 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
DepositionFeb 4, 2014Deposition site: RCSB / Processing site: RCSB
SupersessionApr 23, 2014ID: 3T6M
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 1.3Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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)58,74220
Polymers57,3532
Non-polymers1,38918
Water9,242513
1
A: Succinyl-diaminopimelate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,53812
Polymers28,6771
Non-polymers86211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Succinyl-diaminopimelate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2048
Polymers28,6771
Non-polymers5277
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.898, 49.898, 231.762
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 / 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, 531 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 90.121 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H10O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 513 / 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: 2.9 Å3/Da / Density % sol: 57.65 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 20% (V/V) 1,4-BUTANEDIOL 0.1 M 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
ReflectionResolution: 1.65→40 Å / Num. all: 70716 / Num. obs: 70716 / % possible obs: 91.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.051
Reflection shellResolution: 1.65→1.68 Å / % possible all: 49.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
CCP4model building
MOLREPphasing
REFMAC(phenix.refine: 1.8.4_1496)refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.651→37.714 Å / σ(F): 0 / σ(I): 0 / Phase error: 16.74 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.1659 3630 5.47 %Random
Rwork0.1409 ---
all0.145 70005 --
obs0.1432 66375 42.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.651→37.714 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3947 0 78 513 4538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.024202
X-RAY DIFFRACTIONf_angle_d1.4335670
X-RAY DIFFRACTIONf_dihedral_angle_d15.0551532
X-RAY DIFFRACTIONf_chiral_restr0.057660
X-RAY DIFFRACTIONf_plane_restr0.006748
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6518-1.68030.2859480.2141952X-RAY DIFFRACTION12
1.6803-1.71080.1831720.20261219X-RAY DIFFRACTION16
1.7108-1.74370.2136790.17471562X-RAY DIFFRACTION20
1.7437-1.77920.20681000.17361993X-RAY DIFFRACTION25
1.7792-1.81780.2081150.17212511X-RAY DIFFRACTION33
1.8178-1.86010.1841520.15363142X-RAY DIFFRACTION40
1.8601-1.90650.18851820.15843450X-RAY DIFFRACTION45
1.9065-1.95790.15662100.15063525X-RAY DIFFRACTION46
1.9579-2.01540.16361890.15073628X-RAY DIFFRACTION47
2.0154-2.08030.17612020.15413679X-RAY DIFFRACTION47
2.0803-2.15450.19351800.15343655X-RAY DIFFRACTION47
2.1545-2.24050.16331810.15313655X-RAY DIFFRACTION47
2.2405-2.34220.16591800.14873634X-RAY DIFFRACTION47
2.3422-2.46520.17981870.14283687X-RAY DIFFRACTION47
2.4652-2.61890.16732060.15093682X-RAY DIFFRACTION47
2.6189-2.820.16782140.14873582X-RAY DIFFRACTION47
2.82-3.10170.17212050.12943736X-RAY DIFFRACTION48
3.1017-3.54580.14992240.12243688X-RAY DIFFRACTION48
3.5458-4.44970.13592030.10783781X-RAY DIFFRACTION49
4.4497-15.45960.16122280.14784164X-RAY DIFFRACTION54
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)
10.0002-0.0002-0.00020.0004-0.00060.0010.00120.00380.002-0.009-0.00190.0013-0.00870.0006-00.086-0.00220.00940.0680.01660.04648.838413.7216-10.4972
20.003-0.00180.00750.0062-0.00390.0137-0.01550.00730.0092-0.0229-0.00020.0086-0.0148-0.0021-0.00660.0585-0.00550.00880.0586-0.00330.03839.337911.1569-3.5563
30.00290.0019-0.00050.0019-0.00340.00650.0012-0.00310.01050.0023-0.0025-0.00280.0061-0.0022-0.00410.0536-0.03860.01510.0178-0.00640.028312.17295.64559.8252
40.0013-0.0010.00230.0018-0.00320.00550.00270.0020.0032-0.0078-0.00760.00490.01560.00680.0010.0447-0.01180.01380.06170.00090.03439.2092-0.1402-3.0551
50.00060.0002-0.00030.00050.00010.0005-0.0015-0.00930.00020.0030.00360.0034-0.0072-0.00470.00040.0950.01420.00950.0985-0.01020.07148.579913.7979-34.8825
60.0071-0.00180.00050.0050.0070.0115-0.0146-0.02530.01190.0033-0.00610.0064-0.0106-0.0117-0.00590.0559-0.00580.00120.05280.00940.046210.600511.972-41.9588
70.00040.00030.00020.0005-0.00030.00030.0022-0.0006-0.00090.0004-0.0022-0.0018-0.0007-0.003500.05070.0077-0.01180.08150.0030.0712-0.40519.6546-52.8232
80.0028-0.0016-0.00430.0050.00520.0071-0.00170.00470.00570.00690.00220.0120.00310.01130.0033-0.0005-0.00710.01260.04050.02270.010818.5116.2396-51.4672
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 37 )
2X-RAY DIFFRACTION2chain 'A' and (resid 38 through 132 )
3X-RAY DIFFRACTION3chain 'A' and (resid 133 through 230 )
4X-RAY DIFFRACTION4chain 'A' and (resid 231 through 266 )
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 37 )
6X-RAY DIFFRACTION6chain 'B' and (resid 38 through 132 )
7X-RAY DIFFRACTION7chain 'B' and (resid 133 through 153 )
8X-RAY DIFFRACTION8chain 'B' and (resid 154 through 266 )

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