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- PDB-4ppz: Crystal structure of zinc-bound succinyl-diaminopimelate desuccin... -

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Basic information

Entry
Database: PDB / ID: 4ppz
TitleCrystal structure of zinc-bound succinyl-diaminopimelate desuccinylase from Neisseria meningitidis MC58
ComponentsSuccinyl-diaminopimelate desuccinylase
KeywordsHYDROLASE / DapE / M20 / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases / succinyl-diaminopimelate desuccinylase / aminopeptidase
Function / homology
Function and homology information


acetylornithine deacetylase activity / succinyl-diaminopimelate desuccinylase / succinyl-diaminopimelate desuccinylase activity / arginine biosynthetic process / diaminopimelate biosynthetic process / lysine biosynthetic process via diaminopimelate / cobalt ion binding / zinc ion binding
Similarity search - Function
Succinyl-diaminopimelate desuccinylase, proteobacteria / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits ...Succinyl-diaminopimelate desuccinylase, proteobacteria / Alpha-Beta Plaits - #360 / Peptidase M20, dimerisation domain / Bacterial exopeptidase dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Succinyl-diaminopimelate desuccinylase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNocek, B. / Holz, R. / Anderson, W.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: Biochemistry / Year: 2015
Title: Inhibition of the dapE-Encoded N-Succinyl-L,L-diaminopimelic Acid Desuccinylase from Neisseria meningitidis by L-Captopril.
Authors: Starus, A. / Nocek, B. / Bennett, B. / Larrabee, J.A. / Shaw, D.L. / Sae-Lee, W. / Russo, M.T. / Gillner, D.M. / Makowska-Grzyska, M. / Joachimiak, A. / Holz, R.C.
History
DepositionFeb 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Feb 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_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_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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_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_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_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

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Assembly

Deposited unit
A: Succinyl-diaminopimelate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,5994
Polymers41,3741
Non-polymers2263
Water4,270237
1
A: Succinyl-diaminopimelate desuccinylase
hetero molecules

A: Succinyl-diaminopimelate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,1998
Polymers82,7472
Non-polymers4526
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area4020 Å2
ΔGint-186 kcal/mol
Surface area29170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.963, 151.655, 55.464
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-906-

HOH

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Components

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


Mass: 41373.613 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis (bacteria) / Strain: MC58 / Gene: dapE, NMB1530 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9JYL2, succinyl-diaminopimelate desuccinylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 237 / 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: 2.97 Å3/Da / Density % sol: 58.62 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% Peg3350,0.2M LiSO4, 0.1M Hepes, pH 7.5, 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: Dec 10, 2013 / 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: 2→40 Å / Num. all: 33502 / Num. obs: 33502 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.1 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 22.8
Reflection shellResolution: 2→2.03 Å / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
CCP4model building
REFMAC5.7.0029refinement
HKL-3000data reduction
HKL-3000data scaling
CCP4phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→29.38 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.131 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2079 1601 5.1 %RANDOM
Rwork0.17385 ---
obs0.17551 29892 93.67 %-
all-31493 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.334 Å2
Baniso -1Baniso -2Baniso -3
1--0.96 Å20 Å20 Å2
2--1.68 Å20 Å2
3----0.72 Å2
Refinement stepCycle: LAST / Resolution: 2→29.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2871 0 7 237 3115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0192938
X-RAY DIFFRACTIONr_bond_other_d0.0010.022862
X-RAY DIFFRACTIONr_angle_refined_deg1.6921.9613991
X-RAY DIFFRACTIONr_angle_other_deg0.8323.0026520
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6325376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.02424.621132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.39715490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6781518
X-RAY DIFFRACTIONr_chiral_restr0.1240.2453
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213360
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02648
LS refinement shellResolution: 2→2.056 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 99 -
Rwork0.22 1806 -
obs--77.25 %

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