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- PDB-4o23: Crystal structure of mono-zinc form of succinyl diaminopimelate d... -

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Basic information

Entry
Database: PDB / ID: 4o23
TitleCrystal structure of mono-zinc form of succinyl diaminopimelate desuccinylase from Neisseria meningitidis MC58
ComponentsSuccinyl-diaminopimelate desuccinylase
KeywordsHYDROLASE / DapE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


succinyl-diaminopimelate desuccinylase / succinyl-diaminopimelate desuccinylase activity / acetylornithine deacetylase activity / L-arginine biosynthetic process / diaminopimelate biosynthetic process / cobalt ion binding / lysine biosynthetic process via diaminopimelate / zinc ion binding
Similarity search - Function
Succinyl-diaminopimelate desuccinylase, proteobacteria / : / Alpha-Beta Plaits - #360 / Bacterial exopeptidase dimerisation domain / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 / Peptidase family M20/M25/M40 / Zn peptidases / Aminopeptidase ...Succinyl-diaminopimelate desuccinylase, proteobacteria / : / Alpha-Beta Plaits - #360 / Bacterial exopeptidase dimerisation domain / Peptidase M20, 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
Succinyl-diaminopimelate desuccinylase
Similarity search - Component
Biological speciesNeisseria meningitidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 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
DepositionDec 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Sep 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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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)83,6807
Polymers83,2922
Non-polymers3885
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-160 kcal/mol
Surface area29000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.324, 111.389, 132.535
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 Succinyl-diaminopimelate desuccinylase / SDAP desuccinylase / N-succinyl-LL-2 / 6-diaminoheptanedioate amidohydrolase


Mass: 41645.875 Da / Num. of mol.: 2
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) / Strain (production host): BL21(DE3)
References: UniProt: Q9JYL2, succinyl-diaminopimelate desuccinylase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.45 Å3/Da / Density % sol: 49.83 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1 M Succinic Acid, 15% PEG 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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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: Nov 27, 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: 2.09→39.25 Å / Num. all: 49315 / Num. obs: 48738 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 18
Reflection shellResolution: 2.09→2.14 Å / % possible all: 96.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPCCP4phasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1VGY

1vgy


Resolution: 2.09→39.25 Å / SU ML: 0.22 / σ(F): 1.35 / σ(I): 1.5 / Phase error: 25.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 2219 5.01 %RANDOM
Rwork0.2114 ---
obs0.2129 44283 89 %-
all-46492 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.09→39.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5664 0 13 380 6057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035791
X-RAY DIFFRACTIONf_angle_d0.7147877
X-RAY DIFFRACTIONf_dihedral_angle_d11.9572093
X-RAY DIFFRACTIONf_chiral_restr0.027901
X-RAY DIFFRACTIONf_plane_restr0.0021039
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.09-2.13560.3025820.2691482X-RAY DIFFRACTION27
2.1356-2.18530.296710.25911766X-RAY DIFFRACTION31
2.1853-2.240.31230.26661886X-RAY DIFFRACTION34
2.24-2.30050.29441050.25582161X-RAY DIFFRACTION38
2.3005-2.36820.26641170.24922360X-RAY DIFFRACTION43
2.3682-2.44460.31191560.25242697X-RAY DIFFRACTION49
2.4446-2.5320.29281540.25522849X-RAY DIFFRACTION51
2.532-2.63330.29691700.2522878X-RAY DIFFRACTION52
2.6333-2.75320.2471360.23372887X-RAY DIFFRACTION52
2.7532-2.89830.23751530.23252884X-RAY DIFFRACTION52
2.8983-3.07980.27361490.22812934X-RAY DIFFRACTION52
3.0798-3.31750.21591700.2182876X-RAY DIFFRACTION52
3.3175-3.65110.23891460.19632966X-RAY DIFFRACTION53
3.6511-4.17890.20561490.17912955X-RAY DIFFRACTION53
4.1789-5.2630.20531670.15793010X-RAY DIFFRACTION54
5.263-39.25720.21161710.19983473X-RAY DIFFRACTION62
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)
11.8451-0.1520.38823.16110.43781.4736-0.0034-0.33980.08240.2734-0.0529-0.0585-0.016-0.17750.04530.2052-0.01350.0110.25280.02580.1192-19.1341-11.7185-2.0003
23.4468-1.11591.58312.2901-0.8613.2150.0336-0.0330.40310.115-0.22-0.4029-0.14570.28850.21270.2331-0.04150.00720.21120.06290.2322-8.5522-15.0714-9.7721
32.00981.7891-0.27441.7244-0.19510.38850.2526-0.2633-0.85810.6157-0.2919-1.0454-0.09840.15360.03590.3302-0.0689-0.20140.23990.13710.493711.35413.3481-23.0472
41.00670.0235-0.22561.00950.7361.68330.0572-0.01590.0716-0.1038-0.1452-0.0395-0.1684-0.18220.08550.1960.0163-0.02220.15090.0520.1604-18.5781-10.6328-16.5508
53.05710.1601-0.30311.76910.81412.12720.1603-0.9920.00440.31950.4295-0.3211-0.30111.0887-0.30090.4508-0.09010.02651.027-0.25040.524337.292643.8078-3.7075
62.5442-0.26170.43361.5844-0.72540.9797-0.0843-0.19220.2125-0.3830.4686-0.1653-0.8560.8885-0.33550.4764-0.34040.21751.0086-0.29780.590137.832649.085-14.1895
71.85391.0303-0.10022.67610.33361.2210.3208-0.17370.05210.4545-0.2036-0.0682-0.25580.2052-0.07110.2659-0.0634-0.0280.17350.01430.140914.969225.7514-26.7234
81.70471.4229-0.46971.6650.20150.884-0.0141-0.44130.007-0.37750.6839-0.6188-0.24041.20.06170.4081-0.42510.15391.1565-0.2890.700143.287740.7429-18.9246
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 2:132)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 133:173)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 174:300)
4X-RAY DIFFRACTION4CHAIN A AND (RESID 301:377)
5X-RAY DIFFRACTION5CHAIN B AND (RESID 5:102)
6X-RAY DIFFRACTION6CHAIN B AND (RESID 103:173)
7X-RAY DIFFRACTION7CHAIN B AND (RESID 174:300)
8X-RAY DIFFRACTION8CHAIN B AND (RESID 301:376)

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