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- PDB-4h2k: Crystal structure of the catalytic domain of succinyl-diaminopime... -

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Basic information

Entry
Database: PDB / ID: 4h2k
TitleCrystal structure of the catalytic domain of succinyl-diaminopimelate desuccinylase from Haemophilus influenzae
ComponentsSuccinyl-diaminopimelate desuccinylase
KeywordsHYDROLASE / DapE / MCSG / PSI-Biology / Structural Genomics / Midwest Center for Structural Genomics / Zinc-dependent hydrolase
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 1. / 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 ...Succinyl-diaminopimelate desuccinylase, proteobacteria / ArgE / dapE / ACY1 / CPG2 / yscS family signature 1. / 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
Succinyl-diaminopimelate desuccinylase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsNocek, B. / Jedrzejczak, R. / Makowska-Grzyska, M. / Starus, A. / Holz, R. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
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
DepositionSep 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 26, 2015Group: Database references
Revision 1.2Aug 16, 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 / 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)58,0456
Polymers57,7842
Non-polymers2624
Water5,116284
1
A: Succinyl-diaminopimelate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0233
Polymers28,8921
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Succinyl-diaminopimelate desuccinylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0233
Polymers28,8921
Non-polymers1312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.667, 44.721, 92.481
Angle α, β, γ (deg.)90.00, 92.90, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 28891.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: dapE, HI_0102 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3
References: UniProt: P44514, succinyl-diaminopimelate desuccinylase
#2: Chemical
ChemComp-ZN / ZINC ION / SDAP desuccinylase / N-succinyl-LL-2 / 6-diaminoheptanedioate amidohydrolase


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / References: succinyl-diaminopimelate desuccinylase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / 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: 2.2 Å3/Da / Density % sol: 44.19 %
Crystal growTemperature: 289 K / pH: 5.5
Details: 0.2 M Ammonium acetate, 25% PEG 3350, 0.1 M BIS-TRIS, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 3, 2011 / Details: DOUBLE CRYSTAL
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.84→40 Å / Num. obs: 42453 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 2.3 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 10
Reflection shellResolution: 1.84→1.88 Å / % possible all: 97.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
REFMAC5.6.0117refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ISZ

3isz


Resolution: 1.84→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.756 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.154 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 2157 5.1 %RANDOM
Rwork0.194 ---
obs0.197 40252 95.9 %-
all-42421 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.43 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å22.51 Å2
2---1.55 Å20 Å2
3---2.93 Å2
Refinement stepCycle: LAST / Resolution: 1.84→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3799 0 4 284 4087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0193905
X-RAY DIFFRACTIONr_bond_other_d0.0030.022545
X-RAY DIFFRACTIONr_angle_refined_deg2.0351.9665307
X-RAY DIFFRACTIONr_angle_other_deg2.9536293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3485517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93525.769156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.10615659
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6321514
X-RAY DIFFRACTIONr_chiral_restr0.110.2623
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214380
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02698
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.84→1.89 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 148 -
Rwork0.302 2679 -
obs--91.11 %

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