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- PDB-3ic1: Crystal structure of zinc-bound succinyl-diaminopimelate desuccin... -

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Basic information

Entry
Database: PDB / ID: 3ic1
TitleCrystal structure of zinc-bound succinyl-diaminopimelate desuccinylase from Haemophilus influenzae
ComponentsSuccinyl-diaminopimelate desuccinylase
KeywordsHYDROLASE / DapE / PSI2 / MCSG / Zn bound / succinyl-diaminopimelate desuccinylase / Structural Genomics / Protein Structure Initiative / Midwest Center for Structural Genomics / Amino-acid biosynthesis / Cobalt / Diaminopimelate biosynthesis / Lysine biosynthesis / Metal-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 1. / ArgE / dapE / ACY1 / CPG2 / yscS family signature 2. / ArgE/DapE/ACY1/CPG2/YscS, conserved site / : / Alpha-Beta Plaits - #360 / Bacterial exopeptidase dimerisation domain / Peptidase M20, dimerisation domain / Peptidase dimerisation domain / Peptidase M20 ...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 / : / 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 speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNocek, B.P. / Gillner, D.M. / Holz, R.C. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Structural basis for catalysis by the mono- and dimetalated forms of the dapE-encoded N-succinyl-L,L-diaminopimelic acid desuccinylase.
Authors: Nocek, B.P. / Gillner, D.M. / Fan, Y. / Holz, R.C. / Joachimiak, A.
History
DepositionJul 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Sep 6, 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_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.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_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)83,72213
Polymers82,7962
Non-polymers92611
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3820 Å2
ΔGint-235 kcal/mol
Surface area30580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.697, 95.751, 185.426
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: 41397.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: dapE, HI0102 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3
References: UniProt: P44514, succinyl-diaminopimelate desuccinylase
#2: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.4 Å3/Da / Density % sol: 48.67 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.2 M NaCl, 0.1 M NaAcetate, pH 4.5, VAPOR DIFFUSION, HANGING 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 315 / Detector: CCD / Date: May 30, 2009 / 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: 2.3→40 Å / Num. all: 36163 / Num. obs: 34773 / % possible obs: 95.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 17.8
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 3.1 / % possible all: 99.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
MOLREPphasing
REFMAC5.5.0054refinement
HKL-3000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VGY

1vgy


Resolution: 2.3→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.83 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.366 / ESU R Free: 0.251 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1384 4 %RANDOM
Rwork0.194 ---
obs0.195 33237 95.7 %-
all-34621 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20 Å2
2--1.22 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5695 0 41 212 5948
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0225879
X-RAY DIFFRACTIONr_bond_other_d0.0010.023921
X-RAY DIFFRACTIONr_angle_refined_deg1.4291.9697949
X-RAY DIFFRACTIONr_angle_other_deg0.90739662
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4095742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.08325.556252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.229151029
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5681521
X-RAY DIFFRACTIONr_chiral_restr0.080.2898
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216468
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021063
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_it0.7041.53675
X-RAY DIFFRACTIONr_mcbond_other0.1371.51507
X-RAY DIFFRACTIONr_mcangle_it1.3425934
X-RAY DIFFRACTIONr_scbond_it2.07832204
X-RAY DIFFRACTIONr_scangle_it3.3844.52011
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.346 104 -
Rwork0.24 2463 -
obs--96.65 %

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