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- PDB-2prq: X-ray crystallographic characterization of the Co(II)-substituted... -

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Basic information

Entry
Database: PDB / ID: 2prq
TitleX-ray crystallographic characterization of the Co(II)-substituted Tris-bound form of the aminopeptidase from Aeromonas proteolytica
ComponentsBacterial leucyl aminopeptidase
KeywordsHYDROLASE / Tris / peptidase / aminohydrolase / Cobalt / metalloprotease
Function / homology
Function and homology information


bacterial leucyl aminopeptidase / metalloexopeptidase activity / aminopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Peptidase M28E, aminopeptidase AP1 / Peptidase M28 family / Peptidase, C-terminal, archaeal/bacterial / Bacterial pre-peptidase C-terminal domain / Peptidase M28 / Peptidase family M28 / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Bacterial leucyl aminopeptidase
Similarity search - Component
Biological speciesVibrio proteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Model derived phases / Resolution: 2.15 Å
AuthorsMunih, P. / Moulin, A. / Stamper, C.C. / Bennet, B. / Ringe, D. / Petsko, G.A. / Holz, R.C.
CitationJournal: J.Inorg.Biochem. / Year: 2007
Title: X-ray crystallographic characterization of the Co(II)-substituted Tris-bound form of the aminopeptidase from Aeromonas proteolytica.
Authors: Munih, P. / Moulin, A. / Stamper, C.C. / Bennett, B. / Ringe, D. / Petsko, G.A. / Holz, R.C.
History
DepositionMay 4, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 12, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Aug 30, 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 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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: Bacterial leucyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6674
Polymers31,4271
Non-polymers2403
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.200, 106.200, 96.700
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Detailsmonomeric enzyme. The monomer comprises the ASU

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Components

#1: Protein Bacterial leucyl aminopeptidase


Mass: 31427.350 Da / Num. of mol.: 1 / Fragment: residues 107-397
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio proteolyticus (bacteria) / Production host: Escherichia coli (E. coli)
References: UniProt: Q01693, bacterial leucyl aminopeptidase
#2: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Co
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM Tris pH 8.0, 100 mM KSCN, 4.5 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 298KK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.99
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Mar 3, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. all: 18112 / Num. obs: 18085 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.12 / Χ2: 1.088 / Net I/σ(I): 6.5
Reflection shellResolution: 2.15→2.23 Å / Rmerge(I) obs: 0.743 / Num. unique all: 1755 / Χ2: 1.537 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
CNSphasing
RefinementMethod to determine structure: Model derived phases
Starting model: PDB code 1AMP

1amp


Resolution: 2.15→30 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.273 1634 9.1 %random
Rwork0.224 ---
obs0.224 16585 91.9 %-
all-18112 --
Solvent computationBsol: 45.729 Å2
Displacement parametersBiso mean: 34.059 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2211 0 10 76 2297
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.1251.5
X-RAY DIFFRACTIONc_scbond_it1.6012
X-RAY DIFFRACTIONc_mcangle_it1.8662
X-RAY DIFFRACTIONc_scangle_it2.2872.5
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4tris.param

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