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- PDB-1rtq: The 0.95 Angstrom Resolution Crystal Structure of the Aminopeptid... -

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Basic information

Entry
Database: PDB / ID: 1rtq
TitleThe 0.95 Angstrom Resolution Crystal Structure of the Aminopeptidase from Aeromonas proteolytica
ComponentsBacterial leucyl aminopeptidase
KeywordsHYDROLASE / Bimetallic / Zinc / High Resolution / Aminopeptidase
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
THIOCYANATE ION / Bacterial leucyl aminopeptidase
Similarity search - Component
Biological speciesVibrio proteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.95 Å
AuthorsDesmarais, W. / Bienvenue, D.L. / Krzysztof, B.P. / Holz, R.C. / Petsko, G.A. / Ringe, D.
CitationJournal: J.Biol.Inorg.Chem. / Year: 2006
Title: The high-resolution structures of the neutral and the low pH crystals of aminopeptidase from Aeromonas proteolytica.
Authors: Desmarais, W. / Bienvenue, D.L. / Bzymek, K.P. / Petsko, G.A. / Ringe, D. / Holz, R.C.
History
DepositionDec 10, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: Bacterial leucyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5548
Polymers32,2381
Non-polymers3167
Water5,837324
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.936, 109.936, 91.369
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-1085-

HOH

21A-1098-

HOH

31A-1216-

HOH

41A-1295-

HOH

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Components

#1: Protein Bacterial leucyl aminopeptidase


Mass: 32238.150 Da / Num. of mol.: 1 / Fragment: Aminopeptidase
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-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: HEPES, Potassium Thiocyanate, Sodium Chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: Schalk, C., (1992) Arch. Biochem. Biophys., 294, 91.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
116 mg/mlprotein1drop
210 mMHEPES1droppH7.5
310 mM1dropKSCN
40.4 M1dropNaCl
525 mMTris base1reservoir
6160 mMglycine1reservoir
70.8 %(w/v)SDS1reservoir
865 %(v/v)2-mercaptoethanol1reservoir
96.5 %(v/v)glycerol1reservoir
100.02 %(w/v)bromophenol blue1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 1, 1998
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.95→30 Å / Num. all: 191127 / Num. obs: 191127 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 0.95→0.98 Å / % possible all: 59
Reflection
*PLUS
Num. measured all: 3348266 / Rmerge(I) obs: 0.064
Reflection shell
*PLUS
% possible obs: 59 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
SHELXL-97refinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.95→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.151 9556 Random
Rwork0.135 --
obs0.135 191127 -
all-191127 -
Refinement stepCycle: LAST / Resolution: 0.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4300 0 11 324 4635
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 27 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.03

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