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- PDB-1igb: AEROMONAS PROTEOLYTICA AMINOPEPTIDASE COMPLEXED WITH THE INHIBITO... -

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Basic information

Entry
Database: PDB / ID: 1igb
TitleAEROMONAS PROTEOLYTICA AMINOPEPTIDASE COMPLEXED WITH THE INHIBITOR PARA-IODO-D-PHENYLALANINE HYDROXAMATE
ComponentsAMINOPEPTIDASE
KeywordsAMINOPEPTIDASE / HYDROLASE
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
PARA-IODO-D-PHENYLALANINE HYDROXAMIC ACID / Bacterial leucyl aminopeptidase
Similarity search - Component
Biological speciesVibrio proteolyticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT SOFTWARE USED : X-PLOR STARTING MODEL FOR MOLECULAR REPLACEMENT: NATIVE PROTEIN (REFERENCE 1) / Resolution: 2.3 Å
AuthorsChevrier, B. / D'Orchymont, H. / Schalk, C. / Tarnus, C. / Moras, D.
Citation
Journal: Eur.J.Biochem. / Year: 1996
Title: The structure of the Aeromonas proteolytica aminopeptidase complexed with a hydroxamate inhibitor. Involvement in catalysis of Glu151 and two zinc ions of the co-catalytic unit.
Authors: Chevrier, B. / D'Orchymont, H. / Schalk, C. / Tarnus, C. / Moras, D.
#1: Journal: Structure / Year: 1994
Title: Crystal Structure of Aeromonas Proteolytica Aminopeptidase: A Prototypical Member of the Co-Catalytic Zinc Enzyme Family
Authors: Chevrier, B. / Schalk, C. / D'Orchymont, H. / Rondeau, J.M. / Moras, D. / Tarnus, C.
#2: Journal: Arch.Biochem.Biophys. / Year: 1992
Title: Rapid Purification of the Aeromonas Proteolytica Aminopeptidase: Crystallization and Preliminary X-Ray Data
Authors: Schalk, C. / Remy, J.M. / Chevrier, B. / Moras, D. / Tarnus, C.
History
DepositionFeb 27, 1996Processing site: BNL
Revision 1.0Aug 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / 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 / software / 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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 / _software.name / _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.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_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: AMINOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,8644
Polymers31,4271
Non-polymers4373
Water3,963220
1
A: AMINOPEPTIDASE
hetero molecules

A: AMINOPEPTIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,7298
Polymers62,8552
Non-polymers8746
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Unit cell
Length a, b, c (Å)109.150, 109.150, 98.350
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein AMINOPEPTIDASE


Mass: 31427.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Vibrio proteolyticus (bacteria)
References: UniProt: Q01693, bacterial leucyl aminopeptidase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-IPO / PARA-IODO-D-PHENYLALANINE HYDROXAMIC ACID


Mass: 306.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11IN2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 2.69 Å3/Da / Density % sol: 54.27 %
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlAAP1drop
210 mMHEPES1drop
310 mMKSCN1drop
40.4 M1dropNaCl
5110 mMHEPES1reservoir
64.5 M1reservoirNaCl

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: SIEMENS / Wavelength: 1.5418
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Sep 1, 1993
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 15274 / % possible obs: 91.7 % / Observed criterion σ(I): 0 / Redundancy: 7.7 % / Rmerge(I) obs: 0.081
Reflection
*PLUS
Num. measured all: 118144

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Processing

Software
NameVersionClassification
XDSdata scaling
CCP4ROTAVATA-AGROVATAdata reduction
X-PLOR3.1model building
X-PLOR3.1refinement
XDSdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT SOFTWARE USED : X-PLOR STARTING MODEL FOR MOLECULAR REPLACEMENT: NATIVE PROTEIN (REFERENCE 1)
Resolution: 2.3→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.241 -10.2 %
Rwork0.16 --
obs0.16 13958 90.4 %
Displacement parametersBiso mean: 15.3 Å2
Refine analyzeLuzzati coordinate error obs: 0.01 Å
Refinement stepCycle: LAST / Resolution: 2.3→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2210 0 14 220 2444
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.8
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.16 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.8
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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