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- PDB-2nyq: Structure of Vibrio proteolyticus aminopeptidase with a bound Trp... -

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Basic information

Entry
Database: PDB / ID: 2nyq
TitleStructure of Vibrio proteolyticus aminopeptidase with a bound Trp fragment of dLWCF
Components
  • Aminopeptidase
  • Tetrapeptide
KeywordsHYDROLASE / Trp / VpAP / non-covalent
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBennett, B. / Kumar, A. / Narayanan, B. / Kim, J.-J.
CitationJournal: To be Published
Title: Substrate recognition by the leucine aminopeptidase from Vibrio proteolyticus
Authors: Kumar, A. / Narayanan, B. / Kim, J.-J. / Bennett, B.
History
DepositionNov 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Source and taxonomy / Structure summary
Category: audit_author / citation_author / pdbx_entity_src_syn
Item: _audit_author.name / _citation_author.name ..._audit_author.name / _citation_author.name / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 1.3Aug 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
Revision 1.4Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminopeptidase
B: Tetrapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9374
Polymers32,8062
Non-polymers1312
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-83 kcal/mol
Surface area10310 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)107.8, 107.8, 99.6
Angle α, β, γ (deg.)90.00, 90.00, 120
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Aminopeptidase


Mass: 32238.150 Da / Num. of mol.: 1 / Fragment: Bacterial leucyl aminopeptidase, residues 97-405 / Source method: isolated from a natural source / Source: (natural) Vibrio proteolyticus (bacteria) / Strain: ATTC 15338, DSM 30189, NCBM 1326
References: UniProt: Q01693, bacterial leucyl aminopeptidase
#2: Protein/peptide Tetrapeptide


Mass: 567.699 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The tetrapeptide was chemically synthesised using solid-phase manual synthesis via Fmoc-derivatized amino acids, on Rink-amide resin.
Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 2.55 Å3/Da / Density % sol: 51.67 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 5 d., 10/100/100 mM KSCN, 0.4/4.5/4.5 M NaCl, 10/100 mM Tris/100 mM Tricine, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 1, 2005 / Details: CONFOCAL
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 12122 / Num. obs: 12122 / % possible obs: 98.4 % / Biso Wilson estimate: 36.5 Å2 / Rsym value: 0.048
Reflection shellResolution: 2.5→2.59 Å / Rsym value: 0.139 / % possible all: 97.7

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Processing

Software
NameVersionClassification
HKL-3000data collection
AMoREphasing
CNS1.1refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1CP6

1cp6


Resolution: 2.5→50 Å
RfactorNum. reflection% reflection
Rfree0.256 --
Rwork0.191 --
obs0.191 12122 98.4 %
all-12122 -
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2224 0 2 152 2378

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