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- PDB-3b3c: Crystal structure of the M180A mutant of the aminopeptidase from ... -

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Basic information

Entry
Database: PDB / ID: 3b3c
TitleCrystal structure of the M180A mutant of the aminopeptidase from Vibrio proteolyticus in complex with leucine phosphonic acid
ComponentsBacterial leucyl aminopeptidase
KeywordsHYDROLASE / alpha beta / Aminopeptidase / Metal-binding / Protease / Secreted / Zinc / Zymogen
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
: / LEUCINE PHOSPHONIC ACID / THIOCYANATE ION / Bacterial leucyl aminopeptidase
Similarity search - Component
Biological speciesVibrio proteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.46 Å
AuthorsAtaie, N.J. / Hoang, Q.Q. / Petsko, G.A. / Ringe, D.
CitationJournal: Biochemistry / Year: 2008
Title: Zinc coordination geometry and ligand binding affinity: the structural and kinetic analysis of the second-shell serine 228 residue and the methionine 180 residue of the aminopeptidase from Vibrio proteolyticus.
Authors: Ataie, N.J. / Hoang, Q.Q. / Zahniser, M.P. / Tu, Y. / Milne, A. / Petsko, G.A. / Ringe, D.
History
DepositionOct 19, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / 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_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Oct 30, 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: Bacterial leucyl aminopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,90012
Polymers31,3671
Non-polymers53311
Water5,008278
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)108.189, 108.189, 97.206
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-885-

HOH

DetailsAuthors state that the biological unit of this protein is unknown.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bacterial leucyl aminopeptidase


Mass: 31367.232 Da / Num. of mol.: 1 / Fragment: Residues 107-397 / Mutation: M286A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio proteolyticus (bacteria) / Strain: DSM 30189 / IFO 13287 / LMG 3772 / NCIMB 1326 / Gene: AAP / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q01693, bacterial leucyl aminopeptidase

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Non-polymers , 6 types, 289 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-PLU / LEUCINE PHOSPHONIC ACID


Mass: 167.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H14NO3P
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.62 Å3/Da / Density % sol: 53.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: HEPES, KSCN, NaCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9001 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9001 Å / Relative weight: 1
ReflectionResolution: 1.46→30.63 Å / Num. obs: 57867

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3B35

3b35


Resolution: 1.46→30.63 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.213 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.069 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2926 5.1 %RANDOM
Rwork0.197 ---
obs0.198 57867 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.722 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.46→30.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2208 0 22 278 2508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212271
X-RAY DIFFRACTIONr_angle_refined_deg1.2031.9313100
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7935290
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.23825.631103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.64315337
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.968155
X-RAY DIFFRACTIONr_chiral_restr0.0790.2347
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021755
X-RAY DIFFRACTIONr_nbd_refined0.2310.21209
X-RAY DIFFRACTIONr_nbtor_refined0.3050.21617
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2520.2236
X-RAY DIFFRACTIONr_metal_ion_refined0.3860.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.221
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1090.21
X-RAY DIFFRACTIONr_mcbond_it0.6461.51452
X-RAY DIFFRACTIONr_mcangle_it1.1722334
X-RAY DIFFRACTIONr_scbond_it1.7393819
X-RAY DIFFRACTIONr_scangle_it2.664.5766
LS refinement shellResolution: 1.46→1.498 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 192 -
Rwork0.322 3824 -
all-4016 -
obs--94.34 %

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