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- PDB-1lok: The 1.20 Angstrom Resolution Crystal Structure of the Aminopeptid... -

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Basic information

Entry
Database: PDB / ID: 1lok
TitleThe 1.20 Angstrom Resolution Crystal Structure of the Aminopeptidase from Aeromonas proteolytica Complexed with Tris: A Tale of Buffer Inhibition
ComponentsBacterial leucyl aminopeptidase
KeywordsHYDROLASE / metalloenzyme / aminopeptidase / tris / high resolution / metal coordination
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 / FOURIER SYNTHESIS / Resolution: 1.2 Å
AuthorsDesmarais, W.T. / Bienvenue, D.L. / Bzymek, K.P. / Holz, R.C. / Petsko, G.A. / Ringe, D.
CitationJournal: Structure / Year: 2002
Title: The 1.20 Angstrom Resolution Crystal Structure of the Aminopeptidase from Aeromonas proteolytica Complexed with Tris A tale of Buffer Inhibition
Authors: Desmarais, W.T. / Bienvenue, D.L. / Bzymek, K.P. / Holz, R.C. / Petsko, G.A. / Ringe, D.
History
DepositionMay 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Aug 16, 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 / 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.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 / _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
Revision 1.5Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)31,7616
Polymers31,4271
Non-polymers3345
Water6,269348
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.338, 108.338, 93.519
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-1062-

HOH

21A-1063-

HOH

31A-1067-

HOH

41A-1115-

HOH

51A-1168-

HOH

DetailsThe biological assembly is a monomer.

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Bacterial leucyl aminopeptidase / Aeromonas Proteolytica 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

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Non-polymers , 5 types, 353 molecules

#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#5: 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
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris, potassium thiocyanate, sodium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
116 mg/mlprotein1drop
210 mMTris1droppH8.0
310 mMKSCN1drop
40.4 M1dropNaCl
5100 mMTris1reservoirpH8.0
6100 mMKSCN1reservoir
74.5 M1reservoirNaCl

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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: Feb 11, 2000
RadiationMonochromator: Germanium / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.94→27.08 Å / Num. all: 89053 / Num. obs: 89053 / % possible obs: 88.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 15 %
Reflection shellResolution: 0.94→1.25 Å / % possible all: 98
Reflection
*PLUS
Highest resolution: 1.2 Å / Lowest resolution: 30 Å / Num. obs: 117248 / % possible obs: 99 % / Num. measured all: 1348266 / Rmerge(I) obs: 0.057
Reflection shell
*PLUS
Highest resolution: 1.2 Å / % possible obs: 98 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1AMP

1amp


Resolution: 1.2→27.08 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.198 9943 RANDOM
Rwork0.158 --
all0.154 89053 -
obs0.145 89053 -
Refinement stepCycle: LAST / Resolution: 1.2→27.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2251 0 14 348 2613
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_from_restr_planes0.0289
X-RAY DIFFRACTIONs_zero_chiral_vol0.082
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.08
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å / Rfactor Rfree: 0.176 / Rfactor Rwork: 0.14
Solvent computation
*PLUS
Displacement parameters
*PLUS

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