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- PDB-4dzt: Aqualysin I: the crystal structure of a serine protease from an e... -

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Basic information

Entry
Database: PDB / ID: 4dzt
TitleAqualysin I: the crystal structure of a serine protease from an extreme thermophile, Thermus aquaticus YT-1
ComponentsAqualysin-1
KeywordsHYDROLASE/HYDROLASE INHIBITOR / serine protease / calcium binding / inhibitor / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


aqualysin 1 / serine-type endopeptidase activity / extracellular region
Similarity search - Function
Proteinase K-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. ...Proteinase K-like catalytic domain / Peptidase S8/S53 domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Serine proteases, subtilase domain profile. / Peptidase S8, subtilisin-related / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
phenylmethanesulfonic acid / Aqualysin-1
Similarity search - Component
Biological speciesThermus aquaticus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBarnett, B.L. / Green, P.R. / Strickland, L.C. / Oliver, J.D. / Rydel, T. / Sullivan, J.F.
Citation
Journal: To be Published
Title: Aqualysin I: the crystal structure of a serine protease from an extreme thermophile, Thermus aquaticus YT-1
Authors: Barnett, B.L. / Green, P.R. / Strickland, L.C. / Oliver, J.D. / Rydel, T. / Sullivan, J.F.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1993
Title: Purification, crystallization and preliminary X-ray investigation of aqualysin I, a heat-stable serine protease.
Authors: Green, P.R. / Oliver, J.D. / Strickland, L.C. / Toerner, D.R. / Matsuzawa, H. / Ohta, T.
History
DepositionMar 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 28, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_type.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: Aqualysin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2494
Polymers27,9971
Non-polymers2523
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.906, 64.480, 45.716
Angle α, β, γ (deg.)90.00, 109.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Aqualysin-1 / Aqualysin-I


Mass: 27996.844 Da / Num. of mol.: 1 / Fragment: UNP residues 128-403 / Source method: isolated from a natural source / Source: (natural) Thermus aquaticus (bacteria) / Strain: YT-1 / References: UniProt: P08594, aqualysin 1
#2: Chemical ChemComp-PMS / phenylmethanesulfonic acid


Mass: 172.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8O3S
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O

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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: 2.03 Å3/Da / Density % sol: 39.56 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 21% PEG800, 100 mM phosphate buffer, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU AFC-5R / Detector: DIFFRACTOMETER / Date: Nov 28, 1995 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.95→40 Å / Num. all: 15592 / Num. obs: 15592 / % possible obs: 94.8 % / Observed criterion σ(I): 4 / Rmerge(I) obs: 0.0375 / Rsym value: 0.05 / Net I/σ(I): 22.21
Reflection shellResolution: 1.95→2.05 Å / Redundancy: 0.9 % / Rmerge(I) obs: 0.0557 / Mean I/σ(I) obs: 15.4 / Num. unique all: 2027 / % possible all: 90.5

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Processing

Software
NameClassification
MAR345dtbdata collection
EPMRphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PRK

2prk


Resolution: 1.95→10 Å / σ(I): 4
Details: DATA REDUCTION, STRUCTURE SOLUTION, AND STRUCTURE REFINEMENT WERE PERFORMED WITHOUT A FREE R TEST SET.
RfactorNum. reflection% reflection
Rwork0.1323 --
all0.135 15483 -
obs-15032 94.3 %
Refinement stepCycle: LAST / Resolution: 1.95→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1967 0 12 143 2122
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_angle_d0.04
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.02
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_from_restr_planes0.447
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.1
LS refinement shellHighest resolution: 1.95 Å /
Num. reflection% reflection
Rfree0 -
obs-94.8 %

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