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- PDB-5fsj: Structure of thermolysin prepared by the 'soak-and-freeze' method... -

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Basic information

Entry
Database: PDB / ID: 5fsj
TitleStructure of thermolysin prepared by the 'soak-and-freeze' method under 45 bar of oxygen pressure
ComponentsTHERMOLYSIN
KeywordsHYDROLASE / METALLOPROTEINASE / THERMOLYSINE / DIOXYGEN / PRESSURE / FLASH FREEZING
Function / homology
Function and homology information


thermolysin / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Elastase; domain 1 - #10 / Elastase; domain 1 / PepSY domain / Peptidase propeptide and YPEB domain / : / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain ...Elastase; domain 1 - #10 / Elastase; domain 1 / PepSY domain / Peptidase propeptide and YPEB domain / : / Peptidase M4, C-terminal / FTP domain / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain / Thermolysin metallopeptidase, alpha-helical domain / Fungalysin/Thermolysin Propeptide Motif / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
LYSINE / OXYGEN MOLECULE / VALINE / Thermolysin
Similarity search - Component
Biological speciesBACILLUS THERMOPROTEOLYTICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.201 Å
AuthorsLafumat, B. / Mueller-Dieckmann, C. / Colloc'h, N. / Prange, T. / Royant, A. / van der Linden, P. / Carpentier, P.
CitationJournal: J.Appl.Crystallogr. / Year: 2016
Title: Gas-Sensitive Biological Crystals Processed in Pressurized Oxygen and Krypton Atmospheres: Deciphering Gas Channels in Proteins Using a Novel `Soak-and-Freeze' Methodology.
Authors: Lafumat, B. / Mueller-Dieckmann, C. / Colloc'h, N. / Prange, T. / Royant, A. / van der Linden, P. / Carpentier, P.
History
DepositionJan 6, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2016Group: Structure summary
Revision 1.2Feb 21, 2018Group: Advisory / Database references / Structure summary
Category: audit_author / citation_author / pdbx_unobs_or_zero_occ_residues
Item: _audit_author.name / _citation_author.name
Revision 2.0Jun 20, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / pdbx_struct_conn_angle ...atom_site / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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
Revision 2.1Jan 10, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: THERMOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,98811
Polymers34,3601
Non-polymers62810
Water9,854547
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.922, 92.922, 130.252
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-2023-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein THERMOLYSIN / THERMOSTABLE NEUTRAL PROTEINASE


Mass: 34360.336 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 233-548
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS THERMOPROTEOLYTICUS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P00800, thermolysin

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Non-polymers , 6 types, 557 molecules

#2: Chemical ChemComp-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#3: Chemical ChemComp-LYS / LYSINE


Type: L-peptide linking / Mass: 147.195 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N2O2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 547 / 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: 2.36 Å3/Da / Density % sol: 47.93 % / Description: NONE
Crystal growpH: 6
Details: 1:1 WITH 50 MM MES PH6, 1M NACL 45%(V/V) DMSO RESERVOIR: 35% SATURATED AMONIUM SULPHATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.968
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 100246 / % possible obs: 97 % / Observed criterion σ(I): 2.5 / Redundancy: 15.3 % / Biso Wilson estimate: 11.78 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 23
Reflection shellResolution: 1.2→1.27 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.08 / Mean I/σ(I) obs: 2.65 / % possible all: 88.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DO1

3do1


Resolution: 1.201→46.461 Å / SU ML: 0.08 / σ(F): 1.34 / Phase error: 10.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1216 4921 4.9 %
Rwork0.1039 --
obs0.1048 100245 96.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.16 Å2
Refinement stepCycle: LAST / Resolution: 1.201→46.461 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 26 547 3005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082683
X-RAY DIFFRACTIONf_angle_d1.1493688
X-RAY DIFFRACTIONf_dihedral_angle_d14.208971
X-RAY DIFFRACTIONf_chiral_restr0.087397
X-RAY DIFFRACTIONf_plane_restr0.006492
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2006-1.21430.22741300.232647X-RAY DIFFRACTION82
1.2143-1.22860.21681360.19542859X-RAY DIFFRACTION88
1.2286-1.24360.17871530.17232895X-RAY DIFFRACTION90
1.2436-1.25930.16981460.15432981X-RAY DIFFRACTION91
1.2593-1.27590.1711410.14183002X-RAY DIFFRACTION93
1.2759-1.29330.17741620.13513025X-RAY DIFFRACTION94
1.2933-1.31180.16361200.13263080X-RAY DIFFRACTION94
1.3118-1.33140.16021510.12213085X-RAY DIFFRACTION95
1.3314-1.35220.14491480.12133093X-RAY DIFFRACTION96
1.3522-1.37440.15391680.11353124X-RAY DIFFRACTION97
1.3744-1.39810.14411720.10973169X-RAY DIFFRACTION98
1.3981-1.42350.12721740.10143151X-RAY DIFFRACTION98
1.4235-1.45090.13851480.09693236X-RAY DIFFRACTION99
1.4509-1.48050.11951900.08783180X-RAY DIFFRACTION99
1.4805-1.51270.10631600.08433216X-RAY DIFFRACTION99
1.5127-1.54790.11142080.0833186X-RAY DIFFRACTION99
1.5479-1.58660.11031650.07853229X-RAY DIFFRACTION99
1.5866-1.62950.11141720.07633252X-RAY DIFFRACTION99
1.6295-1.67750.11351710.07653223X-RAY DIFFRACTION99
1.6775-1.73160.09821660.07663260X-RAY DIFFRACTION100
1.7316-1.79350.10391730.07783253X-RAY DIFFRACTION100
1.7935-1.86530.1061670.08043280X-RAY DIFFRACTION100
1.8653-1.95020.09481670.08333274X-RAY DIFFRACTION100
1.9502-2.0530.09751690.08263292X-RAY DIFFRACTION100
2.053-2.18160.11141790.08313296X-RAY DIFFRACTION100
2.1816-2.35010.10351640.08623320X-RAY DIFFRACTION100
2.3501-2.58660.09872070.09463311X-RAY DIFFRACTION100
2.5866-2.96080.12941630.10183377X-RAY DIFFRACTION100
2.9608-3.730.13411720.11393411X-RAY DIFFRACTION100
3.73-46.49580.13181790.13583617X-RAY DIFFRACTION100

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