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

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Basic information

Entry
Database: PDB / ID: 5fsp
TitleStructure of thermolysin prepared by the 'soak-and-freeze' method under 100 bar of krypton pressure
ComponentsTHERMOLYSIN
KeywordsHYDROLASE / METALLOPROTEINASE / THERMOLYSINE / KRYPTON / 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
KRYPTON / LYSINE / VALINE / Thermolysin
Similarity search - Component
Biological speciesBACILLUS THERMOPROTEOLYTICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.2May 10, 2017Group: Structure summary
Revision 1.3Feb 21, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Jan 10, 2024Group: Data collection / Database references ...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 / 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 / _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

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Assembly

Deposited unit
A: THERMOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,52116
Polymers34,3601
Non-polymers1,16015
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.007, 93.007, 129.120
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-2011-

HOH

21A-2151-

HOH

31A-2156-

HOH

41A-2278-

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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BACILLUS THERMOPROTEOLYTICUS (bacteria)
Production host: BACILLUS SUBTILIS (bacteria) / References: UniProt: P00800, thermolysin

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Non-polymers , 6 types, 300 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical
ChemComp-KR / KRYPTON


Mass: 83.798 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Kr
#6: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.3 Å3/Da / Density % sol: 45.79 % / Description: ANOMALOUS DATA
Crystal growpH: 6
Details: 1:1 WITH 50MM MES PH6, 1MNACL 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: ID23-1 / Wavelength: 0.864
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.864 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 68932 / % possible obs: 99.7 % / Observed criterion σ(I): 5.8 / Redundancy: 17.4 % / Biso Wilson estimate: 12.49 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 24.3
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 16.7 % / Rmerge(I) obs: 0.06 / Mean I/σ(I) obs: 5.82 / % possible all: 98.1

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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: 1.7→46.504 Å / SU ML: 0.14 / σ(F): 0.58 / Phase error: 16.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1778 3402 4.9 %
Rwork0.1549 --
obs0.156 37016 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 13.4 Å2
Refinement stepCycle: LAST / Resolution: 1.7→46.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 29 285 2746
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072582
X-RAY DIFFRACTIONf_angle_d1.113532
X-RAY DIFFRACTIONf_dihedral_angle_d13.441909
X-RAY DIFFRACTIONf_chiral_restr0.047380
X-RAY DIFFRACTIONf_plane_restr0.006467
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7210.21811310.24212566X-RAY DIFFRACTION93
1.721-1.74670.2621210.2032763X-RAY DIFFRACTION100
1.7467-1.7740.17981410.18822707X-RAY DIFFRACTION100
1.774-1.80310.26191270.1882757X-RAY DIFFRACTION100
1.8031-1.83420.22321590.17772733X-RAY DIFFRACTION100
1.8342-1.86750.18411630.1742704X-RAY DIFFRACTION100
1.8675-1.90350.19621540.15822751X-RAY DIFFRACTION100
1.9035-1.94230.20291310.15072749X-RAY DIFFRACTION100
1.9423-1.98460.20791490.15752742X-RAY DIFFRACTION100
1.9846-2.03070.20381380.15232709X-RAY DIFFRACTION100
2.0307-2.08150.19631590.14812717X-RAY DIFFRACTION100
2.0815-2.13780.14431710.13982718X-RAY DIFFRACTION100
2.1378-2.20070.18261470.14172727X-RAY DIFFRACTION100
2.2007-2.27170.181420.14892769X-RAY DIFFRACTION100
2.2717-2.35290.1561470.15252708X-RAY DIFFRACTION100
2.3529-2.44710.22841010.15792796X-RAY DIFFRACTION100
2.4471-2.55850.1791250.1542742X-RAY DIFFRACTION100
2.5585-2.69340.14981450.14892744X-RAY DIFFRACTION100
2.6934-2.86210.17211290.14972749X-RAY DIFFRACTION100
2.8621-3.0830.16121430.15732748X-RAY DIFFRACTION100
3.083-3.39320.15851660.15282705X-RAY DIFFRACTION100
3.3932-3.8840.18131380.14492759X-RAY DIFFRACTION100
3.884-4.89260.13771470.13072733X-RAY DIFFRACTION100
4.8926-46.5210.18381280.16882755X-RAY DIFFRACTION100

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