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

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Basic information

Entry
Database: PDB / ID: 5fss
TitleStructure of thermolysin prepared by the 'soak-and-freeze' method under 40 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 / Thermolysin metallopeptidase, alpha-helical 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: 1.5 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 7, 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 1.4Feb 28, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Jun 20, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms ...pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.6Jan 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 / 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_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.ptnr2_auth_seq_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

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Assembly

Deposited unit
A: THERMOLYSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,17512
Polymers34,3601
Non-polymers81511
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.749, 92.749, 128.995
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-2012-

HOH

21A-2183-

HOH

31A-2186-

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 , 7 types, 343 molecules

#2: Chemical ChemComp-VAL / VALINE / Valine


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#3: Chemical ChemComp-LYS / LYSINE / 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.: 4 / 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-KR / KRYPTON / Krypton


Mass: 83.798 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Kr
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 47 % / Description: NONE
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: ID29 / Wavelength: 0.861
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Details: MIRRORS
RadiationMonochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.861 Å / Relative weight: 1
ReflectionResolution: 1.5→46.37 Å / Num. obs: 52712 / % possible obs: 99.5 % / Observed criterion σ(I): 7.9 / Redundancy: 34.9 % / Biso Wilson estimate: 14.11 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 34.3
Reflection shellResolution: 1.5→1.59 Å / Redundancy: 35.2 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 6.7 / % possible all: 98.8

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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: 1.5→46.375 Å / SU ML: 0.12 / σ(F): 1.34 / Phase error: 16.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1796 2582 4.9 %
Rwork0.1615 --
obs0.1624 52712 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.8 Å2
Refinement stepCycle: LAST / Resolution: 1.5→46.375 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 31 332 2795
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082568
X-RAY DIFFRACTIONf_angle_d1.1933505
X-RAY DIFFRACTIONf_dihedral_angle_d13.252892
X-RAY DIFFRACTIONf_chiral_restr0.046374
X-RAY DIFFRACTIONf_plane_restr0.007464
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5001-1.5290.2271500.19022682X-RAY DIFFRACTION98
1.529-1.56020.19671480.18142710X-RAY DIFFRACTION99
1.5602-1.59410.19461400.17932735X-RAY DIFFRACTION99
1.5941-1.63120.21931300.17162733X-RAY DIFFRACTION99
1.6312-1.6720.21191340.17382750X-RAY DIFFRACTION99
1.672-1.71720.17161500.16632727X-RAY DIFFRACTION99
1.7172-1.76770.21171210.16382747X-RAY DIFFRACTION99
1.7677-1.82480.18091430.1622764X-RAY DIFFRACTION100
1.8248-1.890.18891420.16392747X-RAY DIFFRACTION100
1.89-1.96570.18221590.1592746X-RAY DIFFRACTION100
1.9657-2.05510.20541370.15952775X-RAY DIFFRACTION100
2.0551-2.16350.17081490.14982766X-RAY DIFFRACTION100
2.1635-2.2990.16911430.15662796X-RAY DIFFRACTION100
2.299-2.47650.15671380.15972818X-RAY DIFFRACTION100
2.4765-2.72570.19281620.1592811X-RAY DIFFRACTION100
2.7257-3.12010.17731590.16662836X-RAY DIFFRACTION100
3.1201-3.93070.16971280.15472902X-RAY DIFFRACTION100
3.9307-46.39670.16651490.1613085X-RAY DIFFRACTION100

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