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- PDB-4ow3: Thermolysin structure determined by free-electron laser -

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Basic information

Entry
Database: PDB / ID: 4ow3
TitleThermolysin structure determined by free-electron laser
ComponentsThermolysin
KeywordsHYDROLASE / thermolysin / protease
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
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHattne, J. / Echols, N. / Tran, R. / Kern, J. / Gildea, R.J. / Brewster, A.S. / Alonso-Mori, R. / Glockner, C. / Hellmich, J. / Laksmono, H. ...Hattne, J. / Echols, N. / Tran, R. / Kern, J. / Gildea, R.J. / Brewster, A.S. / Alonso-Mori, R. / Glockner, C. / Hellmich, J. / Laksmono, H. / Sierra, R.G. / Lassalle-Kaiser, B. / Lampe, A. / Han, G. / Gul, S. / DiFiore, D. / Milathianaki, D. / Fry, A.R. / Miahnahri, A. / White, W.E. / Schafer, D.W. / Seibert, M.M. / Koglin, J.E. / Sokaras, D. / Weng, T.-C. / Sellberg, J. / Latimer, M.J. / Glatzel, P. / Zwart, P.H. / Grosse-Kunstleve, R.W. / Bogan, M.J. / Messerschmidt, M. / Williams, G.J. / Boutet, S. / Messinger, J. / Zouni, A. / Yano, J. / Bergmann, U. / Yachandra, V.K. / Adams, P.D. / Sauter, N.K.
Funding support United States, 5items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM095887 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM102520 United States
Department of Energy (DOE, United States)DE-AC02-05CH11231 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM055302 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM103393 United States
Citation
Journal: Nat.Methods / Year: 2014
Title: Accurate macromolecular structures using minimal measurements from X-ray free-electron lasers.
Authors: Hattne, J. / Echols, N. / Tran, R. / Kern, J. / Gildea, R.J. / Brewster, A.S. / Alonso-Mori, R. / Glockner, C. / Hellmich, J. / Laksmono, H. / Sierra, R.G. / Lassalle-Kaiser, B. / Lampe, A. ...Authors: Hattne, J. / Echols, N. / Tran, R. / Kern, J. / Gildea, R.J. / Brewster, A.S. / Alonso-Mori, R. / Glockner, C. / Hellmich, J. / Laksmono, H. / Sierra, R.G. / Lassalle-Kaiser, B. / Lampe, A. / Han, G. / Gul, S. / DiFiore, D. / Milathianaki, D. / Fry, A.R. / Miahnahri, A. / White, W.E. / Schafer, D.W. / Seibert, M.M. / Koglin, J.E. / Sokaras, D. / Weng, T.C. / Sellberg, J. / Latimer, M.J. / Glatzel, P. / Zwart, P.H. / Grosse-Kunstleve, R.W. / Bogan, M.J. / Messerschmidt, M. / Williams, G.J. / Boutet, S. / Messinger, J. / Zouni, A. / Yano, J. / Bergmann, U. / Yachandra, V.K. / Adams, P.D. / Sauter, N.K.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2013
Title: New Python-based methods for data processing.
Authors: Sauter, N.K. / Hattne, J. / Grosse-Kunstleve, R.W. / Echols, N.
#2: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Nanoflow electrospinning serial femtosecond crystallography.
Authors: Sierra, R.G. / Laksmono, H. / Kern, J. / Tran, R. / Hattne, J. / Alonso-Mori, R. / Lassalle-Kaiser, B. / Glockner, C. / Hellmich, J. / Schafer, D.W. / Echols, N. / Gildea, R.J. / Grosse- ...Authors: Sierra, R.G. / Laksmono, H. / Kern, J. / Tran, R. / Hattne, J. / Alonso-Mori, R. / Lassalle-Kaiser, B. / Glockner, C. / Hellmich, J. / Schafer, D.W. / Echols, N. / Gildea, R.J. / Grosse-Kunstleve, R.W. / Sellberg, J. / McQueen, T.A. / Fry, A.R. / Messerschmidt, M.M. / Miahnahri, A. / Seibert, M.M. / Hampton, C.Y. / Starodub, D. / Loh, N.D. / Sokaras, D. / Weng, T.C. / Zwart, P.H. / Glatzel, P. / Milathianaki, D. / White, W.E. / Adams, P.D. / Williams, G.J. / Boutet, S. / Zouni, A. / Messinger, J. / Sauter, N.K. / Bergmann, U. / Yano, J. / Yachandra, V.K. / Bogan, M.J.
History
DepositionJan 30, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 18, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Sep 27, 2017Group: Advisory / Author supporting evidence ...Advisory / Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / entity_src_nat ...citation / entity_src_nat / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / pdbx_validate_close_contact / struct_keywords
Item: _citation.country / _citation.journal_id_ASTM ..._citation.country / _citation.journal_id_ASTM / _entity_src_nat.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Aug 16, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_related_exp_data_set / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Sep 27, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)34,5866
Polymers34,3601
Non-polymers2265
Water6,089338
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.8933, 92.8933, 130.438
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Thermolysin / / Thermostable neutral proteinase


Mass: 34360.336 Da / Num. of mol.: 1 / Fragment: UNP residues 233-548 / Source method: isolated from a natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 338 / 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: 13371

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 6.5
Details: 300 ul of the protein stock was mixed in a 1:1 ratio with 40% PEG 2000, 100 mM MES pH 6.5, 5 mM CaCl2. Crystallization occurred within minutes.

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.269, 1.297
DetectorType: CS-PAD detector / Detector: PIXEL / Date: Dec 1, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.2691
21.2971
ReflectionResolution: 2.1→68.5 Å / Num. obs: 19861 / % possible obs: 99.1 % / Redundancy: 209 % / Biso Wilson estimate: 14.3263474589 Å2 / Net I/σ(I): 50.2
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 5.6 / % possible all: 91.2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_1549+SVN) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TLI

2tli


Resolution: 2.1→68.4723333423 Å / SU ML: 0.283633880013 / σ(F): 1.44173097843 / Phase error: 24.4432098669
RfactorNum. reflection% reflection
Rfree0.263168484633 1042 5.24646291728 %
Rwork0.217242670815 18819 -
obs0.219654161884 19861 99.0326601845 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.2875323051 Å2
Refinement stepCycle: LAST / Resolution: 2.1→68.4723333423 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2404 0 5 338 2747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002898529098192462
X-RAY DIFFRACTIONf_angle_d0.6824388498133354
X-RAY DIFFRACTIONf_chiral_restr0.025759577597358
X-RAY DIFFRACTIONf_plane_restr0.00240657682604442
X-RAY DIFFRACTIONf_dihedral_angle_d12.8953940052840
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.21080.3593538396141490.3057509186352468X-RAY DIFFRACTION93.2976827094
2.2108-2.34930.3118595973991570.2567082247482612X-RAY DIFFRACTION99.8557518933
2.3493-2.53070.2893192112581360.2291445493852686X-RAY DIFFRACTION100
2.5307-2.78530.2864987584991690.224525977652653X-RAY DIFFRACTION100
2.7853-3.18840.2597330142161390.2119272416462721X-RAY DIFFRACTION100
3.1884-4.0170.2117767299841440.1815990696012749X-RAY DIFFRACTION100
4.017-68.50870.233078334011480.2017955432582930X-RAY DIFFRACTION100

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