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- PDB-4tnl: 1.8 A resolution room temperature structure of Thermolysin record... -

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Basic information

Entry
Database: PDB / ID: 4tnl
Title1.8 A resolution room temperature structure of Thermolysin recorded using an XFEL
ComponentsThermolysin
KeywordsHYDROLASE / Zn protease / X-ray free electron laser
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
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsKern, J. / Tran, R. / Alonso-Mori, R. / Koroidov, S. / Echols, N. / Hattne, J. / Ibrahim, M. / Gul, S. / Laksmono, H. / Sierra, R.G. ...Kern, J. / Tran, R. / Alonso-Mori, R. / Koroidov, S. / Echols, N. / Hattne, J. / Ibrahim, M. / Gul, S. / Laksmono, H. / Sierra, R.G. / Gildea, R.J. / Han, G. / Hellmich, J. / Lassalle-Kaiser, B. / Chatterjee, R. / Brewster, A. / Stan, C.A. / Gloeckner, C. / Lampe, A. / DiFiore, D. / Milathianaki, D. / Fry, A.R. / Seibert, M.M. / Koglin, J.E. / Gallo, E. / Uhlig, J. / Sokaras, D. / Weng, T.-C. / Zwart, P.H. / Skinner, D.E. / Bogan, M.J. / Messerschmidt, M. / Glatzel, P. / Williams, G.J. / Boutet, S. / Adams, P.D. / Zouni, A. / Messinger, J. / Sauter, N.K. / Bergmann, U. / Yano, J. / Yachandra, V.K.
Citation
Journal: Nat Commun / Year: 2014
Title: Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy.
Authors: Kern, J. / Tran, R. / Alonso-Mori, R. / Koroidov, S. / Echols, N. / Hattne, J. / Ibrahim, M. / Gul, S. / Laksmono, H. / Sierra, R.G. / Gildea, R.J. / Han, G. / Hellmich, J. / Lassalle- ...Authors: Kern, J. / Tran, R. / Alonso-Mori, R. / Koroidov, S. / Echols, N. / Hattne, J. / Ibrahim, M. / Gul, S. / Laksmono, H. / Sierra, R.G. / Gildea, R.J. / Han, G. / Hellmich, J. / Lassalle-Kaiser, B. / Chatterjee, R. / Brewster, A.S. / Stan, C.A. / Glockner, C. / Lampe, A. / DiFiore, D. / Milathianaki, D. / Fry, A.R. / Seibert, M.M. / Koglin, J.E. / Gallo, E. / Uhlig, J. / Sokaras, D. / Weng, T.C. / Zwart, P.H. / Skinner, D.E. / Bogan, M.J. / Messerschmidt, M. / Glatzel, P. / Williams, G.J. / Boutet, S. / Adams, P.D. / Zouni, A. / Messinger, J. / Sauter, N.K. / Bergmann, U. / Yano, J. / Yachandra, V.K.
#1: Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Biol Crystallogr / Year: 2010
Title: PHENIX: a comprehensive Python-based system for macromolecular structure solution.
Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy ...Authors: Paul D Adams / Pavel V Afonine / Gábor Bunkóczi / Vincent B Chen / Ian W Davis / Nathaniel Echols / Jeffrey J Headd / Li-Wei Hung / Gary J Kapral / Ralf W Grosse-Kunstleve / Airlie J McCoy / Nigel W Moriarty / Robert Oeffner / Randy J Read / David C Richardson / Jane S Richardson / Thomas C Terwilliger / Peter H Zwart /
Abstract: Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many ...Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures because of the need for manual interpretation of complex numerical data using many software packages and the repeated use of interactive three-dimensional graphics. PHENIX has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on the automation of all procedures. This has relied on the development of algorithms that minimize or eliminate subjective input, the development of algorithms that automate procedures that are traditionally performed by hand and, finally, the development of a framework that allows a tight integration between the algorithms.
History
DepositionJun 4, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Oct 7, 2015Group: Other
Revision 1.4Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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)34,5866
Polymers34,3601
Non-polymers2265
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.0407, 93.0407, 130.41
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
Components on special symmetry positions
IDModelComponents
11A-588-

HOH

21A-605-

HOH

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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


Mass: 18.015 Da / Num. of mol.: 324 / 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: 120408

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Sample preparation

CrystalDensity Matthews: 2.39 Å3/Da / Density % sol: 48.47 %
Crystal growTemperature: 298 K / Method: batch mode
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: 1.27 Å
DetectorType: CS-PAD detector / Detector: PIXEL / Date: Mar 3, 2013
Details: Collected at the CXI instrument at LCLS/SLAC using the CSPAD
RadiationMonochromator: No monochromator, FEL beam with 20-30 eV bandwidth
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27 Å / Relative weight: 1
ReflectionResolution: 1.8→34.27 Å / Num. obs: 31458 / % possible obs: 100 % / Redundancy: 1468 % / Biso Wilson estimate: 16.3967395539 Å2 / Net I/σ(I): 71.7
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 14.6 % / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1647+SVNrefinement
cctbx.xfeldata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2tli

2tli


Resolution: 1.8→34.27 Å / SU ML: 0.204817582335 / Cross valid method: FREE R-VALUE / σ(F): 1.42149651097 / Phase error: 20.1997292845
RfactorNum. reflection% reflection
Rfree0.232602531993 3063 5.2358974359 %
Rwork0.211866857775 55437 -
obs0.212950766366 58500 99.9128964492 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.1244048785 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2415 0 5 324 2744
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005142269747712473
X-RAY DIFFRACTIONf_angle_d0.9237274396283369
X-RAY DIFFRACTIONf_chiral_restr0.0342922692207359
X-RAY DIFFRACTIONf_plane_restr0.0040116139072445
X-RAY DIFFRACTIONf_dihedral_angle_d12.5608297587845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82810.3751932589951350.3692272075142482X-RAY DIFFRACTION98.3464862834
1.8281-1.85810.3672519720661400.340020054882540X-RAY DIFFRACTION99.7766195086
1.8581-1.89010.3093940299261460.3169467107282482X-RAY DIFFRACTION99.9619627235
1.8901-1.92450.2668887776521380.2797105572322540X-RAY DIFFRACTION100
1.9245-1.96150.2195991003421400.2578731122722498X-RAY DIFFRACTION100
1.9615-2.00160.2344724710721420.2510315694172537X-RAY DIFFRACTION100
2.0016-2.04510.2761279448231350.2372546274752516X-RAY DIFFRACTION100
2.0451-2.09260.263024768471390.2303894325742522X-RAY DIFFRACTION100
2.0926-2.1450.2708426772851360.2194595846132535X-RAY DIFFRACTION100
2.145-2.20290.2514569207131660.2180352078132481X-RAY DIFFRACTION100
2.2029-2.26780.2183705362951530.2038337064372517X-RAY DIFFRACTION100
2.2678-2.34090.2670944531951440.1963869895012503X-RAY DIFFRACTION100
2.3409-2.42460.2477035556021280.2012590371842545X-RAY DIFFRACTION100
2.4246-2.52160.2333296073841240.2032785574612538X-RAY DIFFRACTION100
2.5216-2.63640.2321956841361760.1917352904322477X-RAY DIFFRACTION100
2.6364-2.77530.2371842003321400.1845758143182515X-RAY DIFFRACTION100
2.7753-2.94910.2292608623591280.1919083531592543X-RAY DIFFRACTION100
2.9491-3.17660.1824246594051240.1928204358442524X-RAY DIFFRACTION100
3.1766-3.4960.2298756434731260.1869447554692552X-RAY DIFFRACTION100
3.496-4.00120.1853468455811340.1895702234072523X-RAY DIFFRACTION100
4.0012-5.03860.1787992405481440.1887944210872523X-RAY DIFFRACTION100
5.0386-34.27970.2433430223191250.2128550145742544X-RAY DIFFRACTION100

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