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- PDB-6qf2: X-Ray structure of Thermolysin crystallized on a silicon chip -

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Basic information

Entry
Database: PDB / ID: 6qf2
TitleX-Ray structure of Thermolysin crystallized on a silicon chip
ComponentsThermolysin
KeywordsHYDROLASE / Thermolysin / on-chip crystallization / in-situ crystallization
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
LEUCINE / LYSINE / DI(HYDROXYETHYL)ETHER / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.733 Å
AuthorsLieske, J. / Cerv, M. / Kreida, S. / Barthelmess, M. / Fischer, P. / Pakendorf, T. / Yefanov, O. / Mariani, V. / Seine, T. / Ross, B.H. ...Lieske, J. / Cerv, M. / Kreida, S. / Barthelmess, M. / Fischer, P. / Pakendorf, T. / Yefanov, O. / Mariani, V. / Seine, T. / Ross, B.H. / Crosas, E. / Lorbeer, O. / Burkhardt, A. / Lane, T.J. / Guenther, S. / Bergtholdt, J. / Schoen, S. / Tornroth-Horsefield, S. / Chapman, H.N. / Meents, A.
Funding support Germany, Sweden, United States, 6items
OrganizationGrant numberCountry
European Research Council609920 Germany
European UnionHorizon 2020, No. 654220 Germany
German Federal Ministry for Education and Research05K2018-2017-06727MXD Germany
Swedish Research Council2010-5208 Sweden
Swedish Research Council2012-2849 Sweden
Department of Energy (DOE, United States)DE-AC02-76SF00515 United States
CitationJournal: Iucrj / Year: 2019
Title: On-chip crystallization for serial crystallography experiments and on-chip ligand-binding studies.
Authors: Lieske, J. / Cerv, M. / Kreida, S. / Komadina, D. / Fischer, J. / Barthelmess, M. / Fischer, P. / Pakendorf, T. / Yefanov, O. / Mariani, V. / Seine, T. / Ross, B.H. / Crosas, E. / Lorbeer, O. ...Authors: Lieske, J. / Cerv, M. / Kreida, S. / Komadina, D. / Fischer, J. / Barthelmess, M. / Fischer, P. / Pakendorf, T. / Yefanov, O. / Mariani, V. / Seine, T. / Ross, B.H. / Crosas, E. / Lorbeer, O. / Burkhardt, A. / Lane, T.J. / Guenther, S. / Bergtholdt, J. / Schoen, S. / Tornroth-Horsefield, S. / Chapman, H.N. / Meents, A.
History
DepositionJan 9, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / pdbx_audit_support / pdbx_struct_conn_angle / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _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
Revision 1.3Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / 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)35,95420
Polymers34,3601
Non-polymers1,59419
Water7,728429
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2430 Å2
ΔGint-114 kcal/mol
Surface area13060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.667, 92.667, 128.311
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-816-

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 natural source / Source: (natural) Bacillus thermoproteolyticus (bacteria) / References: UniProt: P00800, thermolysin

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Non-polymers , 9 types, 448 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / 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: Chemical ChemComp-LEU / LEUCINE


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#5: Chemical ChemComp-LYS / LYSINE


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


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400


Mass: 398.489 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#9: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 429 / 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: 46.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M MES-NaOH pH 6.5, 10mM calcium chloride, 25% PEG 2000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.733→46.334 Å / Num. obs: 34527 / % possible obs: 100 % / Redundancy: 13.2 % / Biso Wilson estimate: 12.63 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.168 / Rpim(I) all: 0.048 / Rrim(I) all: 0.175 / Net I/σ(I): 11.4
Reflection shellResolution: 1.733→1.77 Å / Redundancy: 13.6 % / Rmerge(I) obs: 0.976 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 1852 / CC1/2: 0.81 / Rpim(I) all: 0.266 / Rrim(I) all: 1.013 / % possible all: 100
Serial crystallography sample deliveryMethod: fixed target
Serial crystallography sample delivery fixed targetSample dehydration prevention: cryo stream / Sample holding: single crystalline silicon chip / Support base: goniometer

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Processing

Software
NameVersionClassification
PHENIX1.10.1-2155_9999refinement
Coot0.8.2model building
PHASERphasing
PDB_EXTRACT3.24data extraction
Aimless0.5.8data scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2TLX

2tlx


Resolution: 1.733→46.334 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.61
RfactorNum. reflection% reflection
Rfree0.1611 1571 4.56 %
Rwork0.1283 --
obs0.1297 34457 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 58.41 Å2 / Biso mean: 16.57 Å2 / Biso min: 5.52 Å2
Refinement stepCycle: final / Resolution: 1.733→46.334 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 210 429 3071
Biso mean--33.17 29.51 -
Num. residues----316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062728
X-RAY DIFFRACTIONf_angle_d0.8413724
X-RAY DIFFRACTIONf_chiral_restr0.051395
X-RAY DIFFRACTIONf_plane_restr0.006488
X-RAY DIFFRACTIONf_dihedral_angle_d10.9641617
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.7326-1.78860.20441390.164829363075
1.7886-1.85250.18851420.151929193061
1.8525-1.92670.17081370.138529393076
1.9267-2.01440.19171440.125229493093
2.0144-2.12060.15261400.11829273067
2.1206-2.25340.16681410.115329663107
2.2534-2.42740.14671410.112529763117
2.4274-2.67170.14021440.115329693113
2.6717-3.05820.15091410.118630113152
3.0582-3.85270.15061470.126230513198
3.8527-46.35030.16581550.143132433398
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.3947-0.11410.33140.40450.16150.44690.05410.02710.07250.0935-0.0189-0.09040.0254-0.0051-0.00130.08940.00390.00270.0908-0.00080.07127.765127.306310.8603
20.8507-0.05370.26220.5930.14910.70760.02730.0637-0.0030.0033-0.0131-0.0121-0.02520.01990.0030.05510.00890.00840.0772-0.00470.044823.86732.02811.1702
30.52540.26330.32480.37770.05570.40750.02130.0320.1297-0.05080.005-0.0068-0.0859-0.00940.00120.09730.01690.01050.1262-0.00980.127712.511535.7289-4.0367
40.28520.0179-0.09580.31380.26330.27860.0159-0.04780.03220.0162-0.00090.04180.0387-0.033200.08850.00080.00610.1178-0.01060.10246.151628.8779-5.95
50.36930.17410.07251.3040.36410.18390.042-0.22010.10190.2452-0.07140.0606-0.0217-0.1167-0.00080.12770.00150.01860.1824-0.03570.1454.101334.84818.5988
60.76920.24650.53640.36340.64111.2092-0.1097-0.03750.2363-0.0623-0.05310.0635-0.2112-0.2218-0.12060.11870.0336-0.0070.1449-0.01780.1746-4.785338.5888-7.0204
70.8478-0.03510.24830.63570.0760.7267-0.00410.00510.0109-0.0068-0.00030.0050.0292-0.0797-00.0914-0.00090.00360.1279-0.0210.103-0.738926.7389-10.0501
80.21790.2107-0.14980.7377-0.12020.2430.01620.06410.0457-0.0881-0.00950.16020.0783-0.14120.02640.1078-0.02-0.00580.1408-0.01490.1118-5.493520.1341-15.4215
90.3895-1.4640.79075.5032-2.97241.60570.10130.130.103-0.17570.01010.0846-0.2284-0.0549-0.02320.2525-0.0085-0.03950.33330.00510.4128.614541.0395-3.1808
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )A1 - 25
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 122 )A26 - 122
3X-RAY DIFFRACTION3chain 'A' and (resid 123 through 158 )A123 - 158
4X-RAY DIFFRACTION4chain 'A' and (resid 159 through 180 )A159 - 180
5X-RAY DIFFRACTION5chain 'A' and (resid 181 through 200 )A181 - 200
6X-RAY DIFFRACTION6chain 'A' and (resid 201 through 224 )A201 - 224
7X-RAY DIFFRACTION7chain 'A' and (resid 225 through 280 )A225 - 280
8X-RAY DIFFRACTION8chain 'A' and (resid 281 through 316 )A281 - 316
9X-RAY DIFFRACTION9chain 'B' and (resid 317 through 318 )B317 - 318

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