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- PDB-6qf3: X-Ray structure of Thermolysin soaked with sodium aspartate on a ... -

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Basic information

Entry
Database: PDB / ID: 6qf3
TitleX-Ray structure of Thermolysin soaked with sodium aspartate on a silicon chip
ComponentsThermolysin
KeywordsHYDROLASE / Thermolysin / on-chip crystallization / in-situ crystallization / on-chip ligand soaking
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
ASPARTIC ACID / TRIETHYLENE GLYCOL / Thermolysin
Similarity search - Component
Biological speciesBacillus thermoproteolyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.521 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.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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)36,35229
Polymers34,3601
Non-polymers1,99128
Water8,341463
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-58 kcal/mol
Surface area13210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.154, 93.154, 129.294
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-924-

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 , 8 types, 491 molecules

#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: Chemical ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-ASP / ASPARTIC ACID


Type: L-peptide linking / Mass: 133.103 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H7NO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 2.36 Å3/Da / Density % sol: 47.8 %
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: 1.52→46.58 Å / Num. obs: 51432 / % possible obs: 100 % / Redundancy: 29.1 % / Biso Wilson estimate: 11.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.022 / Rrim(I) all: 0.121 / Net I/σ(I): 21.6
Reflection shellResolution: 1.52→1.55 Å / Redundancy: 29.2 % / Rmerge(I) obs: 0.915 / Mean I/σ(I) obs: 4.7 / Num. unique obs: 2484 / CC1/2: 0.939 / Rpim(I) all: 0.17 / Rrim(I) all: 0.932 / % possible all: 99.6
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: 1.521→46.577 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 12.95
RfactorNum. reflection% reflection
Rfree0.1495 1939 3.78 %
Rwork0.1226 --
obs0.1236 51351 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 57.84 Å2 / Biso mean: 16.1262 Å2 / Biso min: 6.65 Å2
Refinement stepCycle: final / Resolution: 1.521→46.577 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2432 0 269 464 3165
Biso mean--33.69 28.88 -
Num. residues----316
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012778
X-RAY DIFFRACTIONf_angle_d1.1623781
X-RAY DIFFRACTIONf_chiral_restr0.069400
X-RAY DIFFRACTIONf_plane_restr0.008498
X-RAY DIFFRACTIONf_dihedral_angle_d10.8641657
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.5213-1.55940.17831350.152434513586
1.5594-1.60160.18781350.146134683603
1.6016-1.64870.1841360.134134523588
1.6487-1.70190.15191370.129634803617
1.7019-1.76270.16771360.125334773613
1.7627-1.83330.15371370.119134903627
1.8333-1.91670.14041370.118434883625
1.9167-2.01780.13531380.117335113649
2.0178-2.14420.13181370.111534973634
2.1442-2.30980.12691390.110535283667
2.3098-2.54220.13271390.112835393678
2.5422-2.910.15661400.116235773717
2.91-3.66610.16431430.121536193762
3.6661-46.5990.14641500.133238353985
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)
10.2405-0.00670.31450.26790.07960.42840.0645-0.08790.06510.10870.0162-0.06720.0310.0254-0.00010.11860.0045-0.00140.12440.00070.108827.745827.80611.008
20.7874-0.19830.270.3464-0.02490.74360.01760.0297-0.02980.0497-0.0088-0.0554-0.0140.027900.08350.00560.00490.0881-0.00490.06725.932831.32294.4873
30.47390.1430.14290.1138-0.01940.31840.0260.13510.0027-0.0479-0.03870.0069-0.032-0.017500.09520.01930.00130.1281-0.01130.082220.481833.9144-4.678
40.52060.16210.34750.3108-0.06530.3584-0.01490.03990.1176-0.03890.01910.0057-0.1006-0.00630.00020.08550.00530.01450.1147-0.01060.104212.61335.9562-4.4069
50.25340.031-0.03820.29320.26260.25630.0522-0.02450.01080.0595-0.00520.0585-0.0255-0.017300.08670.00080.01260.1126-0.00440.09126.228828.69-5.6628
60.88340.26260.58151.47910.48910.50050.0655-0.35640.15490.2776-0.13440.12190.0229-0.26990.10980.1045-0.00480.02770.167-0.03530.10923.773734.61517.788
71.02590.28750.8850.24860.61551.6114-0.1365-0.02790.2281-0.0539-0.02650.1364-0.2488-0.2169-0.34510.08580.0227-0.0050.1107-0.01690.1419-4.937938.8266-7.1016
80.73750.00860.09740.57020.04830.6508-0.00050.02010.0168-0.02260.00840.03720.0549-0.0725-00.0851-0.01130.01350.1139-0.01770.0963-0.845325.3331-11.6493
91.06910.0565-0.5481.3441-0.12950.3112-0.0290.21310.0069-0.1509-0.0270.25970.1266-0.18570.0940.0944-0.03330.00180.1389-0.0220.1078-9.069820.555-13.8253
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 88 )A26 - 88
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 122 )A89 - 122
4X-RAY DIFFRACTION4chain 'A' and (resid 123 through 158 )A123 - 158
5X-RAY DIFFRACTION5chain 'A' and (resid 159 through 180 )A159 - 180
6X-RAY DIFFRACTION6chain 'A' and (resid 181 through 200 )A181 - 200
7X-RAY DIFFRACTION7chain 'A' and (resid 201 through 224 )A201 - 224
8X-RAY DIFFRACTION8chain 'A' and (resid 225 through 296 )A225 - 296
9X-RAY DIFFRACTION9chain 'A' and (resid 297 through 316 )A297 - 316

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