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- PDB-5hqd: Acoustic injectors for drop-on-demand serial femtosecond crystall... -

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Basic information

Entry
Database: PDB / ID: 5hqd
TitleAcoustic injectors for drop-on-demand serial femtosecond crystallography
ComponentsThermolysin
KeywordsHYDROLASE / METALLOPROTEINASE / XFEL
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Elastase; domain 1 - #10 / Elastase; domain 1 / Peptidase M4, C-terminal / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain / Thermolysin metallopeptidase, alpha-helical domain / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily ...Elastase; domain 1 - #10 / Elastase; domain 1 / Peptidase M4, C-terminal / Peptidase M4 domain / Peptidase M4 / Thermolysin metallopeptidase, catalytic domain / Thermolysin metallopeptidase, alpha-helical domain / Neutral Protease Domain 2 / Neutral Protease; domain 2 / Peptidase M4/M1, CTD superfamily / Roll / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Neutral metalloproteinase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / Resolution: 2.52 Å
AuthorsRoesser, C.G. / Agarwal, R. / Allaire, M. / Alonso-Mori, R. / Andi, B. / Bachega, J.F.R. / Bommer, M. / Brewster, A.S. / Browne, M.C. / Chatterjee, R. ...Roesser, C.G. / Agarwal, R. / Allaire, M. / Alonso-Mori, R. / Andi, B. / Bachega, J.F.R. / Bommer, M. / Brewster, A.S. / Browne, M.C. / Chatterjee, R. / Cho, E. / Cohen, A.E. / Cowan, M. / Datwani, S. / Davidson, V.L. / Defever, J. / Eaton, B. / Ellson, R. / Feng, Y. / Ghislain, L.P. / Glownia, J.M. / Han, G. / Hattne, J. / Hellmich, J. / Heroux, A. / Ibrahim, M. / Kern, J. / Kuczewski, A. / Lemke, H.T. / Liu, P. / Majlof, L. / McClintock, W.M. / Myers, S. / Nelsen, S. / Olechno, J. / Orville, A.M. / Sauter, N.K. / Soares, A.S. / Soltis, M.S. / Song, H. / Stearns, R.G. / Tran, R. / Tsai, Y. / Uervirojnangkoorn, M. / Wilmot, C.M. / Yachandra, V. / Yano, J. / Yukl, E.T. / Zhu, D. / Zouni, A.
Funding support United States, 3items
OrganizationGrant numberCountry
Department of Energy (DOE, United States)11-008 United States
National Institutes of HealthP41RR012408 United States
National Institutes of HealthP41GM103473 United States
CitationJournal: Structure / Year: 2016
Title: Acoustic Injectors for Drop-On-Demand Serial Femtosecond Crystallography.
Authors: Roessler, C.G. / Agarwal, R. / Allaire, M. / Alonso-Mori, R. / Andi, B. / Bachega, J.F. / Bommer, M. / Brewster, A.S. / Browne, M.C. / Chatterjee, R. / Cho, E. / Cohen, A.E. / Cowan, M. / ...Authors: Roessler, C.G. / Agarwal, R. / Allaire, M. / Alonso-Mori, R. / Andi, B. / Bachega, J.F. / Bommer, M. / Brewster, A.S. / Browne, M.C. / Chatterjee, R. / Cho, E. / Cohen, A.E. / Cowan, M. / Datwani, S. / Davidson, V.L. / Defever, J. / Eaton, B. / Ellson, R. / Feng, Y. / Ghislain, L.P. / Glownia, J.M. / Han, G. / Hattne, J. / Hellmich, J. / Heroux, A. / Ibrahim, M. / Kern, J. / Kuczewski, A. / Lemke, H.T. / Liu, P. / Majlof, L. / McClintock, W.M. / Myers, S. / Nelsen, S. / Olechno, J. / Orville, A.M. / Sauter, N.K. / Soares, A.S. / Soltis, S.M. / Song, H. / Stearns, R.G. / Tran, R. / Tsai, Y. / Uervirojnangkoorn, M. / Wilmot, C.M. / Yachandra, V. / Yano, J. / Yukl, E.T. / Zhu, D. / Zouni, A.
History
DepositionJan 21, 2016Deposition site: RCSB / Processing site: PDBE
SupersessionFeb 10, 2016ID: 5F80
Revision 1.0Feb 10, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 20, 2016Group: Database references
Revision 1.2Nov 15, 2017Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 1.3Nov 14, 2018Group: Data collection / Category: diffrn / Item: _diffrn.pdbx_serial_crystal_experiment
Revision 1.4Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.5Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)34,6287
Polymers34,3621
Non-polymers2666
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area510 Å2
ΔGint-86 kcal/mol
Surface area12460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.707, 92.707, 129.524
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-634-

HOH

21A-677-

HOH

31A-744-

HOH

41A-765-

HOH

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Components

#1: Protein Thermolysin


Mass: 34362.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Thermus thermophilus (bacteria) / References: UniProt: V5IRV7
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.4 %
Crystal growTemperature: 293 K / Method: batch mode / Details: Batch crystallization 15% ammonium sulfate

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Data collection

DiffractionMean temperature: 293 K / Ambient temp details: Acoustic specimen injector / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: XPP / Wavelength: 1.36 Å
DetectorType: CS-PAD XPP / Detector: PIXEL / Date: Jun 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.36 Å / Relative weight: 1
ReflectionResolution: 2.5→80.3 Å / Num. obs: 11101 / % possible obs: 99.89 % / Redundancy: 22 % / Net I/σ(I): 11.3
Reflection shellResolution: 2.5→2.585 Å / Redundancy: 10.4 % / Mean I/σ(I) obs: 4.4 / % possible all: 99.88

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
cctbx.xfeldata reduction
cctbx.xfeldata scaling
MOLREPphasing
RefinementResolution: 2.52→80.29 Å / Cor.coef. Fo:Fc: 0.835 / Cor.coef. Fo:Fc free: 0.751 / SU B: 11.94 / SU ML: 0.271 / Cross valid method: THROUGHOUT / ESU R: 1.752 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28803 564 4.8 %RANDOM
Rwork0.21876 ---
obs0.22218 11101 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.409 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å2-0.03 Å2-0 Å2
2---0.07 Å2-0 Å2
3---0.21 Å2
Refinement stepCycle: 1 / Resolution: 2.52→80.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2431 0 6 269 2706
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192490
X-RAY DIFFRACTIONr_bond_other_d0.0020.022197
X-RAY DIFFRACTIONr_angle_refined_deg1.5861.9223390
X-RAY DIFFRACTIONr_angle_other_deg2.07835036
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4475315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.7324.435124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.67115356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2151510
X-RAY DIFFRACTIONr_chiral_restr0.0870.2361
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022955
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02623
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6111.3451263
X-RAY DIFFRACTIONr_mcbond_other0.6111.3451262
X-RAY DIFFRACTIONr_mcangle_it1.0772.0161577
X-RAY DIFFRACTIONr_mcangle_other1.0762.0161578
X-RAY DIFFRACTIONr_scbond_it0.4941.3761227
X-RAY DIFFRACTIONr_scbond_other0.4931.3771228
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8562.0491814
X-RAY DIFFRACTIONr_long_range_B_refined3.41211.2593518
X-RAY DIFFRACTIONr_long_range_B_other3.2911.2633460
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.52→2.585 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 38 -
Rwork0.268 807 -
obs--99.88 %

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