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- PDB-6mh6: High-viscosity injector-based Pink Beam Serial Crystallography of... -

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Basic information

Entry
Database: PDB / ID: 6mh6
TitleHigh-viscosity injector-based Pink Beam Serial Crystallography of Micro-crystals at a Synchrotron Radiation Source.
ComponentsProteinase K
KeywordsHYDROLASE / Pink beam serial crystallography / Proteinase K
Function / homology
Function and homology information


phosphorelay signal transduction system / regulation of DNA-templated transcription / DNA binding / membrane
Similarity search - Function
: / VtrA C-terminal periplasmic domain / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Peptidase S8/S53 domain / Signal transduction response regulator, C-terminal effector / Winged helix-like DNA-binding domain superfamily / Rossmann fold ...: / VtrA C-terminal periplasmic domain / OmpR/PhoB-type DNA-binding domain / Transcriptional regulatory protein, C terminal / OmpR/PhoB-type DNA-binding domain profile. / Transcriptional regulatory protein, C terminal / Peptidase S8/S53 domain / Signal transduction response regulator, C-terminal effector / Winged helix-like DNA-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / Putative transcriptional regulator ToxR
Similarity search - Component
Biological speciesParengyodontium album (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMartin-Garcia, J.M. / Zhu, L. / Mendez, D. / Lee, M. / Chun, E. / Li, C. / Hu, H. / Subramanian, G. / Kissick, D. / Ogata, C. ...Martin-Garcia, J.M. / Zhu, L. / Mendez, D. / Lee, M. / Chun, E. / Li, C. / Hu, H. / Subramanian, G. / Kissick, D. / Ogata, C. / Henning, R. / Ishchenko, A. / Dobson, Z. / Zhan, S. / Weierstall, U. / Spence, J.C.H. / Fromme, P. / Zatsepin, N.A. / Fischetti, R.F. / Cherezov, V. / Liu, W.
Funding support United States, 10items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306 United States
National Science Foundation (NSF, United States)1565180 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R21DA042298 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM124152 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM095583 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM127086 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R24GM111072 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)ACB-12002 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)AGM12006 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Iucrj / Year: 2019
Title: High-viscosity injector-based pink-beam serial crystallography of microcrystals at a synchrotron radiation source.
Authors: Martin-Garcia, J.M. / Zhu, L. / Mendez, D. / Lee, M.Y. / Chun, E. / Li, C. / Hu, H. / Subramanian, G. / Kissick, D. / Ogata, C. / Henning, R. / Ishchenko, A. / Dobson, Z. / Zhang, S. / ...Authors: Martin-Garcia, J.M. / Zhu, L. / Mendez, D. / Lee, M.Y. / Chun, E. / Li, C. / Hu, H. / Subramanian, G. / Kissick, D. / Ogata, C. / Henning, R. / Ishchenko, A. / Dobson, Z. / Zhang, S. / Weierstall, U. / Spence, J.C.H. / Fromme, P. / Zatsepin, N.A. / Fischetti, R.F. / Cherezov, V. / Liu, W.
History
DepositionSep 17, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 29, 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Aug 21, 2019Group: Data collection / Category: reflns / Item: _reflns.pdbx_R_split / _reflns.pdbx_Rmerge_I_obs
Revision 1.3Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Proteinase K
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1014
Polymers28,9591
Non-polymers1423
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.300, 68.300, 108.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-474-

HOH

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Components

#1: Protein Proteinase K / Endopeptidase K / Tritirachium alkaline proteinase


Mass: 28958.791 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Parengyodontium album (fungus) / References: UniProt: P06873, peptidase K
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.6 % / Description: Diamond-like crystals
Crystal growTemperature: 293 K / Method: batch mode / pH: 6.5
Details: 0.1 M MES pH 6.5, 0.5 M sodium nitrate, 0.1 M calcium chloride

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1.03 Å
DetectorType: RAYONIX MX340-HS / Detector: CCD / Date: Aug 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.8→57.8 Å / Num. obs: 14910 / % possible obs: 61.3 % / Redundancy: 9 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 23.3
Reflection shellResolution: 1.8→1.85 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Precognitiondata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UVL

5uvl


Resolution: 1.8→57.8 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.902 / SU B: 2.764 / SU ML: 0.082 / Cross valid method: THROUGHOUT / ESU R: 0.193 / ESU R Free: 0.155 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17493 1463 9.8 %RANDOM
Rwork0.12955 ---
obs0.13408 13447 61.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 9.764 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.8→57.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2032 0 6 137 2175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192076
X-RAY DIFFRACTIONr_bond_other_d0.0020.021862
X-RAY DIFFRACTIONr_angle_refined_deg1.8021.9372821
X-RAY DIFFRACTIONr_angle_other_deg1.09734276
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3655278
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.29823.6984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67815299
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.8871512
X-RAY DIFFRACTIONr_chiral_restr0.1130.2312
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022461
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02491
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_it0.6860.8371115
X-RAY DIFFRACTIONr_mcbond_other0.6850.8351114
X-RAY DIFFRACTIONr_mcangle_it1.0941.251392
X-RAY DIFFRACTIONr_mcangle_other1.0941.2531393
X-RAY DIFFRACTIONr_scbond_it1.61.063961
X-RAY DIFFRACTIONr_scbond_other1.6011.057958
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6251.5081426
X-RAY DIFFRACTIONr_long_range_B_refined4.4997.632470
X-RAY DIFFRACTIONr_long_range_B_other4.3647.5132429
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.127 10 -
Rwork0.141 142 -
obs--8.67 %

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