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- PDB-7ku3: Data clustering and dynamics of chymotrypsinogen cluster 141 (cya... -

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Basic information

Entry
Database: PDB / ID: 7ku3
TitleData clustering and dynamics of chymotrypsinogen cluster 141 (cyan) structure
ComponentsChymotrypsinogen A
KeywordsHYDROLASE / Clustering / dynamics / data analysis / chymotrypsinogen
Function / homology
Function and homology information


chymotrypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsNguyen, T. / Phan, K.L. / Kreitler, D.F. / Andrews, L.C. / Gabelli, S.B. / Kozakov, D. / Jakoncic, J. / Sweet, R.M. / Soares, A.S. / Bernstein, H.J.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R21 GM129570-02 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM111244 United States
Department of Energy (DOE, United States)KP1605010 United States
Department of Energy (DOE, United States)KC0401040 United States
Department of Energy (DOE, United States)CA062924 United States
National Science Foundation (NSF, United States)MCB-1517522 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2022
Title: A simple technique to classify diffraction data from dynamic proteins according to individual polymorphs.
Authors: Nguyen, T. / Phan, K.L. / Kozakov, D. / Gabelli, S.B. / Kreitler, D.F. / Andrews, L.C. / Jakoncic, J. / Sweet, R.M. / Soares, A.S. / Bernstein, H.J.
History
DepositionNov 24, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 16, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chymotrypsinogen A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9744
Polymers25,6861
Non-polymers2883
Water3,513195
1
A: Chymotrypsinogen A
hetero molecules

A: Chymotrypsinogen A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9488
Polymers51,3722
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area2380 Å2
ΔGint-87 kcal/mol
Surface area19180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.330, 111.330, 51.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Chymotrypsinogen A


Mass: 25686.037 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P00766, chymotrypsin
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.18 Å3/Da / Density % sol: 61.3 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 1.0 M-2.0 M ammonium sulfate, 0.1 M MES pH 6.5, and 10% or 15% dioxane

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Data collection

Diffraction
IDMean temperature (K)Crystal-IDSerial crystal experiment
11001Y
21001Y
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS-II 17-ID-110.9201
SYNCHROTRONNSLS-II 17-ID-221.89
Detector
TypeIDDetectorDate
DECTRIS EIGER X 9M1PIXELOct 16, 2019
DECTRIS EIGER X 16M2PIXELOct 16, 2019
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.92011
21.891
ReflectionResolution: 2→50 Å / Num. obs: 22533 / % possible obs: 100 % / Redundancy: 181 % / Biso Wilson estimate: 33.72 Å2 / CC1/2: 1 / Net I/σ(I): 29.17
Reflection shellResolution: 2→2.12 Å / Num. unique obs: 3507 / CC1/2: 0.934
Serial crystallography sample delivery
IDMethod
1fixed target
2fixed target

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Processing

Software
NameVersionClassification
REFMACrefinement
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EX3

1ex3


Resolution: 2→29.13 Å / SU ML: 0.2272 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.1716 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2101 1097 4.87 %
Rwork0.1815 21436 -
obs0.183 22533 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.19 Å2
Refinement stepCycle: LAST / Resolution: 2→29.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1771 0 15 195 1981
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00631849
X-RAY DIFFRACTIONf_angle_d0.76742530
X-RAY DIFFRACTIONf_chiral_restr0.0526295
X-RAY DIFFRACTIONf_plane_restr0.0045317
X-RAY DIFFRACTIONf_dihedral_angle_d20.0551648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.090.35051340.30272605X-RAY DIFFRACTION99.42
2.09-2.20.23471620.20192591X-RAY DIFFRACTION99.78
2.2-2.340.19581380.172632X-RAY DIFFRACTION99.6
2.34-2.520.23611230.17862658X-RAY DIFFRACTION99.89
2.52-2.770.25871260.18172683X-RAY DIFFRACTION99.89
2.77-3.170.21851350.19392679X-RAY DIFFRACTION99.93
3.17-40.20291290.1622735X-RAY DIFFRACTION99.93
4-29.130.17551500.17532853X-RAY DIFFRACTION100

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