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- PDB-8cik: Altai wapiti (Cervus elaphus sibiricus) chymosin at 2.2 A resolution -

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Basic information

Entry
Database: PDB / ID: 8cik
TitleAltai wapiti (Cervus elaphus sibiricus) chymosin at 2.2 A resolution
ComponentsChymosin
KeywordsHYDROLASE / gastric aspartic protein
Function / homology
Function and homology information


chymosin / digestion / aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Pepsin catalytic domain / Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site ...Pepsin catalytic domain / Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesCervus canadensis sibiricus (Altai wapiti)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsDiusenova, S.E. / Shevtsov, M.B. / Borshchevskiy, V.I. / Belenkaya, S.V. / Kolybalov, D.S. / Arkhipov, S.G. / Volosnikova, E.A. / Elchaninov, V.V. / Shcherbakov, D.N.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federation075-15-2021-1355 Russian Federation
Citation
History
DepositionFeb 9, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chymosin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7842
Polymers35,6921
Non-polymers921
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-1 kcal/mol
Surface area13780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)142.390, 41.630, 54.550
Angle α, β, γ (deg.)90.000, 98.310, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-501-

HOH

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Components

#1: Protein Chymosin


Mass: 35691.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cervus canadensis sibiricus (Altai wapiti)
Gene: CYM / Production host: Kluyveromyces lactis (yeast) / Strain (production host): SVB-1 / References: UniProt: A0A7D3Q7Y7, chymosin
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.25 Å3/Da / Density % sol: 45.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: PEG 6000, tris, calcium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.22→50 Å / Num. obs: 15426 / % possible obs: 96.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 50.95 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.114 / Net I/σ(I): 7.58
Reflection shellResolution: 2.22→2.35 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.661 / Mean I/σ(I) obs: 0.78 / Num. unique obs: 2365 / CC1/2: 0.516 / Rrim(I) all: 1.972 / % possible all: 92.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.22→46.19 Å / SU ML: 0.4652 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.5975
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.243 1076 7 %
Rwork0.1981 14299 -
obs0.2012 15375 96.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.44 Å2
Refinement stepCycle: LAST / Resolution: 2.22→46.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2469 0 6 83 2558
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212586
X-RAY DIFFRACTIONf_angle_d0.50583533
X-RAY DIFFRACTIONf_chiral_restr0.0457390
X-RAY DIFFRACTIONf_plane_restr0.0038466
X-RAY DIFFRACTIONf_dihedral_angle_d11.45899
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.320.49821270.46131676X-RAY DIFFRACTION91.9
2.32-2.440.40621330.35641797X-RAY DIFFRACTION98.07
2.44-2.60.33241370.28011806X-RAY DIFFRACTION97.69
2.6-2.80.31851340.2641782X-RAY DIFFRACTION98.21
2.8-3.080.26711350.22051805X-RAY DIFFRACTION97.73
3.08-3.530.19981290.18091697X-RAY DIFFRACTION91.53
3.53-4.440.20781370.15681829X-RAY DIFFRACTION98.94
4.44-46.190.20871440.16171907X-RAY DIFFRACTION98.94
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)
10.5798254600460.296280002726-1.234487483972.94550955953-0.008115463537254.805919202060.0950919745127-0.234004092861-0.08201822544020.153702410828-0.2042175560810.1010364121890.221098199841-0.3472699037010.09348281111940.371075526988-0.0330955233809-0.09103163122460.7153200628910.00174251981610.62825073376549.181398589821.379364849545.1063290975
23.77286285523-1.279840842830.04121613977983.6731964383-1.329339543195.614165180070.1416598347050.0268398648007-0.2019527620580.069872330126-0.0484434087671-0.0197359451869-0.03585260786560.306228577809-0.1267979534550.246273268999-0.00296035098258-0.03285385607330.439339495833-0.02147960700220.48244643877356.224220904624.449710233524.8701159073
32.528835510231.5174000877-0.6517786698273.548980163690.7611967784922.09611099912-0.1622543940120.0827707928103-0.0798279273042-0.2358861643350.1739752639620.232224740825-0.0314785331444-0.379000208509-0.001992541883490.3430870438590.0699757184584-0.05872341242410.6144749345580.06097074883220.54373375614539.275481650719.547845251717.713542385
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 150 )1 - 1501 - 150
22chain 'A' and (resid 151 through 186 or resid 299 through 323)151 - 323151 - 323
33chain 'A' and (resid 187 through 298 )187 - 298187 - 298

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