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- PDB-4cms: X-RAY ANALYSES OF ASPARTIC PROTEINASES IV. STRUCTURE AND REFINEME... -

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Basic information

Entry
Database: PDB / ID: 4cms
TitleX-RAY ANALYSES OF ASPARTIC PROTEINASES IV. STRUCTURE AND REFINEMENT AT 2.2 ANGSTROMS RESOLUTION OF BOVINE CHYMOSIN
ComponentsCHYMOSIN B
KeywordsHYDROLASE (ACID PROTEINASE)
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 speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsNewman, M. / Frazao, C. / Khan, G. / Tickle, I.J. / Blundell, T.L. / Safro, M. / Andreeva, N. / Zdanov, A.
Citation
Journal: J.Mol.Biol. / Year: 1991
Title: X-ray analyses of aspartic proteinases. IV. Structure and refinement at 2.2 A resolution of bovine chymosin.
Authors: Newman, M. / Safro, M. / Frazao, C. / Khan, G. / Zdanov, A. / Tickle, I.J. / Blundell, T.L. / Andreeva, N.
#1: Journal: Biochemistry / Year: 1990
Title: Engineering Enzyme Sub-Site Specificity: Preparation, Kinetic Characterization and X-Ray Analysis at 2.0-Angstroms Resolution of Val111Phe Site-Mutated Calf Chymosin
Authors: Strop, P. / Sedlacek, J. / Stys, J. / Kaderabkova, Z. / Blaha, I. / Pavlickova, L. / Pohl, J. / Fabry, M. / Kostka, V. / Newman, M. / Frazao, C. / Shearer, A. / Tickle, I.J. / Blundell, T.L.
History
DepositionNov 1, 1991Processing site: BNL
Revision 1.0Nov 7, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHYMOSIN B


Theoretical massNumber of molelcules
Total (without water)35,6731
Polymers35,6731
Non-polymers00
Water2,360131
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.980, 114.120, 72.760
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Atom site foot note1: RESIDUE PRO 23 IS A CIS-PROLINE.
2: THESE RESIDUES ARE IN POORLY DEFINED REGIONS IN THE ELECTRON DENSITY MAP: GLY -2 TO VAL 1, ASN 8 TO GLN 13, ASN 158 TO SER 163, GLN 239 TO GLU 244, GLN 277 TO PHE 281, AND GLU 289 TO GLN 297.

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Components

#1: Protein CHYMOSIN B


Mass: 35672.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / References: UniProt: P00794, chymosin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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

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Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.12 %
Crystal grow
*PLUS
Temperature: 6 ℃ / pH: 6 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein11
250 mM11NaH2PO4
31 M12NaCl
40.1 M12NaH2PO4

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Data collection

Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 16823 / % possible obs: 96.6 % / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.089

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Processing

SoftwareName: RESTRAIN / Classification: refinement
RefinementResolution: 2.2→8 Å / σ(F): 2
Details: THE QUANTITY PRESENTED IN THE TEMPERATURE FACTOR FIELD IS U.
RfactorNum. reflection
obs0.158 13089
Refinement stepCycle: LAST / Resolution: 2.2→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2487 0 0 131 2618
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d0.032
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 8 Å / Num. reflection obs: 13089 / σ(F): 2 / Rfactor obs: 0.158
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_plane_restr / Dev ideal: 0.007

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