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- PDB-1cms: THE THREE-DIMENSIONAL STRUCTURE OF RECOMBINANT BOVINE CHYMOSIN AT... -

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Basic information

Entry
Database: PDB / ID: 1cms
TitleTHE THREE-DIMENSIONAL STRUCTURE OF RECOMBINANT BOVINE CHYMOSIN AT 2.3 ANGSTROMS RESOLUTION
ComponentsPROCHYMOSIN A/B PRECURSOR
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: 2.3 Å
AuthorsGilliland, G.L. / Winborne, E.L. / Nachman, J. / Wlodawer, A.
CitationJournal: Proteins / Year: 1990
Title: The three-dimensional structure of recombinant bovine chymosin at 2.3 A resolution.
Authors: Gilliland, G.L. / Winborne, E.L. / Nachman, J. / Wlodawer, A.
History
DepositionOct 12, 1989Processing site: BNL
Revision 1.0Jan 15, 1990Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4Oct 30, 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: PROCHYMOSIN A/B PRECURSOR


Theoretical massNumber of molelcules
Total (without water)35,6731
Polymers35,6731
Non-polymers00
Water5,350297
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.700, 80.300, 114.800
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 25 IS A CIS-PROLINE.

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Components

#1: Protein PROCHYMOSIN A/B PRECURSOR


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.: 297 / 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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
Conc.: 30 %sat / Common name: sodium chloride

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 9999 Å / Num. obs: 15628 / Observed criterion σ(I): 1.5 / Num. measured all: 34846 / Rmerge(I) obs: 0.048

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.165 / Highest resolution: 2.3 Å
Refinement stepCycle: LAST / Highest resolution: 2.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2511 0 0 297 2808
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.0440.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0510.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.3241
X-RAY DIFFRACTIONp_mcangle_it2.1682
X-RAY DIFFRACTIONp_scbond_it2.062
X-RAY DIFFRACTIONp_scangle_it3.1873
X-RAY DIFFRACTIONp_plane_restr0.0180.02
X-RAY DIFFRACTIONp_chiral_restr0.2170.15
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: 2.3 Å / Lowest resolution: 20 Å / Num. reflection obs: 12410 / σ(I): 1.5 / Rfactor obs: 0.165
Solvent computation
*PLUS
Displacement parameters
*PLUS

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