4CMS

X-RAY ANALYSES OF ASPARTIC PROTEINASES IV. STRUCTURE AND REFINEMENT AT 2.2 ANGSTROMS RESOLUTION OF BOVINE CHYMOSIN

> Summary

Summary for 4CMS

DescriptorCHYMOSIN B (FORMERLY KNOWN AS RENNIN) (E.C.3.4.23.4)
Functional Keywordshydrolase (acid proteinase)
Biological sourceBos taurus (cattle)
Total number of polymer chains1
Total molecular weight35672.98
Authors
Newman, M.,Frazao, C.,Khan, G.,Tickle, I.J.,Blundell, T.L.,Safro, M.,Andreeva, N.,Zdanov, A. (deposition date: 1991-11-01, release date: 1991-11-07, modification date: 2009-02-24)
Primary citation
Newman, M.,Safro, M.,Frazao, C.,Khan, G.,Zdanov, A.,Tickle, I.J.,Blundell, T.L.,Andreeva, N.
X-ray analyses of aspartic proteinases. IV. Structure and refinement at 2.2 A resolution of bovine chymosin.
J.Mol.Biol., 221:1295-1309, 1991
PubMed: 1942052
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2.2 Å)
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Structure validation

ClashscoreRamachandran outliersSidechain outliers2209.7%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 4cms
no rotation
Molmil generated image of 4cms
rotated about x axis by 90°
Molmil generated image of 4cms
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
ACHYMOSIN Bpolymer32335673.01
UniProt (P00794)
Pfam (PF00026)
Bos taurus (cattle)@PDBj
waterwater18.0131

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight35673.0
Non-Polymers*Number of molecules0
Total molecular weight0.0
All*Total molecular weight35673.0
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2.2 Å)

Cell axes79.980114.12072.760
Cell angles90.0090.0090.00
SpacegroupI 2 2 2
Resolution limits8.00 - 2.20
the highest resolution shell value -
R-factor0.158
RMSD bond length0.018
RMSD bond angle0.032

Data Collection Statistics

Resolution limits - 2.20*
the highest resolution shell value -
Number of reflections16823*
Rmerge_l_obs0.089*
Completeness96.6*
I/sigma(I)3.*

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1Microdialysis*6.0*6**

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
111protein10 (mg/ml)
21150 (mM)
3121 (M)
4120.1 (M)
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0004190molecular_functionaspartic-type endopeptidase activity
A0007586biological_processdigestion
A0030163biological_processprotein catabolic process
A0006508biological_processproteolysis
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC11active site
ChainResidue
AASP34

AC21active site
ChainResidue
AASP216

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
PS001412Eukaryotic and viral aspartyl proteases active site. [LIVMFGAC]-[LIVMTADN]-[LIVFSA]-D-[ST]-G-[STAV]-[STAPDENQ]-{GQ}
ChainResidueDetails
ANA*
ANA*

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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI12
ChainResidueDetails
AASP34
AASP216

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Catalytic Information from CSA

site_idNumber of ResiduesDetails
CSA11Annotated By Reference To The Literature 1am5
ChainResidueDetails
AASP32

CSA21Annotated By Reference To The Literature 1am5
ChainResidueDetails
AASP215

CSA34Annotated By Reference To The Literature 1am5
ChainResidueDetails
AASP215
ASER35
ATHR218
AASP32

CSA44Annotated By Reference To The Literature 1am5
ChainResidueDetails
AASP215
ATHR216
AASP32
ATHR33

CSA53Annotated By Reference To The Literature 1am5
ChainResidueDetails
AASP215
ASER35
AASP32

CSA64Annotated By Reference To The Literature 1am5
ChainResidueDetails
AASP215
ATYR75
ASER35
AASP32

CSA74Annotated By Reference To The Literature 1am5
ChainResidueDetails
AASP215
ATHR218
AASP32
ATHR33

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Catalytic Information from CATRES

site_idNumber of ResiduesDetails
extCATRES14Mapped from 1mpp to 4cms using BLAST. All catalytic residues present. Original details record follows: a catalytic site defined by CATRES, Medline 77255056, 87247286
ChainResidueDetails
AASP32activates water, cofactor or residue. Activates water molecule for attack at carbonyl group
AASP215activates substrate. polarises carbonyl group of substrate
ASER35activates water, cofactor or residue. Hydrogen bonds to D32 and partially holds water
ATYR75acid/base. protonates amide nitrogen of scissile bond

> Sequence Neighbor

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