1SRP

STRUCTURAL ANALYSIS OF SERRATIA PROTEASE

> Summary

Summary for 1SRP

DescriptorSERRATIA PROTEASE (E.C.3.4.24.40) (SERRALYSIN) COMPLEXED WITH ZINC
Functional Keywordshydrolase (metalloprotease)
Biological sourceSerratia sp.
Cellular locationSecreted P07268
Total number of polymer chains1
Total molecular weight50839.87
Authors
Hamada, K.,Hiramatsu, H.,Katsuya, Y.,Hata, Y.,Katsube, Y. (deposition date: 1994-11-02, release date: 1995-02-14, modification date: 2011-07-13)
Primary citation
Hamada, K.,Hata, Y.,Katsuya, Y.,Hiramatsu, H.,Fujiwara, T.,Katsube, Y.
Crystal structure of Serratia protease, a zinc-dependent proteinase from Serratia sp. E-15, containing a beta-sheet coil motif at 2.0 A resolution.
J.Biochem.(Tokyo), 119:844-851, 1996
PubMed: 8797082
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (2 Å)
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Structure validation

ClashscoreRamachandran outliersSidechain outliers120.4%6.6%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 1srp
no rotation
Molmil generated image of 1srp
rotated about x axis by 90°
Molmil generated image of 1srp
rotated about y axis by 90°

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
ASERRALYSINpolymer47150493.91
UniProt (P07268)
Serratia sp.
CALCIUM IONnon-polymer40.17
ZINC IONnon-polymer65.41
waterwater18.0212

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight50493.9
Non-Polymers*Number of molecules8
Total molecular weight345.9
All*Total molecular weight50839.9
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (2 Å)
Cell axes109.140150.89042.640
Cell angles90.0090.0090.00
SpacegroupP 21 21 21
Resolution limits8.00 - 2.00
the highest resolution shell value -
R-factor0.193 (0.184*)
R-free0.18400 (0.00000*)
RMSD bond length0.012
RMSD bond angle0.038

Data Collection Statistics

Resolution limits -
the highest resolution shell value -
Number of reflections42930
Completeness88.2
I/sigma(I)0

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1Microdialysis*unknown*

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
111enzyme20 (mg/ml)
211PEG80002 (%(w/v))
312ammonium sulfate27 (%sat)
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
A0031012cellular_componentextracellular matrix
A0005615cellular_componentextracellular space
A0005509molecular_functioncalcium ion binding
A0004222molecular_functionmetalloendopeptidase activity
A0008270molecular_functionzinc ion binding
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
CAT4
ChainResidue
AHIS176
AHIS180
AHIS186
ATYR216

AC16BINDING SITE FOR RESIDUE CA A 911
ChainResidue
AARG253
AGLY255
ATHR257
AASP285
AGLY287
AASP290

AC26BINDING SITE FOR RESIDUE CA A 912
ChainResidue
AGLY288
AASP290
ATHR327
AGLU329
AHOH
AHOH

AC36BINDING SITE FOR RESIDUE CA A 913
ChainResidue
AGLY334
AGLY336
AASP338
AGLY351
AALA353
AASP356

AC46BINDING SITE FOR RESIDUE CA A 914
ChainResidue
AASN343
AALA345
AASN347
AGLY360
AGLY362
AASP365

AC56BINDING SITE FOR RESIDUE CA A 915
ChainResidue
AGLY352
AGLY354
AASP356
AGLY369
AALA371
AASP374

AC67BINDING SITE FOR RESIDUE CA A 916
ChainResidue
AGLY361
AGLY362
AGLY363
AASP365
AASP383
AASP390
AHOH

AC74BINDING SITE FOR RESIDUE CA A 917
ChainResidue
AGLY370
AGLY372
AASP374
AASP400

AC85BINDING SITE FOR RESIDUE ZN A 920
ChainResidue
AHIS176
AHIS180
AHIS186
ATYR216
AHOH

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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
PS001421Neutral zinc metallopeptidases, zinc-binding region signature. [GSTALIVN]-{PCHR}-{KND}-H-E-[LIVMFYW]-{DEHRKP}-H-{EKPC}-[LIVMFYWGSPQ]
ChainResidueDetails
ANA*

PS003301Hemolysin-type calcium-binding region signature. D-x-[LI]-x(4)-G-x-D-x-[LI]-x-G-G-x(3)-D
ChainResidueDetails
ANA*

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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
SWS_FT_FI11
ChainResidueDetails
AGLU177

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Catalytic Information from CSA

site_idNumber of ResiduesDetails
CSA12Annotated By Reference To The Literature 1hfs
ChainResidueDetails
AGLU177
AGLU194

CSA21Annotated By Reference To The Literature 1hfs
ChainResidueDetails
AGLU177

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Catalytic Information from CATRES

site_idNumber of ResiduesDetails

> Sequence Neighbor

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