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- PDB-1cv8: STAPHOPAIN, CYSTEINE PROTEINASE FROM STAPHYLOCOCCUS AUREUS V8 -

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Basic information

Entry
Database: PDB / ID: 1cv8
TitleSTAPHOPAIN, CYSTEINE PROTEINASE FROM STAPHYLOCOCCUS AUREUS V8
ComponentsSTAPHOPAIN
KeywordsCYSTEINE PROTEASE / THIOL PROTEASE / PAPAIN FAMILY
Function / homology
Function and homology information


staphopain / : / cysteine-type peptidase activity / extracellular region
Similarity search - Function
Staphopain peptidase C47 / Staphopain proregion / Staphopain proregion superfamily / Staphopain peptidase C47 / Staphopain proregion / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily ...Staphopain peptidase C47 / Staphopain proregion / Staphopain proregion superfamily / Staphopain peptidase C47 / Staphopain proregion / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Cysteine proteinases / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-E64 / Staphopain A
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.75 Å
AuthorsHofmann, B. / Schomburg, D. / Hecht, H.-J.
CitationJournal: Acta Crystallogr.,Sect.A / Year: 1993
Title: Crystal Structure of a Thiol Proteinase from Staphylococcus Aureus V-8 in the E-64 Inhibitor Complex
Authors: Hofmann, B. / Schomburg, D. / Hecht, H.J.
History
DepositionMay 8, 1998-
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: STAPHOPAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2903
Polymers19,8701
Non-polymers4192
Water2,216123
1
A: STAPHOPAIN
hetero molecules

A: STAPHOPAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5796
Polymers39,7402
Non-polymers8394
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_564x,x-y+1,-z-1/61
Unit cell
Length a, b, c (Å)61.139, 61.139, 195.063
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein STAPHOPAIN / / THIOL PROTEINASE FROM STAPHYLOCOCCUS AUREUS V-8


Mass: 19870.131 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Staphylococcus aureus (bacteria) / Cellular location: EXTRACELLULARGlossary of biology / Strain: V-8
References: UniProt: P81297, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-E64 / N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE


Mass: 360.429 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H30N5O5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O

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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: 2.62 Å3/Da / Density % sol: 53 %
Crystal growpH: 6
Details: 5 M AMMONIUM ACETATE, 2MM DTT, 5MM E-64, 50 MM MES/TRIS BUFFER PH 6.0 5MM E-64

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Data collection

DiffractionMean temperature: 283 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1994 / Details: MIRRORS
RadiationMonochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→46.6 Å / Num. obs: 19765 / % possible obs: 82.3 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 16.85 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 20.8
Reflection shellResolution: 1.72→1.8 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 10 / % possible all: 63

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Processing

Software
NameClassification
CCP4model building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 1.75→50 Å / Cross valid method: AT LAST STEPS OF REFINEMENT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.239 981 5 %RANDOM
Rwork0.2 ---
obs0.183 18172 82.5 %-
Displacement parametersBiso mean: 20.66 Å2
Refinement stepCycle: LAST / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1387 0 29 121 1537
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0210.02
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.92
X-RAY DIFFRACTIONp_mcangle_it2.73
X-RAY DIFFRACTIONp_scbond_it2.62
X-RAY DIFFRACTIONp_scangle_it3.93
X-RAY DIFFRACTIONp_plane_restr0.0240.03
X-RAY DIFFRACTIONp_chiral_restr0.180.15
X-RAY DIFFRACTIONp_singtor_nbd0.1790.3
X-RAY DIFFRACTIONp_multtor_nbd0.2550.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1180.3
X-RAY DIFFRACTIONp_planar_tor4.57
X-RAY DIFFRACTIONp_staggered_tor15.615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor34.420
X-RAY DIFFRACTIONp_special_tor00

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