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- PDB-1op8: Crystal Structure of Human Granzyme A -

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Basic information

Entry
Database: PDB / ID: 1op8
TitleCrystal Structure of Human Granzyme A
ComponentsGranzyme A
KeywordsHYDROLASE / Granzyme A / Serine proteinase / Apoptosis
Function / homology
Function and homology information


granzyme A / negative regulation of endodeoxyribonuclease activity / cytotoxic T cell pyroptotic cell death / granzyme-mediated programmed cell death signaling pathway / negative regulation of oxidoreductase activity / pyroptotic inflammatory response / negative regulation of DNA binding / protein maturation / immunological synapse / proteolysis involved in protein catabolic process ...granzyme A / negative regulation of endodeoxyribonuclease activity / cytotoxic T cell pyroptotic cell death / granzyme-mediated programmed cell death signaling pathway / negative regulation of oxidoreductase activity / pyroptotic inflammatory response / negative regulation of DNA binding / protein maturation / immunological synapse / proteolysis involved in protein catabolic process / response to bacterium / killing of cells of another organism / immune response / positive regulation of apoptotic process / serine-type endopeptidase activity / apoptotic process / protein homodimerization activity / extracellular space / nucleus / cytoplasm
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHink-Schauer, C. / Estebanez-Perpina, E. / Bode, W. / Jenne, D.
CitationJournal: NAT.STRUCT.BIOL. / Year: 2003
Title: Crystal structure of the apoptosis-inducing human granzyme A dimer
Authors: Hink-Schauer, C. / Estebanez-Perpina, E. / Kurschus, F. / Bode, W. / Jenne, D.
History
DepositionMar 5, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 1, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Granzyme A
B: Granzyme A
C: Granzyme A
D: Granzyme A
E: Granzyme A
F: Granzyme A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,28318
Polymers155,1306
Non-polymers1,15312
Water12,701705
1
A: Granzyme A
B: Granzyme A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1907
Polymers51,7102
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-70 kcal/mol
Surface area21840 Å2
MethodPISA
2
C: Granzyme A
D: Granzyme A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0946
Polymers51,7102
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-72 kcal/mol
Surface area21590 Å2
MethodPISA
3
E: Granzyme A
F: Granzyme A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9985
Polymers51,7102
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-71 kcal/mol
Surface area21860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.480, 94.550, 94.870
Angle α, β, γ (deg.)117.12, 100.25, 100.12
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Granzyme A /


Mass: 25855.055 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P12544, granzyme A
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 705 / 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: 2.29 Å3/Da / Density % sol: 45.8 %
Crystal grow
*PLUS
pH: 4.7 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1-0.3 Mammonium sulfate11
20.1 Msodium acetate11pH4.7
330-40 %(v/v)PEG550 MME11
45.6-11.2 mg/mlprotein12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 6, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 46779 / Num. obs: 44569 / % possible obs: 85 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.045
Reflection shellResolution: 2.5→20 Å / Rmerge(I) obs: 0.045 / Num. unique all: 44569 / % possible all: 85
Reflection
*PLUS
Lowest resolution: 20 Å / % possible obs: 85.1 % / Num. measured all: 49835
Reflection shell
*PLUS
% possible obs: 80 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / Stereochemistry target values: Engh & Huber
RfactorNum. reflection
Rfree0.2843 4496
Rwork0.2182 -
all-49835
obs-44564
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10843 0 60 705 11608
Refinement
*PLUS
Lowest resolution: 20 Å / Num. reflection obs: 40073 / Rfactor Rfree: 0.284 / Rfactor Rwork: 0.217
Solvent computation
*PLUS
Displacement parameters
*PLUS

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