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- PDB-1c8o: 2.9 A STRUCTURE OF CLEAVED VIRAL SERPIN CRMA -

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Basic information

Entry
Database: PDB / ID: 1c8o
Title2.9 A STRUCTURE OF CLEAVED VIRAL SERPIN CRMA
Components(ICE INHIBITOR) x 2
KeywordsVIRAL PROTEIN / SERPIN FOLD
Function / homology
Function and homology information


Microbial modulation of RIPK1-mediated regulated necrosis / symbiont-mediated suppression of host apoptosis / cysteine-type endopeptidase inhibitor activity / protein sequestering activity / Regulation of TNFR1 signaling / serine-type endopeptidase inhibitor activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of TBK1 activity / host cell cytoplasm / extracellular space / cytoplasm
Similarity search - Function
Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily ...Antithrombin; Chain I, domain 2 / Antithrombin, subunit I, domain 2 / Alpha-1-antitrypsin; domain 1 / Alpha-1-antitrypsin, domain 1 / Serpin, conserved site / Serpins signature. / Serpin superfamily, domain 2 / Serpin family / Serpin domain / Serpin superfamily / Serpin superfamily, domain 1 / Serpin (serine protease inhibitor) / SERine Proteinase INhibitors / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Serine proteinase inhibitor 2
Similarity search - Component
Biological speciesCowpox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsSimonovic, M. / Gettins, P.G.W. / Volz, K.
CitationJournal: Protein Sci. / Year: 2000
Title: Crystal structure of viral serpin crmA provides insights into its mechanism of cysteine proteinase inhibition.
Authors: Simonovic, M. / Gettins, P.G.W. / Volz, K.
History
DepositionJun 1, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ICE INHIBITOR
B: ICE INHIBITOR


Theoretical massNumber of molelcules
Total (without water)37,9842
Polymers37,9842
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-33 kcal/mol
Surface area13720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.67, 93.15, 101.63
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein ICE INHIBITOR / CYTOKINE RESPONSE MODIFIER PROTEIN


Mass: 33465.551 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-300 / Mutation: C93S,C102S,C124S,C223S,C269S,C298S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cowpox virus / Genus: Orthopoxvirus / Description: VIRUS; / Plasmid: PQE60 / Production host: Escherichia coli (E. coli) / References: UniProt: P07385
#2: Protein/peptide ICE INHIBITOR / CYTOKINE RESPONSE MODIFIER PROTEIN


Mass: 4517.984 Da / Num. of mol.: 1 / Fragment: RESIDUES 301-341 / Mutation: C304S,C313S,C336S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cowpox virus / Genus: Orthopoxvirus / Plasmid: PQE60 / Production host: Escherichia coli (E. coli) / References: UniProt: P07385
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.66 Å3/Da / Density % sol: 53.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: sodium/potassium phosphate 1.6M, pH 5.4, vapor diffusion/hanging drop, temperature 298K
Crystal
*PLUS
Density % sol: 56 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mg/mlprotein1drop
21.6 Msodium potassium phosphate1reservoir
30.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1
DetectorType: ADSC / Detector: CCD / Date: Feb 7, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 9406 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Biso Wilson estimate: 23.5 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.5
Reflection shellResolution: 2.9→3 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.42 / Num. unique all: 930 / % possible all: 91.1
Reflection
*PLUS
Num. obs: 9406 / Num. measured all: 318152
Reflection shell
*PLUS
% possible obs: 91.1 % / Mean I/σ(I) obs: 4.9

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Processing

Software
NameClassification
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementResolution: 2.9→38.79 Å / Rfactor Rfree error: 0.009 / Data cutoff high rms absF: 335401.38 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.287 968 10.5 %RANDOM
Rwork0.223 ---
all-9444 --
obs-9238 97.9 %-
Solvent computationSolvent model: flat model / Bsol: 44.8062 Å2 / ksol: 0.437705 e/Å3
Displacement parametersBiso mean: 36.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.9→38.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2546 0 0 18 2564
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it1.421.5
X-RAY DIFFRACTIONc_mcangle_it2.512
X-RAY DIFFRACTIONc_scbond_it1.852
X-RAY DIFFRACTIONc_scangle_it2.962.5
LS refinement shellResolution: 2.9→3.08 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.348 170 12.1 %
Rwork0.299 1239 -
obs--91.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 10.5 % / Rfactor obs: 0.224
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 36.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.89
X-RAY DIFFRACTIONc_mcbond_it1.421.5
X-RAY DIFFRACTIONc_scbond_it1.852
X-RAY DIFFRACTIONc_mcangle_it2.512
X-RAY DIFFRACTIONc_scangle_it2.962.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.348 / % reflection Rfree: 12.1 % / Rfactor Rwork: 0.299

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