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- PDB-1f0c: STRUCTURE OF THE VIRAL SERPIN CRMA -

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Basic information

Entry
Database: PDB / ID: 1f0c
TitleSTRUCTURE OF THE VIRAL SERPIN CRMA
Components(ICE INHIBITOR) x 2
KeywordsVIRAL PROTEIN / Apoptosis / caspase inhibitor / protease inhibitor / serpin
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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / Serine proteinase inhibitor 2
Similarity search - Component
Biological speciesCowpox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.26 Å
AuthorsRenatus, M. / Zhou, Q. / Stennicke, H.R. / Snipas, S.J. / Turk, D. / Bankston, L.A. / Liddington, R.C. / Salvesen, G.S.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Crystal structure of the apoptotic suppressor CrmA in its cleaved form.
Authors: Renatus, M. / Zhou, Q. / Stennicke, H.R. / Snipas, S.J. / Turk, D. / Bankston, L.A. / Liddington, R.C. / Salvesen, G.S.
History
DepositionMay 15, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Advisory / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / software
Item: _software.name
Revision 1.4Feb 7, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2823
Polymers38,1282
Non-polymers1541
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-37 kcal/mol
Surface area14260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.203, 92.455, 100.454
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 / CRMA


Mass: 34021.449 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-305
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cowpox virus / Genus: Orthopoxvirus / Plasmid: PET23D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
Keywords: PROTEIN HAS BEEN CLEAVED WITH SUBTILISIN CARLSBERG
References: UniProt: P07385
#2: Protein/peptide ICE INHIBITOR / CYTOKINE RESPONSE MODIFIER PROTEIN / CRMA


Mass: 4106.662 Da / Num. of mol.: 1 / Fragment: RESIDUES 306-341
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cowpox virus / Genus: Orthopoxvirus / Plasmid: PET23D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
Keywords: PROTEIN HAS BEEN CLEAVED WITH SUBTILISIN CARLSBERG
References: UniProt: P07385
#3: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 3 Å3/Da / Density % sol: 58.93 %
Crystal growTemperature: 296 K / Method: vapor diffusion
Details: 0.1 M Na-Acetate, 15% PEG 4000, 0.1 M MgCl2, VAPOR DIFFUSION, temperature 296K
Crystal grow
*PLUS
Temperature: 23 ℃ / pH: 5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
17-10 mg/mlprotein1drop
20.1 Msodium acetate1drop
320 %PEG40001drop
40.1 Msodium acetate1reservoir
515 %PEG40001reservoir
60.1 M1reservoirMgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.15
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Sep 23, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 2.26→35 Å / Num. all: 75617 / Num. obs: 21897 / % possible obs: 96.2 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 35.9 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 26.3
Reflection shellResolution: 2.26→2.31 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.281 / % possible all: 94.1
Reflection
*PLUS
Num. measured all: 75617
Reflection shell
*PLUS
% possible obs: 94.7 %

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Processing

Software
NameClassification
AMoREphasing
CNSrefinement
MADNESSdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.26→500 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.272 2100 RANDOM
Rwork0.228 --
all-22143 -
obs-21293 -
Refinement stepCycle: LAST / Resolution: 2.26→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2601 0 8 167 2776
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.72
X-RAY DIFFRACTIONc_bond_d0.015
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 50 Å / σ(F): 2 / Rfactor obs: 0.2277
Solvent computation
*PLUS
Displacement parameters
*PLUS

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