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- PDB-1m93: 1.65 A Structure of Cleaved Viral Serpin CRMA -

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Basic information

Entry
Database: PDB / ID: 1m93
Title1.65 A Structure of Cleaved Viral Serpin CRMA
Components(Serine proteinase inhibitor 2) x 3
KeywordsVIRAL PROTEIN / SERPIN / CRMA / APOPTOSIS / ICE INHIBITOR
Function / homology
Function and homology information


Microbial modulation of RIPK1-mediated regulated necrosis / symbiont-mediated perturbation of host apoptosis / 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
Helix hairpin bin / 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 ...Helix hairpin bin / 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 / Helix Hairpins / Roll / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Serine proteinase inhibitor 2
Similarity search - Component
Biological speciesCowpox virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsSimonovic, M. / Gettins, P.G.W. / Volz, K.
Citation
Journal: 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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2000
Title: Crystallization and preliminary X-ray diffraction analysis of a recombinant cysteine-free mutant of crmA
Authors: Simonovic, M. / Gettins, P.G.W. / Volz, K.
History
DepositionJul 26, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine proteinase inhibitor 2
B: Serine proteinase inhibitor 2
C: Serine proteinase inhibitor 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0974
Polymers38,0023
Non-polymers951
Water2,630146
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8010 Å2
ΔGint-67 kcal/mol
Surface area13730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.520, 92.590, 100.630
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 Serine proteinase inhibitor 2 / cytokine response modifier protein A / Serpin 2 / Serp-2 / ICE inhibitor / Hemorrhage-inducing 38 kDa protein


Mass: 6079.818 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-55
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cowpox virus / Genus: Orthopoxvirus / Gene: crmA / Plasmid: pQE-60 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: P07385
#2: Protein Serine proteinase inhibitor 2 / cytokine response modifier protein A / Serpin 2 / Serp-2 / ICE inhibitor / Hemorrhage-inducing 38 kDa protein


Mass: 27403.771 Da / Num. of mol.: 1 / Fragment: RESIDUES 56-300 / Mutation: C93S, C102S, C124S, C223S, C269S, C298S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cowpox virus / Genus: Orthopoxvirus / Gene: crmA / Plasmid: pQE-60 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: P07385
#3: Protein/peptide Serine proteinase inhibitor 2 / cytokine response modifier protein A / Serpin 2 / Serp-2 / ICE inhibitor / Hemorrhage-inducing 38 kDa 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 / Gene: crmA / Plasmid: pQE-60 / Production host: Escherichia coli (E. coli) / Strain (production host): SG13009 / References: UniProt: P07385
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.76 Å3/Da / Density % sol: 59.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: sodium/potassium phosphate 1.6M, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 12, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→31.54 Å / Num. all: 54375 / Num. obs: 53225 / % possible obs: 94.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.6 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 32.6
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.1 / % possible all: 83.5

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Processing

Software
NameClassification
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
DENZOdata reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1C8O

1c8o


Resolution: 1.65→31.54 Å / Num. parameters: 25438 / Num. restraintsaints: 31394 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?. Following side-chains are disordered: ...Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28(1995)53-56 ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?. Following side-chains are disordered: ILE57, and ASP122 Following amino-acids are missing: 47 GLU LYS GLU ALA ASP LYS ASN LYS ASP 55; 301 VAL ALA ASP SER ALA SER THR VAL 308
RfactorNum. reflection% reflectionSelection details
Rfree0.2454 5422 10 %RANDOM
Rwork0.1881 ---
all-53172 --
obs-53172 96.3 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 18 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2777
Refinement stepCycle: LAST / Resolution: 1.65→31.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2569 0 5 146 2720
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.009
X-RAY DIFFRACTIONs_angle_d0.027
X-RAY DIFFRACTIONs_similar_dist0.015
X-RAY DIFFRACTIONs_from_restr_planes0.0277
X-RAY DIFFRACTIONs_zero_chiral_vol0.043
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.055
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.013
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.003
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.057
X-RAY DIFFRACTIONs_approx_iso_adps0.077

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