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- PDB-2aip: Crystal structure of native protein C activator from the venom of... -

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Basic information

Entry
Database: PDB / ID: 2aip
TitleCrystal structure of native protein C activator from the venom of copperhead snake Agkistrodon contortrix contortrix
ComponentsProtein C activator
KeywordsHYDROLASE / Protein C activator / snake venom / trypsin-like enzyme
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / toxin activity / serine-type endopeptidase activity / proteolysis / extracellular space
Similarity search - Function
: / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H ...: / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / 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
ACETATE ION / Protein C activator
Similarity search - Component
Biological speciesAgkistrodon contortrix contortrix (southern copperhead)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsMurakami, M.T. / Arni, R.K.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Thrombomodulin-independent Activation of Protein C and Specificity of Hemostatically Active Snake Venom Serine Proteinases: CRYSTAL STRUCTURES OF NATIVE AND INHIBITED AGKISTRODON CONTORTRIX ...Title: Thrombomodulin-independent Activation of Protein C and Specificity of Hemostatically Active Snake Venom Serine Proteinases: CRYSTAL STRUCTURES OF NATIVE AND INHIBITED AGKISTRODON CONTORTRIX CONTORTRIX PROTEIN C ACTIVATOR.
Authors: Murakami, M.T. / Arni, R.K.
History
DepositionJul 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_special_symmetry / pdbx_validate_chiral / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein C activator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2369
Polymers25,1331
Non-polymers1,1038
Water3,297183
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.867, 63.295, 48.237
Angle α, β, γ (deg.)90.00, 99.80, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-954-

HOH

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Components

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Protein / Sugars , 2 types, 4 molecules A

#1: Protein Protein C activator / Venombin A / Ancrod / ACC-C


Mass: 25132.881 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Agkistrodon contortrix contortrix (southern copperhead)
Species: Agkistrodon contortrix / Strain: contortrix / References: UniProt: P09872, EC: 3.4.21.74
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 188 molecules

#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / 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: 2.15 Å3/Da / Density % sol: 42.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: ammonium sulfate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.438 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 19, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.438 Å / Relative weight: 1
ReflectionResolution: 1.65→19.03 Å / Num. obs: 28664 / % possible obs: 99.8 % / Observed criterion σ(F): 2.5 / Observed criterion σ(I): 2.5 / Rmerge(I) obs: 0.09
Reflection shellResolution: 1.65→1.71 Å / % possible all: 99.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1BQY

1bqy


Resolution: 1.65→19.03 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 1.643 / SU ML: 0.057 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2.5 / ESU R: 0.092 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19692 1440 5 %RANDOM
Rwork0.16949 ---
all0.1743 ---
obs0.17086 27223 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.121 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 67 183 2007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221878
X-RAY DIFFRACTIONr_angle_refined_deg1.4931.9962561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2195230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60224.15677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.54815294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.611512
X-RAY DIFFRACTIONr_chiral_restr0.0970.2288
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021397
X-RAY DIFFRACTIONr_nbd_refined0.2170.21030
X-RAY DIFFRACTIONr_nbtor_refined0.3230.21320
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2232
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.269
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.20.225
X-RAY DIFFRACTIONr_mcbond_it0.8021.51168
X-RAY DIFFRACTIONr_mcangle_it1.39321862
X-RAY DIFFRACTIONr_scbond_it2.033779
X-RAY DIFFRACTIONr_scangle_it2.9994.5699
LS refinement shellResolution: 1.65→1.687 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 85 -
Rwork0.225 1905 -
obs--94 %

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