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- PDB-3c05: Crystal structure of Acostatin from Agkistrodon Contortrix Contortrix -

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Basic information

Entry
Database: PDB / ID: 3c05
TitleCrystal structure of Acostatin from Agkistrodon Contortrix Contortrix
Components
  • Disintegrin acostatin alpha
  • Disintegrin acostatin-beta
KeywordsBLOOD CLOTTING/ANTITUMOR PROTEIN / beta-sheets / disulfide bridges / Blood coagulation / Cell adhesion / Secreted / Hydrolase / Metal-binding / Metalloprotease / Protease / Zinc / Zymogen / BLOOD CLOTTING-ANTITUMOR PROTEIN COMPLEX
Function / homology
Function and homology information


negative regulation of blood coagulation / Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / toxin activity / cell adhesion / extracellular region / metal ion binding
Similarity search - Function
Disintegrin domain / Echistatin / Disintegrin, conserved site / Disintegrins signature. / Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Disintegrin / Disintegrin domain profile. ...Disintegrin domain / Echistatin / Disintegrin, conserved site / Disintegrins signature. / Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily / Peptidase M12B, ADAM/reprolysin / ADAM type metalloprotease domain profile. / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Zinc metalloproteinase/disintegrin / Disintegrin acostatin-alpha
Similarity search - Component
Biological speciesAgkistrodon contortrix contortrix (southern copperhead)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 Å
AuthorsMoiseeva, N. / Bau, R. / Allaire, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Crystal structure of acostatin, a dimeric disintegrin from southern copperhead (Agkistrodon contortrix contortrix) at 1.7 A resolution
Authors: Moiseeva, N. / Bau, R. / Swenson, S.D. / Markland, F.S. / Choe, J.-Y. / Liu, Z.-J. / Allaire, M.
History
DepositionJan 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 2.0Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _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: Disintegrin acostatin alpha
B: Disintegrin acostatin-beta
C: Disintegrin acostatin alpha
D: Disintegrin acostatin-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3837
Polymers27,0954
Non-polymers2883
Water5,459303
1
A: Disintegrin acostatin alpha
B: Disintegrin acostatin-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8365
Polymers13,5472
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
MethodPISA
2
C: Disintegrin acostatin alpha
D: Disintegrin acostatin-beta


Theoretical massNumber of molelcules
Total (without water)13,5472
Polymers13,5472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.449, 59.808, 121.307
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 Disintegrin acostatin alpha


Mass: 6747.774 Da / Num. of mol.: 2 / Fragment: UNP residues 48-109 / Source method: isolated from a natural source
Source: (natural) Agkistrodon contortrix contortrix (southern copperhead)
References: UniProt: Q805F7
#2: Protein Disintegrin acostatin-beta


Mass: 6799.651 Da / Num. of mol.: 2 / Fragment: UNP residues 419-482 / Source method: isolated from a natural source
Source: (natural) Agkistrodon contortrix contortrix (southern copperhead)
References: UniProt: Q805F6
#3: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.48 Å3/Da / Density % sol: 50.43 %
Crystal growpH: 8.5
Details: 1.8M AMMONIUM SULFATE, 0.1M TRIS-HCL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 8.50

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
31
41
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONALS 5.0.210.9486
SYNCHROTRONNSLS X6A2
SYNCHROTRONSSRL BL9-13
SYNCHROTRONSSRL BL7-14
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDOct 19, 2002
ADSC QUANTUM 2102CCD
MAR scanner 345 mm plate3IMAGE PLATE
MAR scanner 345 mm plate4IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9486 Å / Relative weight: 1
ReflectionResolution: 1.7→20 Å / Num. obs: 30457 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 13.7 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 13.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.156 / Mean I/σ(I) obs: 8.5 / % possible all: 90.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementStarting model: PDB ENTRY 1J2L

1j2l


Resolution: 1.7→19.67 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.941 / SU B: 1.838 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.099 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS ADDITIONAL RESIDUAL ELECTRON DENSITIES HAVE BEEN TENTATIVELY MODELED BY SULFATE ION A66 AND 10 WATER MOLECULES (A149-A152,C132-C137)
RfactorNum. reflection% reflectionSelection details
Rfree0.215 1543 5.1 %RANDOM
Rwork0.186 ---
obs0.188 28838 98.8 %-
all-30750 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1686 0 15 303 2004
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0211738
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3291.9782345
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8835228
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8292475
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.96215289
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3051517
X-RAY DIFFRACTIONr_chiral_restr0.0970.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021320
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1890.2668
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.21203
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1360.2182
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.257
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.239
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.161.51182
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.85121813
X-RAY DIFFRACTIONr_scbond_it2.9593611
X-RAY DIFFRACTIONr_scangle_it4.7554.5532
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.745 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 97 -
Rwork0.192 1901 -
obs--90.08 %

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