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- PDB-2ero: Crystal structure of vascular apoptosis-inducing protein-1(orthor... -

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Basic information

Entry
Database: PDB / ID: 2ero
TitleCrystal structure of vascular apoptosis-inducing protein-1(orthorhombic crystal form)
Componentsvascular apoptosis-inducing protein 1
KeywordsTOXIN / metalloprotease / disintegrin / calcium-binding / ADAM / SVMP / MDC protein
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / toxin activity / apoptotic process / protein homodimerization activity / proteolysis / zinc ion binding / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
ADAM cysteine-rich / ADAM, cysteine-rich domain / ADAM Cysteine-Rich Domain / Disintegrin, conserved site / Disintegrins signature. / Peptidase M12B, propeptide / Reprolysin family propeptide / Reprolysin domain, adamalysin-type / Reprolysin (M12B) family zinc metalloprotease / Disintegrin ...ADAM cysteine-rich / ADAM, cysteine-rich domain / ADAM Cysteine-Rich Domain / 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. / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COBALT (III) ION / : / Zinc metalloproteinase-disintegrin-like VAP1
Similarity search - Component
Biological speciesCrotalus atrox (western diamondback rattlesnake)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsTakeda, S. / Igarashi, T. / Araki, S.
Citation
Journal: Embo J. / Year: 2006
Title: Crystal structures of VAP1 reveal ADAMs' MDC domain architecture and its unique C-shaped scaffold
Authors: Takeda, S. / Igarashi, T. / Mori, H. / Araki, S.
#1: Journal: To be Published
Title: Crystallization and preliminary X-ray crystallographic analysis of two vascular apoptosis-inducing proteins (VAPs) from Crotalus atrox venom
Authors: Igarashi, T. / Oishi, Y. / Araki, S. / Mori, H. / Takeda, S.
History
DepositionOct 25, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / 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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 25, 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
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: vascular apoptosis-inducing protein 1
B: vascular apoptosis-inducing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,95511
Polymers94,7562
Non-polymers1,1999
Water3,657203
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-107 kcal/mol
Surface area43480 Å2
MethodPISA
2
A: vascular apoptosis-inducing protein 1
hetero molecules

B: vascular apoptosis-inducing protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,95511
Polymers94,7562
Non-polymers1,1999
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area4510 Å2
ΔGint-111 kcal/mol
Surface area41910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.710, 93.270, 137.740
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAsymmetric unit contains one disulfide-linked homodimer molecule that is the biological unit.

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Components

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein vascular apoptosis-inducing protein 1 / VAP-1


Mass: 47378.000 Da / Num. of mol.: 2 / Fragment: residues 184-610 / Source method: isolated from a natural source
Source: (natural) Crotalus atrox (western diamondback rattlesnake)
Secretion: venom / References: GenBank: 11320556, UniProt: Q9DGB9*PLUS
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 210 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-3CO / COBALT (III) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.94 Å3/Da / Density % sol: 58.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 15% PEG, 100mM sodium/cacodylate, 20mM cobaltous chloride, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45PX / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Apr 15, 2004
RadiationMonochromator: double diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 39161 / Num. obs: 38926 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.91 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.4
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2.9 / Num. unique all: 3800 / % possible all: 98.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1QUA

1qua


Resolution: 2.5→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.258 1946 -random
Rwork0.212 ---
all0.214 39161 --
obs0.214 38874 98.8 %-
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6558 0 63 203 6824
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.18
X-RAY DIFFRACTIONc_bond_d0.0052
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_improper_angle_d0.751
LS refinement shellResolution: 2.5→2.59 Å
RfactorNum. reflection% reflection
Rfree0.3717 162 -
Rwork0.3028 --
obs-3570 92.3 %

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