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- PDB-1tej: Crystal structure of a disintegrin heterodimer at 1.9 A resolution. -

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Basic information

Entry
Database: PDB / ID: 1tej
TitleCrystal structure of a disintegrin heterodimer at 1.9 A resolution.
Components
  • disintegrin chain A
  • disintegrin chain B
KeywordsPROTEIN BINDING / cryatal structure / disintegrin / heterodimer
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
Disintegrin domain / Echistatin / Disintegrin, conserved site / Disintegrins signature. / Disintegrin / Disintegrin domain profile. / Homologues of snake disintegrins / Disintegrin domain / Disintegrin domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Disintegrin schistatin-like subunit A / Disintegrin schistatin-like subunit B / Disintegrin schistatin
Similarity search - Component
Biological speciesEchis carinatus (saw-scaled viper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsBilgrami, S. / Kaur, P. / Yadav, S. / Perbandt, M. / Betzel, C. / Singh, T.P.
CitationJournal: Biochemistry / Year: 2005
Title: Crystal Structure of the Disintegrin Heterodimer from Saw-Scaled Viper (Echis carinatus) at 1.9 A Resolution
Authors: Bilgrami, S. / Yadav, S. / Kaur, P. / Sharma, S. / Perbandt, M. / Betzel, C. / Singh, T.P.
History
DepositionMay 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id
Remark 999SEQUENCE A SUITABLE DATABASE REFERENCE SEQUENCE COULD NOT BE FOUND FOR THE PROTEINS IN THIS ...SEQUENCE A SUITABLE DATABASE REFERENCE SEQUENCE COULD NOT BE FOUND FOR THE PROTEINS IN THIS STRUCTURE AT THE TIME OF PROCESSING.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: disintegrin chain A
B: disintegrin chain B


Theoretical massNumber of molelcules
Total (without water)14,0852
Polymers14,0852
Non-polymers00
Water2,900161
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area760 Å2
ΔGint-10 kcal/mol
Surface area9000 Å2
MethodPISA
2
A: disintegrin chain A
B: disintegrin chain B

A: disintegrin chain A
B: disintegrin chain B


Theoretical massNumber of molelcules
Total (without water)28,1704
Polymers28,1704
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556-y,-x,-z+3/21
Buried area3990 Å2
ΔGint-36 kcal/mol
Surface area15540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.718, 90.718, 55.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-107-

HOH

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Components

#1: Protein disintegrin chain A


Mass: 7016.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echis carinatus (saw-scaled viper) / References: UniProt: P83658, UniProt: P0C6B4*PLUS
#2: Protein disintegrin chain B


Mass: 7067.947 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echis carinatus (saw-scaled viper) / References: UniProt: P83658, UniProt: P0C6B5*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 161 / 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: 4.1 Å3/Da / Density % sol: 69.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: sodium cacodylate, ammonium sulphate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 273 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.815 Å
DetectorType: ENRAF-NONIUS / Detector: CCD / Date: Dec 12, 2002
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.815 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 18372 / Num. obs: 18372 / % possible obs: 99.9 % / Biso Wilson estimate: 50 Å2 / Rsym value: 0.062 / Net I/σ(I): 10.8
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.659 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementStarting model: 1RMR

1rmr


Resolution: 1.9→19.96 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.925 / SU B: 2.766 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. origin shifts applied to the model solved in i4122 to get the spacegroup p43212.
RfactorNum. reflection% reflectionSelection details
Rfree0.25295 955 5.1 %RANDOM
Rwork0.21286 ---
obs0.21483 17734 100 %-
all-17734 --
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: 43.873 Å2
Baniso -1Baniso -2Baniso -3
1-1.43 Å20 Å20 Å2
2--1.43 Å20 Å2
3----2.85 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 4 Å / Luzzati sigma a obs: 0.15 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms940 0 0 161 1101
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021973
X-RAY DIFFRACTIONr_angle_refined_deg1.4081.9561324
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2335123
X-RAY DIFFRACTIONr_chiral_restr0.110.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.0180.02774
X-RAY DIFFRACTIONr_nbd_refined0.2880.2373
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2480.293
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.5150.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.214
X-RAY DIFFRACTIONr_mcbond_it2.4841.5622
X-RAY DIFFRACTIONr_mcangle_it4.05721008
X-RAY DIFFRACTIONr_scbond_it6.4013351
X-RAY DIFFRACTIONr_scangle_it9.3664.5316
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.307 69
Rwork0.281 1256

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