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- PDB-1rmr: Crystal Structure of Schistatin, a Disintegrin Homodimer from saw... -

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Basic information

Entry
Database: PDB / ID: 1rmr
TitleCrystal Structure of Schistatin, a Disintegrin Homodimer from saw-scaled Viper (Echis carinatus) at 2.5 A resolution
ComponentsDisintegrin schistatin
KeywordsPROTEIN BINDING / disintegrin / homodimer / echis carinatus
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
Similarity search - Component
Biological speciesEchis carinatus (saw-scaled viper)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 2.5 Å
AuthorsBilgrami, S. / Tomar, S. / Yadav, S. / Kaur, P. / Kumar, J. / Jabeen, T. / Sharma, S. / Singh, T.P.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of schistatin, a disintegrin homodimer from saw-scaled viper (Echis carinatus) at 2.5 A resolution
Authors: Bilgrami, S. / Tomar, S. / Yadav, S. / Kaur, P. / Kumar, J. / Jabeen, T. / Sharma, S. / Singh, T.P.
History
DepositionNov 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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: Disintegrin schistatin


Theoretical massNumber of molelcules
Total (without water)7,0911
Polymers7,0911
Non-polymers00
Water39622
1
A: Disintegrin schistatin

A: Disintegrin schistatin


Theoretical massNumber of molelcules
Total (without water)14,1822
Polymers14,1822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_755-x+2,-y,z1
Unit cell
Length a, b, c (Å)91.645, 91.645, 55.049
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Detailsthe biological assembly is a dimer, with only the monomer forming the asymmetric unit. The other monomer is generated by the symmetry operation: -X+2,-Y,Z

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Components

#1: Protein Disintegrin schistatin


Mass: 7090.936 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Echis carinatus (saw-scaled viper) / Secretion: venom / References: UniProt: P83658
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O
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: 4.07 Å3/Da / Density % sol: 69.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: ammonium sulfate, cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.541 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 12, 2000
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 3943 / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 10.3 % / Rsym value: 0.12 / Net I/σ(I): 17.8
Reflection shellResolution: 2.5→2.54 Å / Mean I/σ(I) obs: 2.7 / Rsym value: 0.3 / % possible all: 55

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIRAS / Resolution: 2.5→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.916 / SU B: 7.268 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22974 197 5 %RANDOM
Rwork0.19037 ---
obs0.19216 3943 100 %-
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: 56.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å20 Å2
2--0.54 Å20 Å2
3----1.07 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å / Luzzati d res low obs: 4 Å / Luzzati sigma a obs: 0.37 Å
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms485 0 0 22 507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.021501
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.958682
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.761563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1080.268
X-RAY DIFFRACTIONr_gen_planes_refined0.020.02408
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2540.2162
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.215
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.510.244
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it3.0041.5320
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.1512517
X-RAY DIFFRACTIONr_scbond_it7.2983181
X-RAY DIFFRACTIONr_scangle_it11.9654.5165
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.562 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.244 8
Rwork0.287 128

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