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- PDB-3uci: Crystal structure of Rhodostomin ARLDDL mutant -

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Basic information

Entry
Database: PDB / ID: 3uci
TitleCrystal structure of Rhodostomin ARLDDL mutant
Componentsdisintegrin
KeywordsTOXIN / disintegrin / integrin alphaVbeta3
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases / metalloendopeptidase activity / toxin activity / proteolysis / extracellular region / metal ion binding / plasma membrane
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
Similarity search - Component
Biological speciesCalloselasma rhodostoma (Malayan pit viper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsShiu, J.H. / Chen, C.Y. / Chen, Y.C. / Chang, Y.T. / Chang, Y.S. / Huang, C.H. / Chuang, W.J.
CitationJournal: To be Published
Title: Design of Integrin AlphaVbeta3-Specific Disintegrin for Cancer Therapy
Authors: Shiu, J.H. / Chen, C.Y. / Chen, Y.C. / Chang, Y.T. / Chang, Y.S. / Huang, C.H. / Chuang, W.J.
History
DepositionOct 27, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 21, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: disintegrin


Theoretical massNumber of molelcules
Total (without water)7,8481
Polymers7,8481
Non-polymers00
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)26.221, 33.437, 73.253
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 / Disintegrin rhodostomin / RHO / Disintegrin kistrin / Platelet aggregation activation inhibitor


Mass: 7847.845 Da / Num. of mol.: 1 / Mutation: P48A, G50L, M52D, P53L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Calloselasma rhodostoma (Malayan pit viper)
Gene: RHOD / Plasmid: pPICZa / Production host: Pichia pastoris (fungus) / Strain (production host): X33 / References: UniProt: P30403
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 2.05 Å3/Da / Density % sol: 39.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl, 0.8M sodium citrate tribasic dihydrate, 0.24M lithium sulfide, 0.5% glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 9, 2010
Details: Vertically Collimating Premirror, Toroidal Focusing Mirror
RadiationMonochromator: LN2-Cooled Fixed-Exit Double Crystal Si(111) Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→30 Å / Num. all: 14777 / Num. obs: 14629 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 6.5 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 34.15
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.559 / Mean I/σ(I) obs: 4.76 / Num. unique all: 1438 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J2L

1j2l


Resolution: 1.35→20 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.95 / SU B: 1.468 / SU ML: 0.028 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R Free: 0.056 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18924 737 5.1 %RANDOM
Rwork0.14506 ---
obs0.14729 14516 98.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.435 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20 Å2
2--0.04 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms536 0 0 102 638
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.021549
X-RAY DIFFRACTIONr_angle_refined_deg2.2841.976739
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.115571
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.62124.07427
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.1251594
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.769156
X-RAY DIFFRACTIONr_chiral_restr0.1310.274
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021426
X-RAY DIFFRACTIONr_mcbond_it2.681.5357
X-RAY DIFFRACTIONr_mcangle_it3.8672564
X-RAY DIFFRACTIONr_scbond_it5.9443192
X-RAY DIFFRACTIONr_scangle_it8.584.5175
X-RAY DIFFRACTIONr_rigid_bond_restr3.0113549
LS refinement shellResolution: 1.351→1.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 56 -
Rwork0.257 1007 -
obs-1063 98.06 %
Refinement TLS params.Method: refined / Origin x: 0.8356 Å / Origin y: -4.7989 Å / Origin z: -7.0177 Å
111213212223313233
T0.0091 Å2-0.0018 Å20.0018 Å2-0.0163 Å2-0.0002 Å2--0.0192 Å2
L0.0115 °20.0628 °20.0773 °2-0.3304 °20.2147 °2--0.1104 °2
S0.0072 Å °-0.0146 Å °-0.0036 Å °0.0332 Å °-0.0093 Å °0.0044 Å °0.0252 Å °-0.0186 Å °0.002 Å °

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