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- PDB-4r5r: Crystal structure of Rhodostomin KKKRT mutant -

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Basic information

Entry
Database: PDB / ID: 4r5r
TitleCrystal structure of Rhodostomin KKKRT mutant
ComponentsDisintegrin rhodostomin
KeywordsTOXIN / RGD motif / disintegrin / integrin / rhodostomin / linker region
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: 0.96 Å
AuthorsHuang, C.H. / Shiu, J.H. / Chang, Y.T. / Jeng, W.Y. / Chuang, W.J.
CitationJournal: To be Published
Title: Effects of the regions adjacent to the RGD motif in disintegrins on their inhibitory activities and structures
Authors: Huang, C.H. / Shiu, J.H. / Chang, Y.T. / Jeng, W.Y. / Chuang, W.J.
History
DepositionAug 21, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 26, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Disintegrin rhodostomin
B: Disintegrin rhodostomin


Theoretical massNumber of molelcules
Total (without water)14,9712
Polymers14,9712
Non-polymers00
Water4,756264
1
A: Disintegrin rhodostomin


Theoretical massNumber of molelcules
Total (without water)7,4861
Polymers7,4861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Disintegrin rhodostomin


Theoretical massNumber of molelcules
Total (without water)7,4861
Polymers7,4861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)18.083, 79.986, 39.497
Angle α, β, γ (deg.)90.00, 91.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Disintegrin rhodostomin / RHO / RHOD / Disintegrin kistrin / Platelet aggregation activation inhibitor


Mass: 7485.618 Da / Num. of mol.: 2 / Fragment: disintegrin mutant, UNP residues 408-475 / Mutation: S39K, R40K, A41K, G42R, K43T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Calloselasma rhodostoma (Malayan pit viper)
Gene: RHOD / Plasmid: pPICZalphaA / Production host: Pichia pastoris (fungus) / References: UniProt: P30403
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 264 / 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: 1.91 Å3/Da / Density % sol: 35.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2M CH3COONH4, 0.1M pH 4.6 CH3COONa, 28% PEG4000, 2% PEG300, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 6, 2013
Details: Vertically Focusing Mirror, Horizontally Focusing Single Crystal Si(111) Bent Monochromator
RadiationMonochromator: Horizontally Focusing Single Crystal Monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 0.96→30 Å / Num. all: 68465 / Num. obs: 68199 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 6.7 %
Reflection shellResolution: 0.96→0.99 Å / % possible all: 99.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 0.96→30 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.977 / SU B: 0.758 / SU ML: 0.018 / Cross valid method: THROUGHOUT / ESU R: 0.023 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.168 3425 5.1 %RANDOM
Rwork0.14763 ---
obs0.14868 64234 99.23 %-
all-67658 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.012 Å2
Baniso -1Baniso -2Baniso -3
1-0.43 Å20 Å2-0.58 Å2
2---0.49 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 0.96→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1020 0 0 264 1284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221052
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.1191.9951417
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6015136
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.87323.47846
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.31115191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.231512
X-RAY DIFFRACTIONr_chiral_restr0.1450.2139
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.022810
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.6681.5683
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.69721094
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.143369
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.3764.5322
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.7731052
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 0.96→1.012 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.302 479 -
Rwork0.285 9150 -
obs-9629 96.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.27910.42470.25670.720.30090.32250.0080.00880.00030.01320.00750.0070.00910.0071-0.01550.0068-0.0040.00450.0216-0.00130.0183-2.539411.1468-12.5887
20.38830.2928-0.19850.2978-0.21110.23330.0171-0.0227-0.03160.0271-0.0209-0.0216-0.01610.00540.00380.0211-0.0095-0.00150.01720.00460.0111-4.297420.7574-32.5234
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 68
2X-RAY DIFFRACTION2B1 - 68

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