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- PDB-4r5u: Crystal structure of Rhodostomin R46E mutant -

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Basic information

Entry
Database: PDB / ID: 4r5u
TitleCrystal structure of Rhodostomin R46E 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: 1.81 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 22, 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)14,6272
Polymers14,6272
Non-polymers00
Water1,31573
1
A: Disintegrin rhodostomin


Theoretical massNumber of molelcules
Total (without water)7,3131
Polymers7,3131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Disintegrin rhodostomin


Theoretical massNumber of molelcules
Total (without water)7,3131
Polymers7,3131
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)29.010, 74.046, 29.010
Angle α, β, γ (deg.)90.00, 115.55, 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: 7313.281 Da / Num. of mol.: 2 / Fragment: disintegrin mutant, UNP residues 408-475 / Mutation: R46E
Source method: isolated from a genetically manipulated source
Details: pPICZalphaA
Source: (gene. exp.) Calloselasma rhodostoma (Malayan pit viper)
Gene: RHOD / Production host: Pichia pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P30403
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 1.92 Å3/Da / Density % sol: 36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: pH 8.5 0.1M Tris, 0.2M (NH4)2SO4, 25% PEG4000,, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97512 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 29, 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: 0.97512 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 10761 / Num. obs: 10307 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 4.2 % / Net I/σ(I): 24.7
Reflection shellResolution: 1.8→1.86 Å / % possible all: 96

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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: 1.81→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.943 / SU B: 9.2 / SU ML: 0.121 / Cross valid method: THROUGHOUT / ESU R: 0.459 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23648 478 4.8 %RANDOM
Rwork0.16636 ---
obs0.16986 9431 98.19 %-
all-9909 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.682 Å2
Baniso -1Baniso -2Baniso -3
1--0.91 Å20 Å2-2.4 Å2
2---0.46 Å20 Å2
3----0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.81→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms924 0 0 73 997
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.022950
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9451.9941285
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0945126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.57724.63441
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.25615155
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.429159
X-RAY DIFFRACTIONr_chiral_restr0.1390.2128
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022739
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_it2.0281.5638
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.44721015
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.6223312
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it9.1124.5270
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.6463950
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.809→1.907 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.279 64 -
Rwork0.189 1212 -
obs--89.99 %
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)
10.01060.0394-0.01590.42350.12170.1220.0022-0.0081-0.0076-0.0006-0.00170.00120.00190.0033-0.00040.1020.0017-0.03440.02490.00170.0794-0.815717.414-1.9695
20.10140.0810.04020.04420.03930.01530.0059-0.0047-0.00970.0077-0.0077-0.0148-0.0039-0.00810.00180.11510.0013-0.03610.02540.00080.0762-6.86929.0969-11.2974
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 67
2X-RAY DIFFRACTION2B4 - 67

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