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- PDB-7x4v: Crystal structure of Rhodostomin ARGDDP mutant -

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Basic information

Entry
Database: PDB / ID: 7x4v
TitleCrystal structure of Rhodostomin ARGDDP mutant
ComponentsDisintegrin rhodostomin
KeywordsBLOOD CLOTTING / Disintegrin / Platelet aggregation inhibitor
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, 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, 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.
Similarity search - Domain/homology
Zinc metalloproteinase/disintegrin
Similarity search - Component
Biological speciesCalloselasma rhodostoma (Malayan pit viper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsChang, Y.T. / Chuang, W.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
Citation
Journal: To be published
Title: Crystal structure of Rhodostomin ARGDDP mutant
Authors: Chang, Y.T. / Chuang, W.J.
#1: Journal: PLoS One / Year: 2017
Title: Effects of the RGD loop and C-terminus of rhodostomin on regulating integrin alphaIIbbeta3 recognition
Authors: Chang, Y.T. / Shiu, J.H. / Chen, C.Y. / Chuang, W.J.
History
DepositionMar 3, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)14,5982
Polymers14,5982
Non-polymers00
Water2,810156
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1040 Å2
ΔGint-1 kcal/mol
Surface area8530 Å2
Unit cell
Length a, b, c (Å)78.293, 62.092, 34.756
Angle α, β, γ (deg.)90.00, 105.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 7299.216 Da / Num. of mol.: 2 / Mutation: P455A, M459D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Calloselasma rhodostoma (Malayan pit viper)
Production host: Pichia (fungus) / References: UniProt: P30403
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.79 Å3/Da / Density % sol: 55.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M NH4OAc, 0.05 M Sodium cacodylate pH 6.5, 30% PEG 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→30 Å / Num. obs: 32038 / % possible obs: 97.1 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.117 / Net I/σ(I): 13.4
Reflection shellResolution: 1.38→1.43 Å / Rmerge(I) obs: 0.55 / Num. unique obs: 3211

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-20002.3.10data reduction
HKL-20002.3.10data scaling
HKL-30002.3.10phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4RQG

4rqg


Resolution: 1.38→18.09 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.246 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21689 1658 5.2 %RANDOM
Rwork0.18295 ---
obs0.18469 30379 97.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.221 Å2
Baniso -1Baniso -2Baniso -3
1-1.22 Å2-0 Å2-0.26 Å2
2--1.13 Å20 Å2
3----1.91 Å2
Refinement stepCycle: 1 / Resolution: 1.38→18.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms950 0 0 156 1106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.013993
X-RAY DIFFRACTIONr_bond_other_d0.0020.013866
X-RAY DIFFRACTIONr_angle_refined_deg1.4441.6781343
X-RAY DIFFRACTIONr_angle_other_deg1.4641.6092025
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.165132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.79220.16162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.70415165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4171514
X-RAY DIFFRACTIONr_chiral_restr0.0810.2128
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021166
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02226
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_it1.851.237522
X-RAY DIFFRACTIONr_mcbond_other1.8511.233521
X-RAY DIFFRACTIONr_mcangle_it2.0331.856650
X-RAY DIFFRACTIONr_mcangle_other2.0311.858651
X-RAY DIFFRACTIONr_scbond_it2.6761.668471
X-RAY DIFFRACTIONr_scbond_other2.6781.67472
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2782.371692
X-RAY DIFFRACTIONr_long_range_B_refined3.11216.8541081
X-RAY DIFFRACTIONr_long_range_B_other2.96516.4351056
X-RAY DIFFRACTIONr_rigid_bond_restr2.69531858
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.38→1.415 Å
RfactorNum. reflection% reflection
Rfree0.296 111 -
Rwork0.26 2210 -
obs--96.59 %
Refinement TLS params.

S13: 0.0005 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (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)
10.0084-0.01630.00830.0512-0.00970.02220.00250.0009-0.0015-0.00240.0018-0.003-0.0047-00.00350.00250.0020.00240.00060.013923.11567.425313.8533
20.04120.0373-0.04080.069-0.04120.05480.00040.00080.0002-0.0037-0.00190.0053-0.00480.00330.0023-0.00190.00120.0021-0.00050.01324.9622-3.81916.4563
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 68
2X-RAY DIFFRACTION2B4 - 67

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