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- PDB-7x4z: Crystal structure of Rhodostomin ARGDWP mutant -

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Basic information

Entry
Database: PDB / ID: 7x4z
TitleCrystal structure of Rhodostomin ARGDWP 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: 1.48 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 ARGDWP 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 ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Disintegrin rhodostomin
B: Disintegrin rhodostomin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,0295
Polymers14,7412
Non-polymers2883
Water2,342130
1
A: Disintegrin rhodostomin


Theoretical massNumber of molelcules
Total (without water)7,3701
Polymers7,3701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5070 Å2
MethodPISA
2
B: Disintegrin rhodostomin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,6594
Polymers7,3701
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area4970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.709, 79.281, 92.011
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-161-

HOH

21B-269-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 3 - 68 / Label seq-ID: 3 - 68

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AA
22BB

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Components

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


Mass: 7370.339 Da / Num. of mol.: 2 / Mutation: P455A, M459W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Calloselasma rhodostoma (Malayan pit viper)
Production host: Pichia (fungus) / References: UniProt: P30403
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.09 Å3/Da / Density % sol: 41.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5, 2M (NH4)2SO4

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.48→30 Å / Num. obs: 20726 / % possible obs: 99.8 % / Redundancy: 7 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 28.8
Reflection shellResolution: 1.48→1.53 Å / Rmerge(I) obs: 0.714 / Num. unique obs: 2042

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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: 1.48→23.8 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.591 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.082 / ESU R Free: 0.077 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21392 1103 5.3 %RANDOM
Rwork0.1625 ---
obs0.1652 19620 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.683 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å20 Å2
2--0.11 Å20 Å2
3---0.33 Å2
Refinement stepCycle: 1 / Resolution: 1.48→23.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms982 0 15 130 1127
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0131028
X-RAY DIFFRACTIONr_bond_other_d00.013869
X-RAY DIFFRACTIONr_angle_refined_deg1.4911.6691395
X-RAY DIFFRACTIONr_angle_other_deg1.4821.6032033
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.065132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.73420.66760
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.04215163
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.2661512
X-RAY DIFFRACTIONr_chiral_restr0.0750.2129
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021193
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02231
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_it1.931.379528
X-RAY DIFFRACTIONr_mcbond_other1.927527
X-RAY DIFFRACTIONr_mcangle_it2.3892.074657
X-RAY DIFFRACTIONr_mcangle_other2.38722.337658
X-RAY DIFFRACTIONr_scbond_it3.0741.828500
X-RAY DIFFRACTIONr_scbond_other3.093488
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.7292.757719
X-RAY DIFFRACTIONr_long_range_B_refined3.3721114
X-RAY DIFFRACTIONr_long_range_B_other3.3071094
X-RAY DIFFRACTIONr_rigid_bond_restr2.66431016
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1727 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.481→1.519 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 95 -
Rwork0.277 1382 -
obs--98.86 %
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)
10.19050.15420.28730.44970.32690.46880.0021-0.02430.0160.0225-0.0181-0.00470.0299-0.03150.01610.03830.00140.00210.0336-0.01390.0074.1424-22.5477-17.6405
20.21380.02870.09350.17410.03360.17990.02210.0037-0.01090.0104-0.0093-0.01780.01740.0273-0.01270.02510.002-0.00330.0225-0.00020.002511.4676-6.08121.5764
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 68
2X-RAY DIFFRACTION2B3 - 68

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