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- PDB-4rqg: Crystal structure of Rhodostomin -

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Basic information

Entry
Database: PDB / ID: 4rqg
TitleCrystal structure of Rhodostomin
ComponentsDisintegrin rhodostomin
KeywordsTOXIN / RGD motif / disintegrin / integrin / rhodostomin
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: 1.66 Å
AuthorsShiu, J.H. / Huang, C.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: Shiu, J.H. / Huang, C.H. / Chang, Y.T. / Jeng, W.Y. / Chuang, W.J.
History
DepositionNov 3, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software
Revision 1.2Nov 8, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)14,6832
Polymers14,6832
Non-polymers00
Water2,396133
1
A: Disintegrin rhodostomin


Theoretical massNumber of molelcules
Total (without water)7,3411
Polymers7,3411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Disintegrin rhodostomin


Theoretical massNumber of molelcules
Total (without water)7,3411
Polymers7,3411
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)93.956, 34.179, 53.946
Angle α, β, γ (deg.)90.00, 119.26, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Disintegrin rhodostomin


Mass: 7341.361 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Calloselasma rhodostoma (Malayan pit viper)
Gene: RHOD / Plasmid: pPICZalphaA / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33 / References: UniProt: P30403
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 133 / 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: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2
Details: 50mM MOPS, 32% PEG1500, 5% PEG200, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 15, 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: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. all: 18571 / Num. obs: 17798 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 2.3 % / Net I/σ(I): 15.9
Reflection shellHighest resolution: 1.66 Å / Num. unique all: 3376 / % possible all: 90.1

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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
Starting model: 3UCI

3uci


Resolution: 1.66→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.815 / SU ML: 0.057 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20786 909 5.1 %RANDOM
Rwork0.16024 ---
obs0.16268 16836 99.1 %-
all-17745 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.723 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å20 Å2-0.85 Å2
2---1.46 Å20 Å2
3---1.09 Å2
Refinement stepCycle: LAST / Resolution: 1.66→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms974 0 0 133 1107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0211009
X-RAY DIFFRACTIONr_angle_refined_deg2.1731.9861365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8865132
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.92923.47846
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.49115168
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.451512
X-RAY DIFFRACTIONr_chiral_restr0.1510.2134
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.022794
X-RAY DIFFRACTIONr_mcbond_it2.3411.5664
X-RAY DIFFRACTIONr_mcangle_it3.58321061
X-RAY DIFFRACTIONr_scbond_it5.8593345
X-RAY DIFFRACTIONr_scangle_it8.954.5304
X-RAY DIFFRACTIONr_rigid_bond_restr3.16931009
LS refinement shellResolution: 1.661→1.751 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.278 125 -
Rwork0.199 2400 -
obs-3376 97.68 %
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)
10.16540.24210.4351.19540.95071.6181-0.0003-0.00330.0328-0.08140.02460.05150.00140.0094-0.02430.06130.0082-0.00320.0562-0.00730.0425-20.129313.880911.7988
21.0966-0.7222-0.78021.11620.44560.58690.0536-0.0084-0.0073-0.0952-0.02740.1428-0.01390.0364-0.02620.03190.0189-0.01280.0501-0.00370.0943-25.14096.322419.6132
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 68
2X-RAY DIFFRACTION2B3 - 68

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