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- PDB-4m4c: Crystal structure of Rhodostomin ARGDP mutant -

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Basic information

Entry
Database: PDB / ID: 4m4c
TitleCrystal structure of Rhodostomin ARGDP mutant
ComponentsZinc metalloproteinase/disintegrin
KeywordsTOXIN / Rhodostomin / disintegrin / integrin / ARGDP / Loss-of-function
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: 1.8 Å
AuthorsChang, Y.T. / Jeng, W.Y. / Shiu, J.H. / Chen, C.Y. / Chuang, W.J.
CitationJournal: To be Published
Title: Effect of C-terminal proline residue adjacent to the RGD motif in rhodostomin on its activity and structure
Authors: Chang, Y.T. / Jeng, W.Y. / Shiu, J.H. / Chen, C.Y. / Chuang, W.J.
History
DepositionAug 7, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Zinc metalloproteinase/disintegrin
B: Zinc metalloproteinase/disintegrin
C: Zinc metalloproteinase/disintegrin
D: Zinc metalloproteinase/disintegrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,70110
Polymers29,1254
Non-polymers5766
Water1,802100
1
A: Zinc metalloproteinase/disintegrin


Theoretical massNumber of molelcules
Total (without water)7,2811
Polymers7,2811
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Zinc metalloproteinase/disintegrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4733
Polymers7,2811
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Zinc metalloproteinase/disintegrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4733
Polymers7,2811
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Zinc metalloproteinase/disintegrin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,4733
Polymers7,2811
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)31.619, 42.637, 46.538
Angle α, β, γ (deg.)106.84, 103.86, 97.23
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 4 / Auth seq-ID: 4 - 40 / Label seq-ID: 4 - 40

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Zinc metalloproteinase/disintegrin / Snake venom metalloproteinase rhodostoxin / SVMP / Hemorrhagic protein / Disintegrin rhodostomin / ...Snake venom metalloproteinase rhodostoxin / SVMP / Hemorrhagic protein / Disintegrin rhodostomin / RHO / Disintegrin kistrin / Platelet aggregation activation inhibitor


Mass: 7281.243 Da / Num. of mol.: 4 / Fragment: UNP residues 408-475 / Mutation: P48A, M52P
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) / Strain (production host): X-33
References: UniProt: P30403, Hydrolases; Acting on peptide bonds (peptidases); Metalloendopeptidases
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.96 Å3/Da / Density % sol: 37.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG4000, 0.2M Ammonium sulfate, 5% PEG3350, 2% PEG200, 0.5% 2-propanol(External) , pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 2, 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: 1.8→30 Å / Num. all: 20296 / Num. obs: 19633 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 23.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 2.3 / % possible all: 91.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
CNSrefinement
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UCI

3uci


Resolution: 1.8→23.58 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.938 / SU B: 9.14 / SU ML: 0.126 / Isotropic thermal model: Isotropic with TLS / Cross valid method: THROUGHOUT / ESU R: 0.843 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23787 1005 5.1 %RANDOM
Rwork0.17742 ---
obs0.18057 18626 96.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.953 Å2
Baniso -1Baniso -2Baniso -3
1--2.75 Å2-0.46 Å2-1.72 Å2
2--0.67 Å20.11 Å2
3---1.21 Å2
Refinement stepCycle: LAST / Resolution: 1.8→23.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1892 0 30 100 2022
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0211983
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.2572.0032687
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7255260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.30723.55690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.42715320
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2561525
X-RAY DIFFRACTIONr_chiral_restr0.1570.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0221541
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_it2.3481.51302
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.83822072
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.3963681
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it8.324.5613
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.82631983
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Number: 263 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDTypeRms dev position (Å)Weight position
Amedium positional0.590.5
Bmedium positional0.570.5
Cmedium positional0.590.5
Dmedium positional0.690.5
Amedium thermal7.332
Bmedium thermal9.052
Cmedium thermal7.232
Dmedium thermal9.42
LS refinement shellResolution: 1.8→1.901 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.31 132 -
Rwork0.21 2574 -
obs--91.02 %
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)
10.0766-0.1214-0.52011.14880.50791.1771-0.01720.0107-0.0137-0.0187-0.00520.00490.02610.02490.02230.0992-0.0070.03660.0469-0.00160.0448-7.046920.2086-23.9661
20.0032-0.0244-0.1210.06930.14160.29940.0009-0.0303-0.0022-0.011-0.0097-0.01270.02390.00460.00880.0950.00250.04130.0450.00230.0561-13.8361-1.5561-32.9543
30.32450.1052-0.31350.21840.05260.204-0.00310.0160.0304-0.02990.0149-0.0128-0.0141-0.0391-0.01180.0931-0.00110.0380.05180.00330.0526-2.0274-5.0702-12.2658
4-0.07530.1927-0.03850.2185-0.13850.08870.01350.01380.02160.03160.0170.02960.00420.0193-0.03050.1026-0.00170.04090.04630.00380.05620.09159.4864-3.3522
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 67
2X-RAY DIFFRACTION2B3 - 67
3X-RAY DIFFRACTION3C3 - 67
4X-RAY DIFFRACTION4D3 - 67

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