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- PDB-2vrp: Structure of rhodocytin -

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Basic information

Entry
Database: PDB / ID: 2vrp
TitleStructure of rhodocytin
Components
  • AGGRETIN ALPHA CHAIN
  • AGGRETIN BETA CHAIN
KeywordsSUGAR BINDING PROTEIN / C-TYPE LECTIN-LIKE / SUGAR-BINDING PROTEIN / LECTIN / CLEC-2 / VENOM / AGGRETIN
Function / homology
Function and homology information


regulation of cytokine activity / toxin activity / extracellular region / metal ion binding
Similarity search - Function
: / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily ...: / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Snaclec rhodocytin subunit beta / Snaclec rhodocytin subunit alpha
Similarity search - Component
Biological speciesCALLOSELASMA RHODOSTOMA (Malayan pit viper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsWatson, A.A. / O'Callaghan, C.A.
CitationJournal: Protein Sci. / Year: 2008
Title: Crystal Structure of Rhodocytin, a Ligand for the Platelet-Activating Receptor Clec-2.
Authors: Watson, A.A. / Eble, J.A. / O'Callaghan, C.A.
History
DepositionApr 9, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AGGRETIN ALPHA CHAIN
B: AGGRETIN BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3638
Polymers30,2012
Non-polymers1636
Water79344
1
A: AGGRETIN ALPHA CHAIN
B: AGGRETIN BETA CHAIN
hetero molecules

A: AGGRETIN ALPHA CHAIN
B: AGGRETIN BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,72716
Polymers60,4014
Non-polymers32612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z1
Buried area10650 Å2
ΔGint-61.9 kcal/mol
Surface area28040 Å2
MethodPQS
2
A: AGGRETIN ALPHA CHAIN
B: AGGRETIN BETA CHAIN
hetero molecules

A: AGGRETIN ALPHA CHAIN
B: AGGRETIN BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,72716
Polymers60,4014
Non-polymers32612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)61.933, 89.368, 120.996
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A1 - 132
2115B1 - 132

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Components

#1: Protein AGGRETIN ALPHA CHAIN / RHODOCYTIN


Mass: 15812.376 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) CALLOSELASMA RHODOSTOMA (Malayan pit viper)
References: UniProt: Q9I841
#2: Protein AGGRETIN BETA CHAIN / RHODOCYTIN


Mass: 14388.200 Da / Num. of mol.: 1 / Fragment: RESIDUES 24-146 / Source method: isolated from a natural source
Source: (natural) CALLOSELASMA RHODOSTOMA (Malayan pit viper)
References: UniProt: Q9I840
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 44 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsFIRST THREE RESIDUES OF THE Q9I840 SEQUENCE OF CHAIN A ARE ABSENT FROM THE STRUCTURE. FIRST TWENTY- ...FIRST THREE RESIDUES OF THE Q9I840 SEQUENCE OF CHAIN A ARE ABSENT FROM THE STRUCTURE. FIRST TWENTY-THREE RESIDUES OF THE Q9I841 SEQUENCE OF CHAIN B ARE ABSENT FROM THE STRUCTURE, BECAUSE THESE RESIDUES ARE ABSENT FROM THE NATIVE PROTEIN (AS DETERMINED BY N-TERMINAL SEQUENCING, PMID 11728470)

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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: 2.77 Å3/Da / Density % sol: 55.65 % / Description: NONE
Crystal growpH: 8 / Details: 2M AMMONIUM SULPHATE, 5% 2-PROPANOL, pH 8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.9762
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 8, 2007 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 13367 / % possible obs: 94.7 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 37.75
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 7.05 / % possible all: 80.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: COMPOSITE MODEL CONSISTING OF PDB ENTRY 1IOD, PDB ENTRY 1J34, PDB ENTRY 1C3A, PDB ENTRY 1UMR

1iod

1j34

1c3a

1umr


Resolution: 2.41→36.76 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.89 / SU B: 26.314 / SU ML: 0.272 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.396 / ESU R Free: 0.287 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.272 618 4.9 %RANDOM
Rwork0.201 ---
obs0.204 12040 94.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.1 Å20 Å20 Å2
2--0.56 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 2.41→36.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2101 0 6 44 2151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212173
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9161.92947
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.8225254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.54724.746118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.43615353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.569158
X-RAY DIFFRACTIONr_chiral_restr0.1430.2284
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021709
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2440.2987
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21405
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1780.289
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2940.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2730.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8721.51273
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.70422030
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1613978
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.4384.5917
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
120medium positional1.150.5
136loose positional1.865
120medium thermal1.462
136loose thermal2.2310
LS refinement shellResolution: 2.41→2.47 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.371 44
Rwork0.3 698
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)
10.9940.160.59471.88650.58946.8846-0.06360.0693-0.05160.03130.12290.11850.08420.0554-0.0593-0.053-0.0226-0.03280.0210.00830.089719.035-13.273-6.2032
20.37160.1333-0.25661.694-1.20288.22920.0773-0.0501-0.11210.3717-0.0515-0.1382-0.0406-0.2186-0.0258-0.0055-0.02070.0612-0.0021-0.0060.102618.1874-12.463922.6175
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 133
2X-RAY DIFFRACTION2B1 - 123

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