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- PDB-4zqy: Ringhalexin from hemachatus haemachatus: A novel inhibitor of ext... -

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Basic information

Entry
Database: PDB / ID: 4zqy
TitleRinghalexin from hemachatus haemachatus: A novel inhibitor of extrinsic tenase complex
ComponentsRinghalexin
KeywordsTOXIN / Ringhalexin / three finger toxin / Anticoagulant
Function / homology
Function and homology information


envenomation resulting in negative regulation of blood coagulation in another organism / toxin activity / extracellular region
Similarity search - Function
Snake toxin and toxin-like protein / Snake three-finger toxin / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / CD59 / CD59 / Snake toxin-like superfamily / Ribbon / Mainly Beta
Similarity search - Domain/homology
Biological speciesHemachatus haemachatus (ringhals)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9515 Å
AuthorsJobichen, C. / Sivaraman, J.
CitationJournal: Sci Rep / Year: 2016
Title: Ringhalexin from Hemachatus haemachatus: A novel inhibitor of extrinsic tenase complex.
Authors: Barnwal, B. / Jobichen, C. / Girish, V.M. / Foo, C.S. / Sivaraman, J. / Kini, R.M.
History
DepositionMay 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 11, 2016Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references
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 / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ringhalexin
B: Ringhalexin
C: Ringhalexin


Theoretical massNumber of molelcules
Total (without water)22,3703
Polymers22,3703
Non-polymers00
Water00
1
A: Ringhalexin

A: Ringhalexin


Theoretical massNumber of molelcules
Total (without water)14,9132
Polymers14,9132
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-y+1/2,x+1/2,z+1/41
2
B: Ringhalexin
C: Ringhalexin


Theoretical massNumber of molelcules
Total (without water)14,9132
Polymers14,9132
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.160, 82.160, 82.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Ringhalexin


Mass: 7456.717 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Hemachatus haemachatus (ringhals) / References: UniProt: C0HJT5*PLUS
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.53 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: 29% MPD, 0.1M HEPES

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.9515→15 Å / Num. obs: 6253 / % possible obs: 99.36 % / Redundancy: 8.5 % / Rsym value: 0.122 / Net I/σ(I): 14.7

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
MOSFLMdata reduction
MOSFLMdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2H8U

2h8u


Resolution: 2.9515→15 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.268 286 4.57 %
Rwork0.2174 --
obs0.2197 6253 99.36 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.987 Å2 / ksol: 0.337 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.8172 Å20 Å2-0 Å2
2--0.8172 Å2-0 Å2
3----9.8348 Å2
Refinement stepCycle: LAST / Resolution: 2.9515→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1550 0 0 0 1550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091601
X-RAY DIFFRACTIONf_angle_d1.5992146
X-RAY DIFFRACTIONf_dihedral_angle_d15.043600
X-RAY DIFFRACTIONf_chiral_restr0.062228
X-RAY DIFFRACTIONf_plane_restr0.007276
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9501-3.70810.35531500.25472888X-RAY DIFFRACTION99
3.7081-15.32890.22341360.19973079X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 12.6536 Å / Origin y: 20.794 Å / Origin z: 17.345 Å
111213212223313233
T0.2397 Å20.0122 Å2-0.0371 Å2-0.1549 Å20.048 Å2--0.2518 Å2
L0.7932 °2-1.3624 °2-0.8609 °2-4.2103 °22.8189 °2--2.2127 °2
S-0.0022 Å °-0.0543 Å °-0.3058 Å °0.1494 Å °-0.0409 Å °0.1608 Å °0.3533 Å °-0.022 Å °0.0229 Å °
Refinement TLS groupSelection details: all

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