[English] 日本語
Yorodumi
- PDB-4zqy: Ringhalexin from hemachatus haemachatus: A novel inhibitor of ext... -

+
Open data


ID or keywords:

Loading...

-
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


venom-mediated suppression of blood coagulation / toxin activity / extracellular region
Similarity search - Function
Snake toxin and toxin-like protein / Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more