[English] 日本語
Yorodumi
- PDB-1v4l: Crystal structure of a platelet agglutination factor isolated fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1v4l
TitleCrystal structure of a platelet agglutination factor isolated from the venom of Taiwan habu (Trimeresurus mucrosquamatus)
Components
  • mucrocetin alpha chain
  • mucrocetin beta chain
KeywordsBLOOD CLOTTING / lectin-like / square-shaped ring
Function / homology
Function and homology information


toxin activity / extracellular region
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 mucrocetin subunit beta / Snaclec mucrocetin subunit alpha
Similarity search - Component
Biological speciesProtobothrops mucrosquamatus (brown spotted pit viper)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHuang, K.-F. / Ko, T.-P. / Wang, A.H.-J.
CitationJournal: Biochem.J. / Year: 2004
Title: Crystal structure of a platelet-agglutinating factor isolated from the venom of Taiwan habu (Trimeresurus mucrosquamatus).
Authors: Huang, K.F. / Ko, T.P. / Hung, C.C. / Chu, J. / Wang, A.H. / Chiou, S.H.
History
DepositionNov 14, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 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
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: mucrocetin alpha chain
B: mucrocetin beta chain
C: mucrocetin alpha chain
D: mucrocetin beta chain
E: mucrocetin alpha chain
F: mucrocetin beta chain


Theoretical massNumber of molelcules
Total (without water)90,9146
Polymers90,9146
Non-polymers00
Water9,656536
1
A: mucrocetin alpha chain
B: mucrocetin beta chain
C: mucrocetin alpha chain
D: mucrocetin beta chain
E: mucrocetin alpha chain
F: mucrocetin beta chain

A: mucrocetin alpha chain
B: mucrocetin beta chain
C: mucrocetin alpha chain
D: mucrocetin beta chain
E: mucrocetin alpha chain
F: mucrocetin beta chain

A: mucrocetin alpha chain
B: mucrocetin beta chain
C: mucrocetin alpha chain
D: mucrocetin beta chain
E: mucrocetin alpha chain
F: mucrocetin beta chain

A: mucrocetin alpha chain
B: mucrocetin beta chain
C: mucrocetin alpha chain
D: mucrocetin beta chain
E: mucrocetin alpha chain
F: mucrocetin beta chain


Theoretical massNumber of molelcules
Total (without water)363,65724
Polymers363,65724
Non-polymers00
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
2
E: mucrocetin alpha chain
F: mucrocetin beta chain


Theoretical massNumber of molelcules
Total (without water)30,3052
Polymers30,3052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-21 kcal/mol
Surface area13040 Å2
MethodPISA
3
A: mucrocetin alpha chain
B: mucrocetin beta chain


Theoretical massNumber of molelcules
Total (without water)30,3052
Polymers30,3052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-21 kcal/mol
Surface area13040 Å2
MethodPISA
4
C: mucrocetin alpha chain
D: mucrocetin beta chain


Theoretical massNumber of molelcules
Total (without water)30,3052
Polymers30,3052
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-22 kcal/mol
Surface area12860 Å2
MethodPISA
5
A: mucrocetin alpha chain
B: mucrocetin beta chain
C: mucrocetin alpha chain
D: mucrocetin beta chain

A: mucrocetin alpha chain
B: mucrocetin beta chain
C: mucrocetin alpha chain
D: mucrocetin beta chain

A: mucrocetin alpha chain
B: mucrocetin beta chain
C: mucrocetin alpha chain
D: mucrocetin beta chain

A: mucrocetin alpha chain
B: mucrocetin beta chain
C: mucrocetin alpha chain
D: mucrocetin beta chain


Theoretical massNumber of molelcules
Total (without water)242,43816
Polymers242,43816
Non-polymers00
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
MethodPQS
6
E: mucrocetin alpha chain
F: mucrocetin beta chain
x 8


Theoretical massNumber of molelcules
Total (without water)242,43816
Polymers242,43816
Non-polymers00
Water28816
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
crystal symmetry operation5_555-x,y,-z1
crystal symmetry operation6_555x,-y,-z1
crystal symmetry operation7_555y,x,-z1
crystal symmetry operation8_555-y,-x,-z1
MethodPQS
Unit cell
Length a, b, c (Å)119.866, 119.866, 360.815
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-519-

HOH

21A-815-

HOH

31C-912-

HOH

41D-915-

HOH

51E-982-

HOH

61F-562-

HOH

71F-744-

HOH

DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit

-
Components

#1: Protein mucrocetin alpha chain


Mass: 15745.479 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Protobothrops mucrosquamatus (brown spotted pit viper)
Secretion: snake venom / References: UniProt: Q6TPH0
#2: Protein mucrocetin beta chain


Mass: 14559.232 Da / Num. of mol.: 3 / Source method: isolated from a natural source
Source: (natural) Protobothrops mucrosquamatus (brown spotted pit viper)
Secretion: snake venom / References: UniProt: Q6TPG9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 536 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.32 Å3/Da / Density % sol: 62.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 1,6-hexanediol, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
152.3 mg/mlprotein1drop
22.5 M1,6-hexanediol1reservoir
30.1 Msodium citrate1reservoirpH5.6

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL17B2 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 25, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 32858 / Num. obs: 30509 / % possible obs: 92.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.5
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2971 / % possible all: 92.3
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 127650 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 92.33 % / Num. unique obs: 2971 / Num. measured obs: 12356

-
Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1C3A

1c3a


Resolution: 2.8→18 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1465 -random
Rwork0.235 ---
all-29524 --
obs-28059 85.4 %-
Refine analyzeLuzzati coordinate error obs: 0.42 Å / Luzzati sigma a obs: 0.57 Å
Refinement stepCycle: LAST / Resolution: 2.8→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6381 0 0 536 6917
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.68
LS refinement shellResolution: 2.8→2.9 Å
RfactorNum. reflection
Rfree0.385 105
Rwork0.357 -
obs-1865
Refinement
*PLUS
Lowest resolution: 18 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.294
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
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