[English] 日本語
Yorodumi
- PDB-1a7h: GAMMA S CRYSTALLIN C-TERMINAL DOMAIN -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1a7h
TitleGAMMA S CRYSTALLIN C-TERMINAL DOMAIN
ComponentsGAMMAS CRYSTALLIN
KeywordsEYE-LENS PROTEIN / GAMMA CRYSTALLIN S / EYE LENS PROTEIN / MULTIGENE FAMILY
Function / homology
Function and homology information


structural constituent of eye lens / lens development in camera-type eye / visual perception / morphogenesis of an epithelium
Similarity search - Function
Crystallins / Gamma-B Crystallin; domain 1 / Beta/Gamma crystallin / Crystallins beta and gamma 'Greek key' motif profile. / Beta/gamma crystallins / Beta/gamma crystallin / Gamma-crystallin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsBasak, A.K. / Slingsby, C.
CitationJournal: Protein Eng. / Year: 1998
Title: The C-terminal domains of gammaS-crystallin pair about a distorted twofold axis.
Authors: Basak, A.K. / Kroone, R.C. / Lubsen, N.H. / Naylor, C.E. / Jaenicke, R. / Slingsby, C.
History
DepositionMar 13, 1998Processing site: BNL
Revision 1.0May 27, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Refinement description / Category: database_2 / software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: GAMMAS CRYSTALLIN
B: GAMMAS CRYSTALLIN


Theoretical massNumber of molelcules
Total (without water)20,6402
Polymers20,6402
Non-polymers00
Water90150
1
A: GAMMAS CRYSTALLIN


Theoretical massNumber of molelcules
Total (without water)10,3201
Polymers10,3201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GAMMAS CRYSTALLIN


Theoretical massNumber of molelcules
Total (without water)10,3201
Polymers10,3201
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.250, 62.250, 170.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.35584, -0.08497, -0.93068), (-0.60532, -0.73777, 0.2988), (-0.71202, 0.66968, 0.21109)
Vector: 103.14307, 54.72361, 51.32024)
DetailsTHE PROTEIN IN THE CRYSTAL LATTICE IS A DIMER. IN DILUTE SOLUTION IT IS A MONOMER. THERE IS NO NATURALLY OCCURRING BIOLOGICAL EQUIVALENT.

-
Components

#1: Protein GAMMAS CRYSTALLIN


Mass: 10319.770 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN / Mutation: Q87M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Cell line: BL21 / Gene: CRYGS / Organ: EYE / Organelle: EYE-LENS / Plasmid: BL21 / Gene (production host): CRYGS / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P06504
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 43 % / Description: TAKEN FROM WHOLE STRUCTURE.
Crystal growpH: 5
Details: PROTEIN CONCENTRATION 5MGS/ML. 0.1M NA-CITRATE, PH 5.0, 20-22%(W/V) PEG8K, 2% 1,4-DIOXANE, AT ROOM-TEMPERATURE.
Temp details: room temp
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
225 mMMes/NaOH1drop
311 %(w/v)PEG80001reservoir
4Na-citrate1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996 / Details: PLATINUM VERTICAL MIRROR
RadiationMonochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.56→45.64 Å / Num. obs: 6716 / % possible obs: 98.6 % / Redundancy: 5 % / Biso Wilson estimate: 17.84 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 14.7
Reflection shellResolution: 2.56→2.65 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.058 / Mean I/σ(I) obs: 11.5 / % possible all: 97.9
Reflection
*PLUS
Num. measured all: 33311
Reflection shell
*PLUS
% possible obs: 97.9 %

-
Processing

Software
NameVersionClassification
AMoREphasing
X-PLORrefinement
DENZOdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: GAMMA B C-TERMINAL

Resolution: 2.56→30 Å / Isotropic thermal model: RESTRAINED INDIVIDUAL / Cross valid method: THROUGHOUT REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.295 434 6 %RANDOM
Rwork0.208 ---
obs0.208 6709 98.7 %-
Displacement parametersBiso mean: 25.48 Å2
Refine analyzeLuzzati d res low obs: 30 Å / Luzzati sigma a obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.56→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1444 0 0 50 1494
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.68
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.13
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.46
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.571.5
X-RAY DIFFRACTIONx_mcangle_it2.63
X-RAY DIFFRACTIONx_scbond_it4.572.5
X-RAY DIFFRACTIONx_scangle_it2.65
Refine LS restraints NCSNCS model details: RESTRAINED / Rms dev position: 0.406 Å / Weight position: 300
LS refinement shellResolution: 2.56→2.68 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.358 56 7 %
Rwork0.276 738 -
obs--97.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.13
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.46
LS refinement shell
*PLUS
Rfactor obs: 0.276

+
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