[English] 日本語
Yorodumi
- PDB-1oki: Crystal structure of truncated human beta-B1-crystallin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1oki
TitleCrystal structure of truncated human beta-B1-crystallin
ComponentsBETA CRYSTALLIN B1
KeywordsEYE LENS PROTEIN / CRYSTALLIN / CATARACT
Function / homology
Function and homology information


structural constituent of eye lens / lens development in camera-type eye / visual perception
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 speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
Authorsvan Montfort, R.L.M. / Bateman, O.A. / Lubsen, N.H. / Slingsby, C.
CitationJournal: Protein Sci. / Year: 2003
Title: Crystal Structure of Truncated Human Beta-B1-Crystallin
Authors: Van Montfort, R.L.M. / Bateman, O.A. / Lubsen, N.H. / Slingsby, C.
History
DepositionJul 25, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 22, 2004Provider: repository / Type: Initial release
Revision 1.1Nov 5, 2014Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Mar 28, 2018Group: Source and taxonomy / Structure summary / Category: audit_author / entity_src_gen
Item: _audit_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id ..._audit_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.3Dec 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.pdbx_leaving_atom_flag
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BETA CRYSTALLIN B1
B: BETA CRYSTALLIN B1


Theoretical massNumber of molelcules
Total (without water)48,5042
Polymers48,5042
Non-polymers00
Water7,620423
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)45.040, 45.040, 171.111
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.0001, -1, -0.0003), (-1, 0.0001, 0.0001), (-0.0001, 0.0003, -1)
Vector: 67.5623, 67.5594, 12.9483)

-
Components

#1: Protein BETA CRYSTALLIN B1


Mass: 24252.088 Da / Num. of mol.: 2 / Fragment: CRYSTALLIN DOMAINS, RESIDUES 42-251
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: EYE LENS / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P53674
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCRYSTALLINS FORM THE DOMINANT STRUCTURAL COMPONENTS OF THE VERTEBRATE EYE LENS. THE PROTEIN EXISTS ...CRYSTALLINS FORM THE DOMINANT STRUCTURAL COMPONENTS OF THE VERTEBRATE EYE LENS. THE PROTEIN EXISTS AS DIMERIC OR HIGHER OLIGOMERIC FORMS.
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.8 Å3/Da / Density % sol: 31 %
Crystal growpH: 8.5
Details: 24-30% PEG4000, 0.1M TRIS/HCL PH 7.0-8.5, 0.2M MGCL2
Crystal grow
*PLUS
pH: 8 / Method: batch method / Details: Bateman, O.A., (2001) Exp. Eye Res., 73, 321.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
125 mMTris-HCl11pH8.0
21 mMdithiothreitol11
310 mg/mlprotein11

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: MARRESEARCH / Detector: CCD
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.4→35 Å / Num. obs: 60531 / % possible obs: 85.6 % / Redundancy: 2 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 8.9
Reflection
*PLUS
Highest resolution: 1.4 Å / Num. measured all: 315295 / Rmerge(I) obs: 0.043

-
Processing

Software
NameVersionClassification
REFMAC5.1.29refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BB2

2bb2


Resolution: 1.4→45.17 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.26 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.075 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INITIAL DATASET PROCESSED IN P43212. TYR130 AT THE CRYSTALLOGRAPHIC TWOFOLD CLASHED WITH TYR130 OF A SYMMETRY RELATED MOLECULE. AS MOLECULE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. INITIAL DATASET PROCESSED IN P43212. TYR130 AT THE CRYSTALLOGRAPHIC TWOFOLD CLASHED WITH TYR130 OF A SYMMETRY RELATED MOLECULE. AS MOLECULE IS A DIMER IN SOLULTION, LOWERED SPACE GROUP TO P43 WITH TWOFOLD NCS SYMMETRY. TYR130 POSSIBLY IN TWO CONFORMATIONS. PRIMARY CONFORMATION MODELLED.
RfactorNum. reflection% reflectionSelection details
Rfree0.201 2902 5 %RANDOM
Rwork0.171 ---
obs0.172 55136 87.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.61 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å20 Å2
2--0.14 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.4→45.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3039 0 0 423 3462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0213154
X-RAY DIFFRACTIONr_bond_other_d0.0020.022711
X-RAY DIFFRACTIONr_angle_refined_deg1.2421.9164255
X-RAY DIFFRACTIONr_angle_other_deg0.78236268
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8525364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.080.2394
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023585
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02788
X-RAY DIFFRACTIONr_nbd_refined0.1780.2501
X-RAY DIFFRACTIONr_nbd_other0.2460.23367
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0860.21884
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2314
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0840.21
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2810.280
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.238
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.55751812
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.49962894
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.72761342
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.177.51361
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
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.281 161
Rwork0.254 3332
Refinement
*PLUS
Highest resolution: 1.4 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.211 / Rfactor Rwork: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.023
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.87

+
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