[English] 日本語
Yorodumi
- PDB-3ph6: Bovine beta lactoglobulin crytsallized through ligandation of yttrium -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3ph6
TitleBovine beta lactoglobulin crytsallized through ligandation of yttrium
ComponentsBeta-lactoglobulin
KeywordsTRANSPORT PROTEIN
Function / homology
Function and homology information


retinol binding / long-chain fatty acid binding / extracellular region / identical protein binding
Similarity search - Function
Beta-lactoglobulin / Lipocalin / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin/cytosolic fatty-acid binding domain / Lipocalin / cytosolic fatty-acid binding protein family / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
YTTRIUM (III) ION / Beta-lactoglobulin
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.53 Å
AuthorsZocher, G. / Stehle, T.
CitationJournal: J.Appl.Crystallogr. / Year: 2011
Title: Novel Approach to Protein Crystallization through Ligandation of Yttrium Cations
Authors: Zhang, F. / Zocher, G. / Sauter, A. / Stehle, T. / Schreiber, F.
History
DepositionNov 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jan 15, 2020Group: Data collection / Category: reflns / reflns_shell
Item: _reflns.number_all / _reflns.number_obs ..._reflns.number_all / _reflns.number_obs / _reflns.pdbx_Rmerge_I_obs / _reflns.pdbx_redundancy / _reflns_shell.Rmerge_I_obs / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_redundancy
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-lactoglobulin
B: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,8038
Polymers36,3762
Non-polymers4276
Water77543
1
A: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4375
Polymers18,1881
Non-polymers2494
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Beta-lactoglobulin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3663
Polymers18,1881
Non-polymers1782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.060, 63.710, 134.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Beta-lactoglobulin / Beta-LG


Mass: 18188.018 Da / Num. of mol.: 2 / Fragment: unp residues 18-178
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / References: UniProt: P02754
#2: Chemical
ChemComp-YT3 / YTTRIUM (III) ION


Mass: 88.906 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Y
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 277 K / Method: batch crystallization / pH: 7
Details: 0.3 mM Yttrium, pH 7, Batch crystallization, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 24, 2009
RadiationMonochromator: copper / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.52→20 Å / Num. obs: 21458 / % possible obs: 95 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.7 % / Biso Wilson estimate: 42.4 Å2 / Rmerge(I) obs: 0.097 / Net I/σ(I): 17
Reflection shellResolution: 2.52→2.58 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 3 / Num. unique obs: 1522 / % possible all: 92.4

-
Processing

Software
NameVersionClassification
REFMAC5.5.0110refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.53→19.64 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.892 / SU B: 27.422 / SU ML: 0.273 / Cross valid method: THROUGHOUT / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2652 234 2 %RANDOM
Rwork0.21623 ---
obs0.21722 11428 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.942 Å2
Baniso -1Baniso -2Baniso -3
1-6.44 Å2-0 Å2-0 Å2
2---4.23 Å20 Å2
3----2.22 Å2
Refinement stepCycle: LAST / Resolution: 2.53→19.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2456 0 6 43 2505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222502
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0231.9933400
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1695315
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.5426.538104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.51415453
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.224156
X-RAY DIFFRACTIONr_chiral_restr0.0650.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211842
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.38531593
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.67332566
X-RAY DIFFRACTIONr_scbond_it0.5944909
X-RAY DIFFRACTIONr_scangle_it0.8894834
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.529→2.594 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 16 -
Rwork0.259 771 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.4925-0.30441.2054.9410.74066.5746-0.00580.1097-0.2647-0.3607-0.0184-0.13930.28230.03820.02420.11920.01960.03490.1285-0.01010.1453-0.6053-2.7291-24.0716
22.81781.73311.47165.0503-0.2116.78530.1236-0.1769-0.02550.6386-0.0673-0.2527-0.15930.0949-0.05630.20480.0098-0.04570.1512-0.00830.22127.69962.33495.2258
31.5112-1.31751.8911.2515-2.0574.8387-0.11060.0801-0.19340.1205-0.0591-0.00440.1522-0.26740.16970.5387-0.0743-0.07320.2405-0.11770.53132.4155-1.7892-20.4311
40.44340.94760.83442.35470.66195.58860.0709-0.0211-0.03070.0535-0.0558-0.10210.1848-0.0743-0.01510.03460.05710.02630.15330.00290.2422.8312-0.2258-13.603
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 178
2X-RAY DIFFRACTION2B23 - 178
3X-RAY DIFFRACTION3A1 - 6
4X-RAY DIFFRACTION4A - B1 - 195

+
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