[English] 日本語
Yorodumi
- PDB-2y32: Crystal structure of bradavidin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2y32
TitleCrystal structure of bradavidin
ComponentsBLR5658 PROTEIN
KeywordsBIOTIN-BINDING PROTEIN
Function / homology
Function and homology information


biotin binding / extracellular region
Similarity search - Function
Avidin-like / Avidin/streptavidin / Avidin-like superfamily / Avidin family / Avidin-like domain profile. / Lipocalin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesBRADYRHIZOBIUM JAPONICUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsLeppiniemi, J. / Gronroos, T. / Johnson, M.S. / Kulomaa, M.S. / Hytonen, V.P. / Airenne, T.T.
CitationJournal: Plos One / Year: 2012
Title: Structure of Bradavidin - C-Terminal Residues Act as Intrinsic Ligands.
Authors: Leppiniemi, J. / Gronroos, T. / Maatta, J.A.E. / Johnson, M.S. / Kulomaa, M.S. / Hytonen, V.P. / Airenne, T.T.
History
DepositionDec 17, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2012Group: Other
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN -5-STRANDED BARREL THIS IS REPRESENTED BY A -4-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: BLR5658 PROTEIN
B: BLR5658 PROTEIN
C: BLR5658 PROTEIN
D: BLR5658 PROTEIN


Theoretical massNumber of molelcules
Total (without water)57,5674
Polymers57,5674
Non-polymers00
Water12,250680
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14040 Å2
ΔGint-97 kcal/mol
Surface area19950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.712, 84.868, 120.260
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.96559, -0.2395, -0.1014), (-0.23829, 0.65851, 0.71385), (-0.10419, 0.71345, -0.69292)103.42558, -19.51832, 80.25967
2given(0.91894, 0.10573, 0.37995), (0.10232, -0.99432, 0.02922), (0.38088, 0.01202, -0.92454)-13.49884, -1.16503, 68.3793
3given(-0.94468, 0.12473, -0.30335), (0.14774, -0.66389, -0.73309), (-0.29283, -0.73736, 0.60873)110.60921, 30.35186, 34.37062
4given(-0.95147, 0.13351, -0.27726), (0.11901, -0.67122, -0.73164), (-0.28378, -0.72914, 0.62276)109.76263, 31.62576, 33.18629
5given(0.90724, 0.11422, 0.4048), (0.11455, -0.99314, 0.0235), (0.4047, 0.02504, -0.9141)-14.06161, -1.57557, 66.61932
6given(-0.96454, -0.23421, -0.12168), (-0.25014, 0.66408, 0.70458), (-0.08421, 0.71003, -0.69912)104.30981, -18.65276, 79.51627

-
Components

#1: Protein
BLR5658 PROTEIN / BRADAVIDIN


Mass: 14391.656 Da / Num. of mol.: 4 / Fragment: RESIDUES 26-163
Source method: isolated from a genetically manipulated source
Details: AUTHORS REPORT RESIDUES 1-25 ARE A SIGNAL PEPTIDE THAT IS ABSENT IN CRYSTALLIZED FORM
Source: (gene. exp.) BRADYRHIZOBIUM JAPONICUM (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q89IH6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 680 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1-25 CORRESPOND TO A SIGNAL PEPTIDE THAT IS ASSUMED TO BE ABSENT FROM THE CRYSTALLIZED PROTEIN.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41 % / Description: HOMOLOGY MODELS WERE CREATED USING MODELLER.
Crystal growMethod: vapor diffusion, sitting drop
Details: 0.7 MICROLITER OF WELL SOLUTION CONTAINING 25% PEG 4000, 0.17 M AMMONIUM ACETATE, AND 0.08 M SODIUM ACETATE, PH 4.6 WERE MIXED WITH 0.8 MICROLITER OF PROTEIN SOLUTION CONTAINING 0.4 MG PER ...Details: 0.7 MICROLITER OF WELL SOLUTION CONTAINING 25% PEG 4000, 0.17 M AMMONIUM ACETATE, AND 0.08 M SODIUM ACETATE, PH 4.6 WERE MIXED WITH 0.8 MICROLITER OF PROTEIN SOLUTION CONTAINING 0.4 MG PER ML OF PROTEIN, 50 MM SODIUM ACETATE, PH 4. THE PROTEIN SOLUTION WAS DILUTED WITH SATURATED SOLUTION OF 4-HYDROXYAZOBENZENE-2-CARBOXYLIC ACID IN 1 TO 10 VOLUME RATIO BEFORE CRYSTALLIZATION, WHICH WAS AT RT USING THE VAPOUR DIFFUSION METHOD AND SITTING DROPS.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04192
DetectorType: MARRESEARCH SX-165 / Detector: CCD / Date: Jun 7, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04192 Å / Relative weight: 1
ReflectionResolution: 1.78→25 Å / Num. obs: 46670 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 18
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 5.9 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AN ENSEMBLE OF THREE HOMOLOGY MODELS OF BRADAVIDIN BASED ON PDB ENTRIES 1AVD, 1MK5, AND 2UYW.

1avd

1mk5

2uyw


Resolution: 1.78→28.64 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.123 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.109 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.18243 2365 5.1 %RANDOM
Rwork0.1444 ---
obs0.14639 44303 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.011 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2--0.18 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 1.78→28.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4034 0 0 680 4714
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0214230
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.9015814
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9045591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.52326.121165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.22115610
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1120.2667
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023232
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_it0.761.52743
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.34624383
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.14231487
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1594.51408
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: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 167 -
Rwork0.182 3208 -
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)
11.12510.1887-0.19510.6579-0.35731.01660.01220.02350.07440.00850.02210.0701-0.0145-0.1151-0.03430.07150.0007-0.00450.05210.00940.077239.003-2.31354.971
20.87850.2107-0.11470.7988-0.34531.5088-0.01570.04820.0334-0.0831-0.0501-0.1481-0.10940.21990.06570.1049-0.0202-0.00440.09060.03450.105660.5888.99936.582
30.68460.08770.08320.8069-0.46521.2917-0.03470.08770.0446-0.12550.03490.07610.0244-0.1085-0.00010.1003-0.011-0.0170.07720.01770.086842.855.85232.114
40.8739-0.01380.05840.9148-0.35261.1962-0.0046-0.03050.01950.0651-0.0312-0.06160.00480.09370.03580.0588-0.0024-0.00110.04690.0120.072157.138-3.11758.404
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 150
2X-RAY DIFFRACTION2B1 - 150
3X-RAY DIFFRACTION3C1 - 150
4X-RAY DIFFRACTION4D1 - 150

+
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