[English] 日本語
Yorodumi
- PDB-3zq3: Crystal Structure of Rat Odorant Binding Protein 3 (OBP3) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3zq3
TitleCrystal Structure of Rat Odorant Binding Protein 3 (OBP3)
ComponentsOBP3 PROTEIN
KeywordsODORANT BINDING PROTEIN / LIPOCALIN / ENTHALPY-ENTROPY
Function / homology
Function and homology information


pheromone binding / odorant binding / small molecule binding / extracellular region
Similarity search - Function
Major urinary protein / Lipocalin / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Alpha-2u globulin / Obp3 protein
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPortman, K.L. / Long, J. / Carr, S. / Brand, L. / Winzor, D.J. / Searle, M. / Scott, D.J.
CitationJournal: Biochemistry / Year: 2014
Title: Enthalpy/Entropy Compensation Effects from Cavity Desolvation Underpin Broad Ligand Binding Selectivity for Rat Odorant Binding Protein 3
Authors: Portman, K.L. / Long, J. / Carr, S. / Briand, L. / Winzor, D.J. / Searle, M.S. / Scott, D.J.
History
DepositionMar 5, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Structure summary
Revision 1.2May 7, 2014Group: Database references
Revision 1.3May 14, 2014Group: Database references
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 / struct_ncs_dom_lim
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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: OBP3 PROTEIN
B: OBP3 PROTEIN
C: OBP3 PROTEIN
D: OBP3 PROTEIN


Theoretical massNumber of molelcules
Total (without water)79,7574
Polymers79,7574
Non-polymers00
Water00
1
A: OBP3 PROTEIN


Theoretical massNumber of molelcules
Total (without water)19,9391
Polymers19,9391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: OBP3 PROTEIN


Theoretical massNumber of molelcules
Total (without water)19,9391
Polymers19,9391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: OBP3 PROTEIN


Theoretical massNumber of molelcules
Total (without water)19,9391
Polymers19,9391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: OBP3 PROTEIN


Theoretical massNumber of molelcules
Total (without water)19,9391
Polymers19,9391
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.980, 100.530, 72.410
Angle α, β, γ (deg.)90.00, 110.61, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: GLN / End label comp-ID: GLN / Refine code: _ / Auth seq-ID: 20 - 178 / Label seq-ID: 14 - 172

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

-
Components

#1: Protein
OBP3 PROTEIN / ODORANT BINDING PROTEIN 3 / PROTEIN LOC259244 / RCG31933 / ISOFORM CRA_A / RAT SALIVARY GLAND ...ODORANT BINDING PROTEIN 3 / PROTEIN LOC259244 / RCG31933 / ISOFORM CRA_A / RAT SALIVARY GLAND (ALPHA)2(MU) GLOBULIN / TYPE 1


Mass: 19939.244 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Plasmid: PQE31 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q78E14, UniProt: Q63213*PLUS

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growpH: 6.5
Details: 0.02 M D-GLUCOSE, 0.02 M D-GALACTOSE, 0.02 M L-FUCOSE, 0.02M D-XYLOSE, 0.02M N-ACETYL-D-GLUCOSAMINE, 0.1 M MORPHEUS BUFFER 1 PH 6.5, 10 % W/V POLYETHYLENE GLYCOL, 20 % POLYETHYLENE GLYCOL 550

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2012 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.8→67.8 Å / Num. obs: 19952 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 1.8 % / Biso Wilson estimate: 48.8 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 4.8
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 1.8 / % possible all: 95.1

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
MOSFLMdata reduction
SCALAdata scaling
MrBUMPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2A2U

2a2u


Resolution: 2.8→67.776 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.876 / SU B: 14.313 / SU ML: 0.279 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.376 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1025 5.11 %RANDOM
Rwork0.2176 ---
obs0.219 19938 95.279 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 43.566 Å2
Baniso -1Baniso -2Baniso -3
1--2.367 Å20 Å20.698 Å2
2---0.107 Å20 Å2
3---1.723 Å2
Refinement stepCycle: LAST / Resolution: 2.8→67.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5132 0 0 0 5132
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0195216
X-RAY DIFFRACTIONr_bond_other_d0.0050.024868
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9437020
X-RAY DIFFRACTIONr_angle_other_deg0.9053.00111192
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4235632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.41225.211284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63615952
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8171528
X-RAY DIFFRACTIONr_chiral_restr0.0750.2776
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025960
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021228
X-RAY DIFFRACTIONr_nbd_refined0.1970.2890
X-RAY DIFFRACTIONr_nbd_other0.3580.2137
X-RAY DIFFRACTIONr_nbtor_refined0.1870.22572
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.296
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1070.21
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_it3.2074.1972540
X-RAY DIFFRACTIONr_mcbond_other3.2074.1972539
X-RAY DIFFRACTIONr_mcangle_it5.3436.2863168
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7754.5532676
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.1856.6663852
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
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A99470.04
12B99470.04
21A99860.02
22C99860.02
31A99360.04
32D99360.04
41B99410.05
42C99410.05
51B99730.02
52D99730.02
61C99300.05
62D99300.05
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 63 -
Rwork0.311 1405 -
obs--93.922 %

+
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://pdbjlvh1.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