[English] 日本語
Yorodumi
- PDB-6o1t: BOVINE SALIVARY PROTEIN FORM 30B WITH OLEIC ACID -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6o1t
TitleBOVINE SALIVARY PROTEIN FORM 30B WITH OLEIC ACID
ComponentsShort palate, lung and nasal epithelium carcinoma-associated protein 2B
KeywordsLIPID BINDING PROTEIN / HYDROPHOBIC CHANNEL
Function / homologyLipid-binding serum glycoprotein, N-terminal / Bactericidal permeability-increasing protein, alpha/beta domain superfamily / LBP / BPI / CETP family, N-terminal domain / secretory granule / lipopolysaccharide binding / extracellular region / OLEIC ACID / Short palate, lung and nasal epithelium carcinoma-associated protein 2B
Function and homology information
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhang, H. / Arcus, V.L.
CitationJournal: Plos One / Year: 2019
Title: The three dimensional structure of Bovine Salivary Protein 30b (BSP30b) and its interaction with specific rumen bacteria.
Authors: Zhang, H. / Burrows, J. / Card, G.L. / Attwood, G. / Wheeler, T.T. / Arcus, V.L.
History
DepositionFeb 21, 2019Deposition site: RCSB / Processing site: RCSB
SupersessionMar 13, 2019ID: 6MSZ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 25, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Short palate, lung and nasal epithelium carcinoma-associated protein 2B
B: Short palate, lung and nasal epithelium carcinoma-associated protein 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2897
Polymers44,6042
Non-polymers6855
Water91951
1
A: Short palate, lung and nasal epithelium carcinoma-associated protein 2B
hetero molecules

B: Short palate, lung and nasal epithelium carcinoma-associated protein 2B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2897
Polymers44,6042
Non-polymers6855
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455x-1/2,y+1/2,z1
Buried area2960 Å2
ΔGint-25 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.750, 61.400, 91.090
Angle α, β, γ (deg.)90.00, 107.74, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Short palate, lung and nasal epithelium carcinoma-associated protein 2B / BSP30b / Common salivary protein form b


Mass: 22302.133 Da / Num. of mol.: 2 / Mutation: F52M, F106M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: SPLUNC2B, BSP30B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P79125
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-OLA / OLEIC ACID / Oleic acid


Mass: 282.461 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H34O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.66 Å3/Da / Density % sol: 53.81 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES PH 7.5, 0.2M CALCIUM CHLORIDE, 9% PEG 3350, 5% ISOPROPYL ALCOHOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.15K

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 1, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.3→86.76 Å / Num. obs: 19718 / % possible obs: 99.8 % / Redundancy: 5.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.027 / Rrim(I) all: 0.068 / Net I/σ(I): 15
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.241 / Num. unique obs: 1940 / CC1/2: 0.985 / Rpim(I) all: 0.113 / Rrim(I) all: 0.267 / % possible all: 99.6

-
Processing

Software
NameClassification
REFMACrefinement
iMOSFLMdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WD6

5wd6


Resolution: 2.3→48.7 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.935 / SU B: 20.376 / SU ML: 0.228 / Cross valid method: THROUGHOUT / ESU R: 0.355 / ESU R Free: 0.25
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26505 980 5 %RANDOM
Rwork0.22311 ---
obs0.22525 18652 99.32 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å
Displacement parametersBiso mean: 69.715 Å2
Baniso -1Baniso -2Baniso -3
1--2.7 Å2-0 Å2-0.95 Å2
2--5.16 Å2-0 Å2
3----1.54 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2930 0 43 51 3024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132990
X-RAY DIFFRACTIONr_bond_other_d0.0030.0172926
X-RAY DIFFRACTIONr_angle_refined_deg1.4071.6364045
X-RAY DIFFRACTIONr_angle_other_deg1.2191.5676790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8765373
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.64923.125160
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.17115549
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1781523
X-RAY DIFFRACTIONr_chiral_restr0.0640.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023268
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02545
X-RAY DIFFRACTIONr_mcbond_it1.0372.7921507
X-RAY DIFFRACTIONr_mcbond_other1.032.7911506
X-RAY DIFFRACTIONr_mcangle_it1.734.1761875
X-RAY DIFFRACTIONr_mcangle_other1.7294.1781876
X-RAY DIFFRACTIONr_scbond_it1.3023.1511483
X-RAY DIFFRACTIONr_scbond_other1.3023.1531484
X-RAY DIFFRACTIONr_scangle_other2.1194.592171
X-RAY DIFFRACTIONr_long_range_B_refined7.10834.583093
X-RAY DIFFRACTIONr_long_range_B_other7.10534.4933087
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 82 -
Rwork0.276 1400 -
obs--99.26 %
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)
13.6016-0.01082.0920.9866-0.79437.1820.12460.06860.13630.2449-0.0602-0.18950.65440.6806-0.06440.68620.1151-0.09830.0902-0.04460.096378.25739.41831.284
26.76540.58882.78971.49570.0913.90780.3184-0.3990.01190.1558-0.29140.17690.3463-0.5876-0.0270.5626-0.0073-0.06260.2184-0.1130.113172.37919.77512.359
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A38 - 238
2X-RAY DIFFRACTION2B38 - 237

+
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