[English] 日本語
Yorodumi
- PDB-7yzu: Crystal structure of the sulfoquinovosyl binding protein SmoF com... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yzu
TitleCrystal structure of the sulfoquinovosyl binding protein SmoF complexed with SQMe
ComponentsSulfoquinovosyl binding protein
KeywordsSUGAR BINDING PROTEIN / agrobacterium / sulfoquinovose / SmoF
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / periplasmic space / Chem-DO7 / Maltose-binding periplasmic protein
Function and homology information
Biological speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å
AuthorsSnow, A.J.D. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Leverhulme TrustRPG-2017-190 United Kingdom
CitationJournal: Curr Res Struct Biol / Year: 2022
Title: The sulfoquinovosyl glycerol binding protein SmoF binds and accommodates plant sulfolipids.
Authors: Snow, A.J.D. / Sharma, M. / Lingford, J.P. / Zhang, Y. / Mui, J.W. / Epa, R. / Goddard-Borger, E.D. / Williams, S.J. / Davies, G.J.
History
DepositionFeb 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sulfoquinovosyl binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,3332
Polymers44,0751
Non-polymers2581
Water5,386299
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.270, 99.380, 53.760
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Sulfoquinovosyl binding protein / Maltose-binding periplasmic protein


Mass: 44074.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: SY94_3278 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A083ZKV5
#2: Chemical ChemComp-DO7 / [(2S,3S,4S,5R,6S)-6-methoxy-3,4,5-tris(oxidanyl)oxan-2-yl]methanesulfonic acid / Methylsulfoquinovoside


Mass: 258.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H14O8S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.75 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.3 M sodium acetate, 0.1 M BIS-TRIS (pH 5.5) and 35% PEG 2000 MME

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.59→47.33 Å / Num. obs: 48233 / % possible obs: 99.4 % / Redundancy: 6.9 % / CC1/2: 0.98 / Rmerge(I) obs: 0.28 / Rpim(I) all: 0.148 / Rrim(I) all: 0.302 / Net I/σ(I): 7.7
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsCC1/2Diffraction-ID
1.59-1.625.622700.6791
8.71-47.286.9482330.981

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 70FY

70fy


Resolution: 1.59→47.33 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.915 / SU B: 3.66 / SU ML: 0.119 / Cross valid method: FREE R-VALUE / ESU R: 0.121 / ESU R Free: 0.115
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2669 2429 5.042 %
Rwork0.2377 45750 -
all0.239 --
obs-48179 99.234 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.698 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å20 Å2
2--2.683 Å2-0 Å2
3----1.833 Å2
Refinement stepCycle: LAST / Resolution: 1.59→47.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2915 0 16 299 3230
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0132994
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162805
X-RAY DIFFRACTIONr_angle_refined_deg1.5071.6414073
X-RAY DIFFRACTIONr_angle_other_deg1.3831.5826469
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4225380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.25924.375128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22715488
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.047158
X-RAY DIFFRACTIONr_chiral_restr0.0760.2399
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023377
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02647
X-RAY DIFFRACTIONr_nbd_refined0.2140.2670
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.22637
X-RAY DIFFRACTIONr_nbtor_refined0.1670.21497
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21345
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1580.2230
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.10.28
X-RAY DIFFRACTIONr_nbd_other0.190.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1810.214
X-RAY DIFFRACTIONr_mcbond_it1.2651.8861526
X-RAY DIFFRACTIONr_mcbond_other1.2641.8851525
X-RAY DIFFRACTIONr_mcangle_it1.8532.8251904
X-RAY DIFFRACTIONr_mcangle_other1.8532.8261905
X-RAY DIFFRACTIONr_scbond_it1.7842.0291468
X-RAY DIFFRACTIONr_scbond_other1.7842.0281469
X-RAY DIFFRACTIONr_scangle_it2.6112.972169
X-RAY DIFFRACTIONr_scangle_other2.6112.972170
X-RAY DIFFRACTIONr_lrange_it3.91923.1743532
X-RAY DIFFRACTIONr_lrange_other3.79622.9113481
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.59-1.6310.3321870.3583216X-RAY DIFFRACTION96.1028
1.631-1.6750.3491650.3333240X-RAY DIFFRACTION98.2401
1.675-1.7240.3111630.3063135X-RAY DIFFRACTION98.8017
1.724-1.7770.311550.2873080X-RAY DIFFRACTION98.839
1.777-1.8350.31610.2672984X-RAY DIFFRACTION99.3367
1.835-1.90.2871520.2772909X-RAY DIFFRACTION99.7718
1.9-1.9710.2921530.2452774X-RAY DIFFRACTION99.8295
1.971-2.0520.3181560.242710X-RAY DIFFRACTION99.9303
2.052-2.1430.2731260.2222639X-RAY DIFFRACTION100
2.143-2.2480.3171360.2332488X-RAY DIFFRACTION99.8858
2.248-2.3690.271400.2242357X-RAY DIFFRACTION99.92
2.369-2.5130.2621050.2232270X-RAY DIFFRACTION99.9159
2.513-2.6860.2791210.2182118X-RAY DIFFRACTION99.9108
2.686-2.9010.2811030.2291982X-RAY DIFFRACTION99.9042
2.901-3.1780.2591010.2311836X-RAY DIFFRACTION99.8454
3.178-3.5520.228820.2231677X-RAY DIFFRACTION100
3.552-4.1010.189740.2041482X-RAY DIFFRACTION99.4249
4.101-5.0210.248630.2081266X-RAY DIFFRACTION99.0313
5.021-7.0910.217540.251997X-RAY DIFFRACTION99.8101
7.091-47.330.232320.226590X-RAY DIFFRACTION97.9528

+
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