[English] 日本語
Yorodumi
- PDB-7ylt: Structure of a bacteria protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ylt
TitleStructure of a bacteria protein
ComponentsPutative ABC transporter, substrate-binding protein
KeywordsMETAL BINDING PROTEIN / a bacteria protein / TRANSPORT PROTEIN
Function / homologyLeucine-binding protein domain / Periplasmic binding protein / Periplasmic binding protein-like I / Putative ABC transporter, substrate-binding protein
Function and homology information
Biological speciesVariovorax paradoxus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhang, H. / Ma, Y.J. / Yu, G.M. / Li, X.Z.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: To Be Published
Title: Structure of a bacteria protein
Authors: Zhang, H. / Ma, Y.J. / Yu, G.M. / Li, X.Z.
History
DepositionJul 26, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Putative ABC transporter, substrate-binding protein
D: Putative ABC transporter, substrate-binding protein
C: Putative ABC transporter, substrate-binding protein
A: Putative ABC transporter, substrate-binding protein


Theoretical massNumber of molelcules
Total (without water)153,5044
Polymers153,5044
Non-polymers00
Water9,404522
1
B: Putative ABC transporter, substrate-binding protein


Theoretical massNumber of molelcules
Total (without water)38,3761
Polymers38,3761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Putative ABC transporter, substrate-binding protein


Theoretical massNumber of molelcules
Total (without water)38,3761
Polymers38,3761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative ABC transporter, substrate-binding protein


Theoretical massNumber of molelcules
Total (without water)38,3761
Polymers38,3761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
A: Putative ABC transporter, substrate-binding protein


Theoretical massNumber of molelcules
Total (without water)38,3761
Polymers38,3761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.775, 75.745, 119.706
Angle α, β, γ (deg.)85.600, 89.160, 89.370
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

#1: Protein
Putative ABC transporter, substrate-binding protein


Mass: 38375.887 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variovorax paradoxus (bacteria) / Gene: VAPA_1c15920 / Production host: Escherichia coli (E. coli) / References: UniProt: T1X8R6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 522 / 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: 2.16 Å3/Da / Density % sol: 43.12 %
Crystal growTemperature: 291.15 K / Method: liquid diffusion
Details: Polyethylene glycol 3350, Tris, Cobalt(II) chloride hexahydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→48.67 Å / Num. obs: 52101 / % possible obs: 90.99 % / Redundancy: 3.6 % / Biso Wilson estimate: 24.67 Å2 / CC1/2: 0.998 / Net I/σ(I): 9.78
Reflection shellResolution: 2.3→2.382 Å / Num. unique obs: 4716 / CC1/2: 0.968

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
autoPROCdata reduction
autoPROCdata scaling
PHENIX1.20_4459phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold2

Resolution: 2.3→48.67 Å / SU ML: 0.2522 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 23.9203
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2275 2588 4.98 %
Rwork0.1863 49422 -
obs0.1883 52010 91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.07 Å2
Refinement stepCycle: LAST / Resolution: 2.3→48.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10737 0 0 522 11259
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003310948
X-RAY DIFFRACTIONf_angle_d0.640714878
X-RAY DIFFRACTIONf_chiral_restr0.0431712
X-RAY DIFFRACTIONf_plane_restr0.00741923
X-RAY DIFFRACTIONf_dihedral_angle_d5.05991558
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.28661380.22822556X-RAY DIFFRACTION86.9
2.34-2.390.23171270.21552395X-RAY DIFFRACTION79.46
2.39-2.440.28321430.22212815X-RAY DIFFRACTION90.43
2.44-2.50.26321400.21632801X-RAY DIFFRACTION94.87
2.5-2.560.28871360.20782860X-RAY DIFFRACTION94.6
2.56-2.630.27171630.20762879X-RAY DIFFRACTION94.15
2.63-2.710.24851490.20822778X-RAY DIFFRACTION93.51
2.71-2.80.27661450.21552841X-RAY DIFFRACTION92.91
2.8-2.90.27181470.21962770X-RAY DIFFRACTION92.63
2.9-3.010.25051560.21122753X-RAY DIFFRACTION91.54
3.01-3.150.23051160.20232731X-RAY DIFFRACTION89.84
3.15-3.320.21631680.20132668X-RAY DIFFRACTION88.05
3.32-3.520.2471430.19392410X-RAY DIFFRACTION81.67
3.52-3.80.2161560.17372896X-RAY DIFFRACTION95.46
3.8-4.180.23541530.16642891X-RAY DIFFRACTION95.21
4.18-4.780.16971550.14522830X-RAY DIFFRACTION94.73
4.78-6.020.1791360.16292793X-RAY DIFFRACTION91.39
6.02-48.670.18121170.15672755X-RAY DIFFRACTION90.69
Refinement TLS params.Method: refined / Origin x: 13.0277649281 Å / Origin y: 19.8693634351 Å / Origin z: 3.99097172731 Å
111213212223313233
T0.172065132666 Å20.0171998283761 Å20.0221988045065 Å2-0.187131139227 Å20.0164022506875 Å2--0.27591606755 Å2
L0.0726721197599 °20.0445585111703 °2-0.0372379244475 °2-0.204235802931 °2-0.0506081647089 °2--0.134093321962 °2
S0.0153659636075 Å °0.00315607180232 Å °0.0151504507911 Å °0.0122058863975 Å °-0.0289886908251 Å °0.0287673644006 Å °-0.0193582669947 Å °0.0195327298091 Å °0.0117521797452 Å °
Refinement TLS groupSelection details: all

+
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