[English] 日本語
Yorodumi
- PDB-7c6y: Crystal structure of beta-glycosides-binding protein (W41A) of AB... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7c6y
TitleCrystal structure of beta-glycosides-binding protein (W41A) of ABC transporter in an open state (Form II)
ComponentsSugar ABC transporter, periplasmic sugar-binding protein
KeywordsSUGAR BINDING PROTEIN / Conformational dynamics / substrate-binding protein / Induced-fit mechanism / Two-step ligand binding / Venus Fly-trap mechanism
Function / homologyBacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / CARBON DIOXIDE / Sugar ABC transporter, periplasmic sugar-binding protein
Function and homology information
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å
AuthorsKanaujia, S.P. / Chandravanshi, M. / Samanta, R.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology (DBT, India)BT/563/NE/U-Excel/2016 India
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Conformational Trapping of a beta-Glucosides-Binding Protein Unveils the Selective Two-Step Ligand-Binding Mechanism of ABC Importers.
Authors: Chandravanshi, M. / Samanta, R. / Kanaujia, S.P.
History
DepositionMay 22, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Sugar ABC transporter, periplasmic sugar-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3579
Polymers45,9081
Non-polymers4498
Water7,134396
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-12 kcal/mol
Surface area17340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.350, 63.250, 103.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Sugar ABC transporter, periplasmic sugar-binding protein


Mass: 45908.156 Da / Num. of mol.: 1 / Mutation: W41A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Strain: HB8 / Gene: TTHB082 / Plasmid: pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q53W80

-
Non-polymers , 5 types, 404 molecules

#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CO2 / CARBON DIOXIDE / Carbon dioxide


Mass: 44.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 396 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.25 % / Description: Orthorhombic
Crystal growTemperature: 293 K / Method: microbatch / Details: 0.2 M Ammonium sulphate, 40% PEG 8000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 21, 2019 / Details: VariMax HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→54.03 Å / Num. obs: 41739 / % possible obs: 97.2 % / Redundancy: 8.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.026 / Rrim(I) all: 0.079 / Net I/σ(I): 21.3 / Num. measured all: 373282 / Scaling rejects: 283
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.7-1.738.40.351771521000.9390.1260.3725.794.3
9-54.037.40.07226193560.9910.0270.07837.299.8

-
Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation6.01 Å54.03 Å

-
Processing

Software
NameVersionClassification
HKL-30003000data collection
MOSFLM7.2.2data reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
Coot0.8.9.2model building
REFMAC5.8.0258refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7C63

7c63


Resolution: 1.7→54.03 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.94 / SU B: 3.428 / SU ML: 0.06 / SU R Cruickshank DPI: 0.0245 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.024 / ESU R Free: 0.024 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2108 2102 5.1 %RANDOM
Rwork0.1723 ---
obs0.1743 39504 96.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.71 Å2 / Biso mean: 20.702 Å2 / Biso min: 8.16 Å2
Baniso -1Baniso -2Baniso -3
1--0.55 Å20 Å20 Å2
2---2.77 Å2-0 Å2
3---3.32 Å2
Refinement stepCycle: final / Resolution: 1.7→54.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3185 0 23 396 3604
Biso mean--32.74 29.09 -
Num. residues----417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0133357
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173096
X-RAY DIFFRACTIONr_angle_refined_deg2.1281.644579
X-RAY DIFFRACTIONr_angle_other_deg1.6161.5697182
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7125436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57821.89164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.54915523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3261521
X-RAY DIFFRACTIONr_chiral_restr0.1250.2419
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023816
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02735
LS refinement shellResolution: 1.7→1.744 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 169 -
Rwork0.194 2748 -
all-2917 -
obs--94.07 %
Refinement TLS params.Method: refined / Origin x: -23.4598 Å / Origin y: 1.1248 Å / Origin z: -13.5662 Å
111213212223313233
T0.0095 Å20.0038 Å2-0.0046 Å2-0.0027 Å2-0.0005 Å2--0.0114 Å2
L0.4704 °20.0369 °2-0.0731 °2-0.3687 °2-0.0276 °2--0.2948 °2
S-0.0098 Å °0.0124 Å °0.0074 Å °-0.01 Å °-0.0123 Å °-0.009 Å °0.0328 Å °0.014 Å °0.0221 Å °

+
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