[English] 日本語
Yorodumi
- PDB-3qnq: Crystal structure of the transporter ChbC, the IIC component from... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3qnq
TitleCrystal structure of the transporter ChbC, the IIC component from the N,N'-diacetylchitobiose-specific phosphotransferase system
ComponentsPTS system, cellobiose-specific IIC component
Keywordsmembrane protein / transport protein / transporter / Enzyme IIC / phosphoenolpyruvate-sugar phosphotransferase system / Structural Genomics / PSI-Biology / New York Consortium on Membrane Protein Structure / NYCOMPS / hydrolase
Function / homology
Function and homology information


protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / membrane => GO:0016020 / identical protein binding / plasma membrane
Similarity search - Function
Phosphotransferase system, cellobiose-type IIC component / Phosphotransferase system, EIIC component, type 3 / PTS_EIIC type-3 domain profile. / Phosphotransferase system, EIIC / Phosphotransferase system, EIIC
Similarity search - Domain/homology
alpha-maltose / CITRIC ACID / Permease IIC component
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.295 Å
AuthorsCao, Y. / Jin, X. / Huang, H. / Levin, E.J. / Zhou, M. / New York Consortium on Membrane Protein Structure (NYCOMPS)
CitationJournal: Nature / Year: 2011
Title: Crystal structure of a phosphorylation-coupled saccharide transporter.
Authors: Cao, Y. / Jin, X. / Levin, E.J. / Huang, H. / Zong, Y. / Quick, M. / Weng, J. / Pan, Y. / Love, J. / Punta, M. / Rost, B. / Hendrickson, W.A. / Javitch, J.A. / Rajashankar, K.R. / Zhou, M.
History
DepositionFeb 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 6, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_asym.entity_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PTS system, cellobiose-specific IIC component
B: PTS system, cellobiose-specific IIC component
C: PTS system, cellobiose-specific IIC component
D: PTS system, cellobiose-specific IIC component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)198,73523
Polymers192,4494
Non-polymers6,28619
Water0
1
A: PTS system, cellobiose-specific IIC component
B: PTS system, cellobiose-specific IIC component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,27111
Polymers96,2252
Non-polymers3,0479
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9390 Å2
ΔGint-78 kcal/mol
Surface area35500 Å2
MethodPISA
2
C: PTS system, cellobiose-specific IIC component
D: PTS system, cellobiose-specific IIC component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,46412
Polymers96,2252
Non-polymers3,23910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9680 Å2
ΔGint-76 kcal/mol
Surface area35920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.812, 132.812, 452.954
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsThe biological unit is a dimer. There are 2 biological units in the asymmetric unit (chains A/B and chains C/D)

-
Components

#1: Protein
PTS system, cellobiose-specific IIC component


Mass: 48112.270 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10987 / Gene: BCE_5325, celB, ChbC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q72XQ0, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Polysaccharide
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#4: Sugar
ChemComp-ZDM / nonyl 4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside / nonyl-beta-D-maltoside


Type: saccharideCarbohydrate / Mass: 468.536 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C21H40O11 / Comment: detergent*YM
#5: Chemical
ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H8O7

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
15.1976.3
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop5.630% PEG 400, 100 mM Li2SO4, 0.5% polyvinylpyrrolidone, 100 mM Na Citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
2932vapor diffusion, sitting drop5.630% PEG 400, 100 mM Li2SO4, 0.5% polyvinylpyrrolidone, 100 mM Na Citrate, Ta6Br12 powder., pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21002
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X2511.08097
SYNCHROTRONNSLS X2521.255773
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDApr 5, 2009
ADSC QUANTUM 3152CCDOct 23, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111)SINGLE WAVELENGTHMx-ray1
2Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.080971
21.2557731
ReflectionRedundancy: 10.1 % / Av σ(I) over netI: 26.64 / Number: 478665 / Rmerge(I) obs: 0.117 / Χ2: 0.96 / D res high: 4.5 Å / D res low: 50 Å / Num. obs: 24476 / % possible obs: 98.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
9.675099.610.0710.99912.9
7.699.6710010.089110.9
6.727.6910010.219.6
6.116.7210010.3720.9639.3
5.676.1110010.5590.9269.4
5.335.6710010.5860.9049.5
5.075.3310010.4940.8989.6
4.855.079910.320.9619.7
4.664.8594.910.2970.9669.7
4.54.6687.610.3790.9539.8
ReflectionResolution: 3.295→50 Å / Num. obs: 59563 / % possible obs: 95.7 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.077 / Χ2: 0.871 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.3-3.429.80.70255690.6971,291.4
3.42-3.559.70.44356720.7091,293.1
3.55-3.729.70.30856440.741,292.5
3.72-3.919.60.20856990.7731,292.6
3.91-4.169.50.1457970.831,294.5
4.16-4.489.40.09359020.9181,295.8
4.48-4.939.30.0760780.9461,297.7
4.93-5.649.60.07562040.9651,299.8
5.64-7.110.90.07763371.0111,2100
7.1-5012.90.04266610.9951,299.5

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
DMphasing
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 3.295→19.974 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7701 / SU ML: 0.42 / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2636 2996 5.08 %RANDOM
Rwork0.2275 ---
obs0.2294 58996 95.02 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.794 Å2 / ksol: 0.237 e/Å3
Displacement parametersBiso max: 216.35 Å2 / Biso mean: 106.0916 Å2 / Biso min: 62.72 Å2
Baniso -1Baniso -2Baniso -3
1-20.5653 Å2-0 Å20 Å2
2--20.5653 Å2-0 Å2
3----41.1306 Å2
Refinement stepCycle: LAST / Resolution: 3.295→19.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13147 0 419 0 13566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00613906
X-RAY DIFFRACTIONf_angle_d1.21719014
X-RAY DIFFRACTIONf_chiral_restr0.0782356
X-RAY DIFFRACTIONf_plane_restr0.0052271
X-RAY DIFFRACTIONf_dihedral_angle_d25.425175
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2949-3.41210.35572740.32974978525286
3.4121-3.5480.36712900.3035355564593
3.548-3.70850.32833030.27095329563292
3.7085-3.90260.25932820.24275411569393
3.9026-4.14510.25493040.22395465576994
4.1451-4.46180.25592750.19785602587795
4.4618-4.90480.21832910.17945762605397
4.9048-5.60080.24993160.212558856201100
5.6008-7.00550.2793360.247459866322100
7.0055-19.97430.24713250.22362276552100

+
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