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- PDB-3qnq: Crystal structure of the transporter ChbC, the IIC component from... -

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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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water00
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)

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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: saccharide / 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


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

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Experimental details

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Experiment

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

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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

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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

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Phasing

PhasingMethod: SAD

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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

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