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- PDB-5iws: Crystal structure of the transporter MalT, the EIIC domain from t... -

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Basic information

Entry
Database: PDB / ID: 5iws
TitleCrystal structure of the transporter MalT, the EIIC domain from the maltose-specific phosphotransferase system
ComponentsProtein-N(Pi)-phosphohistidine-sugar phosphotransferase (Enzyme II of the phosphotransferase system) (PTS system glucose-specific IIBC component)
KeywordsTRANSFERASE / transporter / membrane protein / Structural Genomics / New York Consortium on Membrane Protein Structure / NYCOMPS / PSI-Biology
Function / homology
Function and homology information


protein-Npi-phosphohistidine-sugar phosphotransferase / protein-N(pi)-phosphohistidine--N-acetyl-D-glucosamine phosphotransferase activity / protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / phosphorylation / plasma membrane
Similarity search - Function
Phosphotransferase system, IIBC component / Phosphotransferase system, IIB component, type 1 / Phosphotransferase system, EIIC component, type 1 / Phosphotransferase system EIIB, cysteine phosphorylation site / Glucose permease domain IIB / phosphotransferase system, EIIB / PTS EIIB domains cysteine phosphorylation site signature. / PTS_EIIB type-1 domain profile. / PTS_EIIC type-1 domain profile. / Phosphotransferase system, EIIC / Phosphotransferase system, EIIC
Similarity search - Domain/homology
alpha-maltose / Protein-N(Pi)-phosphohistidine-sugar phosphotransferase (Enzyme II of the phosphotransferase system) (PTS system glucose-specific IIBC component)
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.551 Å
AuthorsMcCoy, J.G. / Ren, Z. / Levin, E.J. / Zhou, M. / New York Consortium on Membrane Protein Structure (NYCOMPS)
Funding support United States, 7items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM098878 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R01HL086392 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)R01DK088057 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54GM095315 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U54GM087519 United States
American Heart Association12EIA8850017 United States
Cancer Prevention and Research Institute of Texas (CPRIT)R12MZ United States
CitationJournal: Structure / Year: 2016
Title: The Structure of a Sugar Transporter of the Glucose EIIC Superfamily Provides Insight into the Elevator Mechanism of Membrane Transport.
Authors: McCoy, J.G. / Ren, Z. / Stanevich, V. / Lee, J. / Mitra, S. / Levin, E.J. / Poget, S. / Quick, M. / Im, W. / Zhou, M.
History
DepositionMar 22, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / 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 / struct_conn / 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_atom_id / _atom_site.label_comp_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein-N(Pi)-phosphohistidine-sugar phosphotransferase (Enzyme II of the phosphotransferase system) (PTS system glucose-specific IIBC component)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0572
Polymers51,7151
Non-polymers3421
Water25214
1
A: Protein-N(Pi)-phosphohistidine-sugar phosphotransferase (Enzyme II of the phosphotransferase system) (PTS system glucose-specific IIBC component)
hetero molecules

A: Protein-N(Pi)-phosphohistidine-sugar phosphotransferase (Enzyme II of the phosphotransferase system) (PTS system glucose-specific IIBC component)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,1144
Polymers103,4302
Non-polymers6852
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z1
Buried area6750 Å2
ΔGint-51 kcal/mol
Surface area35260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.633, 108.182, 139.329
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Protein-N(Pi)-phosphohistidine-sugar phosphotransferase (Enzyme II of the phosphotransferase system) (PTS system glucose-specific IIBC component)


Mass: 51714.781 Da / Num. of mol.: 1 / Fragment: PTS EIIC type-1 domain, residues 3-472
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (strain ZK / E33L) (bacteria)
Strain: ZK / E33L / Gene: ptsG, BCE33L0344 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q63GK8, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.43 % / Mosaicity: 1.286 ° / Mosaicity esd: 0.042 °
Crystal growTemperature: 293 K / Method: lipidic cubic phase / pH: 6.7
Details: 39% polyethylene glycol 400, 450 mM NaCl, 3% ethanol, and 100 mM N-(2-Acetamido)iminodiacetic acid

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.97872 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. obs: 17976 / % possible obs: 100 % / Redundancy: 8.7 % / Biso Wilson estimate: 48.04 Å2 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.044 / Rrim(I) all: 0.13 / Χ2: 1.077 / Net I/av σ(I): 15.769 / Net I/σ(I): 7 / Num. measured all: 155607
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.55-2.617.70.85811760.7880.3290.9220.933100
2.61-2.677.60.77111730.8080.2950.8280.968100
2.67-2.758.40.71111830.8680.2610.7590.987100
2.75-2.838.70.57611730.9080.2060.6131.025100
2.83-2.928.30.46711770.9380.1720.4981.024100
2.92-3.028.40.33911910.9670.1240.3611.047100
3.02-3.149.40.2911900.9790.0990.3061.059100
3.14-3.299.40.22311970.9870.0770.2361.023100
3.29-3.469.40.18111810.9880.0620.1911.037100
3.46-3.689.30.13411950.9950.0460.1421.08100
3.68-3.969.10.10812060.9950.0370.1141.001100
3.96-4.368.70.0912000.9970.0320.0950.974100
4.36-4.997.80.0812200.9960.0290.0860.96100
4.99-6.288.60.08312190.9970.0290.0881.312100
6.28-5090.05312950.9990.0180.0561.61199.5

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.551→34.832 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2823 3407 10.04 %RANDOM
Rwork0.2373 30532 --
obs0.2417 33939 99.58 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.2 Å2 / Biso mean: 52.3376 Å2 / Biso min: 24.78 Å2
Refinement stepCycle: final / Resolution: 2.551→34.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3402 0 23 14 3439
Biso mean--45.26 46.63 -
Num. residues----443
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023511
X-RAY DIFFRACTIONf_angle_d0.4474781
X-RAY DIFFRACTIONf_chiral_restr0.039568
X-RAY DIFFRACTIONf_plane_restr0.004587
X-RAY DIFFRACTIONf_dihedral_angle_d7.9032022
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.551-2.58740.35021320.28431197132993
2.5874-2.6260.32151430.287512721415100
2.626-2.6670.28941400.283312741414100
2.667-2.71070.31881420.293912681410100
2.7107-2.75740.30811450.262612781423100
2.7574-2.80760.31511410.27613021443100
2.8076-2.86150.33121440.283912541398100
2.8615-2.91990.34131370.272312571394100
2.9199-2.98340.29411490.263213181467100
2.9834-3.05270.391410.260312381379100
3.0527-3.1290.32891430.26812921435100
3.129-3.21360.39281430.257412751418100
3.2136-3.30810.26681440.262912881432100
3.3081-3.41480.30751400.256912911431100
3.4148-3.53670.27631420.233912591401100
3.5367-3.67810.3031440.226212771421100
3.6781-3.84530.2721430.238812791422100
3.8453-4.04780.27581390.231512721411100
4.0478-4.3010.22011430.23212861429100
4.301-4.63240.30281350.25371240137598
4.6324-5.09720.34041460.215112711417100
5.0972-5.83180.2091490.219612811430100
5.8318-7.33620.29471410.211112921433100
7.3362-34.83550.19711410.182412711412100

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