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- PDB-3lfj: Crystal structure of manxB from Thermoanaerobacter tengcongensis -

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Basic information

Entry
Database: PDB / ID: 3lfj
TitleCrystal structure of manxB from Thermoanaerobacter tengcongensis
ComponentsPhosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IIB
KeywordsTRANSFERASE / manxB PTS
Function / homology
Function and homology information


protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / cytoplasm
Similarity search - Function
Fructose Permease / Phosphotransferase system, sorbose subfamily IIB component / Phosphotransferase system, sorbose subfamily IIB component / Phosphotransferase system, sorbose subfamily IIB component superfamily / PTS system sorbose subfamily IIB component / PTS_EIIB type-4 domain profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IIB
Similarity search - Component
Biological speciesThermoanaerobacter tengcongensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.556 Å
AuthorsFu, T.M. / Su, X.-D.
CitationJournal: To be Published
Title: Crystal structure of manxA and manxB from Thermoanaerobacter tengcongensis
Authors: Fu, T.M. / Su, X.-D.
History
DepositionJan 17, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IIB
B: Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IIB


Theoretical massNumber of molelcules
Total (without water)42,3252
Polymers42,3252
Non-polymers00
Water6,593366
1
A: Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IIB


Theoretical massNumber of molelcules
Total (without water)21,1631
Polymers21,1631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IIB


Theoretical massNumber of molelcules
Total (without water)21,1631
Polymers21,1631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)81.300, 81.300, 170.831
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Phosphotransferase system, mannose/fructose/N-acetylgalactosamine-specific component IIB / manxB


Mass: 21162.621 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobacter tengcongensis (bacteria)
Strain: MB4T / Gene: manxB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8RD54
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / 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: 2.57 Å3/Da / Density % sol: 52.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 20% iso-propanol, 0.1M Na Citrate pH 5.6, 15% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 2, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 60091 / % possible obs: 99.5 % / Redundancy: 10.7 % / Biso Wilson estimate: 21.21 Å2 / Rsym value: 0.075
Reflection shellResolution: 1.55→1.58 Å / Redundancy: 10.2 % / Num. unique all: 6075 / % possible all: 99.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1nrz

1nrz


Resolution: 1.556→33.085 Å / Occupancy max: 1 / Occupancy min: 0.03 / FOM work R set: 0.878 / SU ML: 0.21 / σ(F): 1.98 / Phase error: 19.73 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2076 3031 5.05 %
Rwork0.1888 57048 -
obs0.1897 60079 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.047 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 70.02 Å2 / Biso mean: 24.54 Å2 / Biso min: 11.86 Å2
Baniso -1Baniso -2Baniso -3
1-0.368 Å2-0 Å2-0 Å2
2--0.368 Å20 Å2
3----0.736 Å2
Refinement stepCycle: LAST / Resolution: 1.556→33.085 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2605 0 0 366 2971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092721
X-RAY DIFFRACTIONf_angle_d1.23699
X-RAY DIFFRACTIONf_dihedral_angle_d13.7891019
X-RAY DIFFRACTIONf_chiral_restr0.082437
X-RAY DIFFRACTIONf_plane_restr0.006459
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.556-1.58030.23561310.21442641X-RAY DIFFRACTION100
1.5803-1.60620.22181530.20192615X-RAY DIFFRACTION100
1.6062-1.63390.22251470.2032576X-RAY DIFFRACTION100
1.6339-1.66360.23161330.19962637X-RAY DIFFRACTION100
1.6636-1.69560.23581180.18962603X-RAY DIFFRACTION100
1.6956-1.73020.20851390.19522616X-RAY DIFFRACTION100
1.7302-1.76780.23551410.19442614X-RAY DIFFRACTION100
1.7678-1.8090.21251470.19012580X-RAY DIFFRACTION100
1.809-1.85420.20181490.18382620X-RAY DIFFRACTION100
1.8542-1.90430.2131480.18832586X-RAY DIFFRACTION100
1.9043-1.96040.20581450.18972598X-RAY DIFFRACTION100
1.9604-2.02360.21181320.19072597X-RAY DIFFRACTION100
2.0236-2.09590.20591240.18942622X-RAY DIFFRACTION100
2.0959-2.17980.20211540.17972599X-RAY DIFFRACTION100
2.1798-2.2790.20451320.17422620X-RAY DIFFRACTION100
2.279-2.39920.20331420.18752607X-RAY DIFFRACTION100
2.3992-2.54940.21391440.17912625X-RAY DIFFRACTION100
2.5494-2.74620.19421360.18942595X-RAY DIFFRACTION100
2.7462-3.02240.20841360.18132603X-RAY DIFFRACTION100
3.0224-3.45930.18531450.17852582X-RAY DIFFRACTION100
3.4593-4.35680.17711400.15592546X-RAY DIFFRACTION97
4.3568-33.09230.1547950.17192366X-RAY DIFFRACTION89
Refinement TLS params.Method: refined / Origin x: 19.2069 Å / Origin y: 13.6842 Å / Origin z: -15.9123 Å
111213212223313233
T0.1268 Å20.003 Å2-0.0062 Å2-0.1208 Å2-0.0034 Å2--0.1456 Å2
L0.092 °20.0591 °2-0.0577 °2-0.0021 °2-0.0343 °2--0.7125 °2
S-0.0129 Å °-0.0081 Å °0.0083 Å °-0.0039 Å °-0.0068 Å °0.0065 Å °0.0281 Å °0.0091 Å °0.0192 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA-1 - 165
2X-RAY DIFFRACTION1allB-1 - 164
3X-RAY DIFFRACTION1allA1 - 370

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