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- PDB-3l8r: The crystal structure of PtcA from S. mutans -

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Basic information

Entry
Database: PDB / ID: 3l8r
TitleThe crystal structure of PtcA from S. mutans
ComponentsPutative PTS system, cellobiose-specific IIA component
KeywordsTRANSFERASE / PTS / Helix / PtcA
Function / homology
Function and homology information


phosphoenolpyruvate-dependent sugar phosphotransferase system / transferase activity / metal ion binding
Similarity search - Function
Phosphotransferase system, lactose/cellobiose-type IIA subunit / Phosphotransferase system, lactose/cellobiose-type IIA subunit superfamily / PTS system, Lactose/Cellobiose specific IIA subunit / PTS_EIIA type-3 domain profile. / Phosphotransferase system, lactose/cellobiose-type IIA subunit / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Putative PTS system, cellobiose-specific IIA component
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLei, J. / Liu, X. / Li, L.
CitationJournal: To be Published
Title: The crystal structure of PtcA from Streptococcus mutans
Authors: Lei, J. / Liu, X. / Li, L. / Su, X.
History
DepositionJan 3, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 12, 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: Putative PTS system, cellobiose-specific IIA component
B: Putative PTS system, cellobiose-specific IIA component
C: Putative PTS system, cellobiose-specific IIA component
D: Putative PTS system, cellobiose-specific IIA component
E: Putative PTS system, cellobiose-specific IIA component
F: Putative PTS system, cellobiose-specific IIA component
G: Putative PTS system, cellobiose-specific IIA component
H: Putative PTS system, cellobiose-specific IIA component


Theoretical massNumber of molelcules
Total (without water)107,8598
Polymers107,8598
Non-polymers00
Water4,936274
1
A: Putative PTS system, cellobiose-specific IIA component
B: Putative PTS system, cellobiose-specific IIA component
C: Putative PTS system, cellobiose-specific IIA component


Theoretical massNumber of molelcules
Total (without water)40,4473
Polymers40,4473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6000 Å2
ΔGint-38 kcal/mol
Surface area13430 Å2
MethodPISA
2
D: Putative PTS system, cellobiose-specific IIA component
E: Putative PTS system, cellobiose-specific IIA component
F: Putative PTS system, cellobiose-specific IIA component


Theoretical massNumber of molelcules
Total (without water)40,4473
Polymers40,4473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-44 kcal/mol
Surface area13530 Å2
MethodPISA
3
G: Putative PTS system, cellobiose-specific IIA component

G: Putative PTS system, cellobiose-specific IIA component

G: Putative PTS system, cellobiose-specific IIA component


Theoretical massNumber of molelcules
Total (without water)40,4473
Polymers40,4473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-y,x-y-1,z1
crystal symmetry operation3_655-x+y+1,-x,z1
Buried area5840 Å2
ΔGint-40 kcal/mol
Surface area13750 Å2
MethodPISA
4
H: Putative PTS system, cellobiose-specific IIA component

H: Putative PTS system, cellobiose-specific IIA component

H: Putative PTS system, cellobiose-specific IIA component


Theoretical massNumber of molelcules
Total (without water)40,4473
Polymers40,4473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5620 Å2
ΔGint-45 kcal/mol
Surface area13560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.400, 127.400, 190.600
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11H-107-

HOH

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Components

#1: Protein
Putative PTS system, cellobiose-specific IIA component / PtcA


Mass: 13482.329 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: ptcA, SMU_1598 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE)3
References: UniProt: Q8DT03, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES 7.5, 2.0M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 15, 2007
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→19.4 Å / Num. obs: 39798 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 33.9 Å2
Reflection shellHighest resolution: 2.5 Å

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E2A

1e2a


Resolution: 2.5→19.4 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.861 / WRfactor Rfree: 0.262 / WRfactor Rwork: 0.194 / Occupancy max: 1 / Occupancy min: 0.33 / FOM work R set: 0.778 / SU B: 9.774 / SU ML: 0.222 / SU R Cruickshank DPI: 0.427 / SU Rfree: 0.303 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.427 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.28 2027 5.1 %RANDOM
Rwork0.208 ---
all0.24 39810 --
obs0.212 39798 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 99.35 Å2 / Biso mean: 28.761 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6549 0 0 274 6823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226614
X-RAY DIFFRACTIONr_angle_refined_deg1.811.9628898
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9915810
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.64626.439337
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.467151329
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9041524
X-RAY DIFFRACTIONr_chiral_restr0.1370.21049
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024816
X-RAY DIFFRACTIONr_mcbond_it0.8511.54059
X-RAY DIFFRACTIONr_mcangle_it1.70526518
X-RAY DIFFRACTIONr_scbond_it2.92932555
X-RAY DIFFRACTIONr_scangle_it4.8534.52379
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 138 -
Rwork0.254 2749 -
all-2887 -
obs--99.97 %

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