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- PDB-3czc: The Crystal Structure of a putative PTS IIB(PtxB) from Streptococ... -

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Basic information

Entry
Database: PDB / ID: 3czc
TitleThe Crystal Structure of a putative PTS IIB(PtxB) from Streptococcus mutans
ComponentsRmpB
KeywordsTRANSFERASE / alpha/beta sandwich / Phosphotransferase system / Transport
Function / homology
Function and homology information


protein-N(PI)-phosphohistidine-sugar phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system
Similarity search - Function
Phosphotransferase system, EIIB component, type 2 / PTS_EIIB type-2 domain profile. / Phosphotransferase system, EIIB component, type 2/3 / PTS system IIB component-like superfamily / PTS system, Lactose/Cellobiose specific IIB subunit / Response regulator / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PTS ascorbate transporter subunit IIB
Similarity search - Component
Biological speciesStreptococcus mutans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.02 Å
AuthorsLei, J. / Su, X.D.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Crystal structures of phosphotransferase system enzymes PtxB (IIB(Asc)) and PtxA (IIA(Asc)) from Streptococcus mutans
Authors: Lei, J. / Li, L.F. / Su, X.D.
History
DepositionApr 29, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RmpB


Theoretical massNumber of molelcules
Total (without water)11,9091
Polymers11,9091
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.000, 41.400, 54.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RmpB / PTS EII / Putative PTS system / enzyme IIB component


Mass: 11908.539 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus mutans (bacteria) / Strain: UA159 / Gene: ptxB / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q93DB0, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.717724 Å3/Da / Density % sol: 28.393608 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M MES, 1.5-1.8M (NH4)2SO4, pH 6.5, Vapor diffusion, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.981 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 25, 2007
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.981 Å / Relative weight: 1
ReflectionResolution: 2→19.4 Å / Num. obs: 5665 / % possible obs: 96 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 21.478 Å2 / Rmerge(I) obs: 0.025 / Rsym value: 0.028 / Net I/σ(I): 58.33
Reflection shellResolution: 2→2.3 Å / Redundancy: 7 % / Rmerge(I) obs: 0.04 / Mean I/σ(I) obs: 42.2 / Num. measured obs: 23150 / Num. unique all: 3265 / Num. unique obs: 3265 / Rsym value: 0.038 / % possible all: 89

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
XDSdata reduction
XDSdata scaling
SHELXCDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.02→19.37 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.392 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.203 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23734 264 4.7 %RANDOM
Rwork0.17454 ---
all0.23 6711 --
obs0.1774 5401 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.07 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.02→19.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms700 0 0 59 759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.022712
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.989946
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.432596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.73926.78628
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.95915144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.839153
X-RAY DIFFRACTIONr_chiral_restr0.1050.2114
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02503
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2010.2314
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2920.2467
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2850.243
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2490.228
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2771.5481
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.7692738
X-RAY DIFFRACTIONr_scbond_it2.993245
X-RAY DIFFRACTIONr_scangle_it4.7684.5206
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.024→2.076 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 26 -
Rwork0.225 358 -
all-384 -
obs--100 %

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