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- PDB-4tkz: Crystal structure of phosphotransferase system component EIIA fro... -

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Basic information

Entry
Database: PDB / ID: 4tkz
TitleCrystal structure of phosphotransferase system component EIIA from Streptococcus agalactiae
ComponentsPutative uncharacterized protein gbs1890
KeywordsTRANSFERASE / PHOSPHOTRANSFERASE
Function / homology
Function and homology information


phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / membrane => GO:0016020
Similarity search - Function
PTS system mannose/sorbose specific IIA subunit / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component / Phosphotransferase system, mannose-type IIA component superfamily / PTS system fructose IIA component / PTS_EIIA type-4 domain profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PTS EIIA type-4 domain-containing protein
Similarity search - Component
Biological speciesStreptococcus agalactiae NEM316 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsNakamichi, Y. / Maruyama, Y. / Oiki, S. / Mikami, B. / Murata, K. / Hashimoto, W.
Funding support Japan, 3items
OrganizationGrant numberCountry
Grants-in-Aid for Scientific Research for Japan Society for the Promotion of Science Japan
Targeted Proteins Research Program from the Ministry of Education, Culture, Sports, Science, and Technology Japan
Research Fellowships from the Japan Society for the Promotion of Science for Young Scientists Japan
CitationJournal: To Be Published
Title: Crystal structure of phosphotransferase system component EIIA from Streptococcus agalactiae
Authors: Nakamichi, Y. / Maruyama, Y. / Oiki, S. / Mikami, B. / Murata, K. / Hashimoto, W.
History
DepositionMay 28, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 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 / refine_hist
Item: _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: Putative uncharacterized protein gbs1890
B: Putative uncharacterized protein gbs1890
C: Putative uncharacterized protein gbs1890
D: Putative uncharacterized protein gbs1890
E: Putative uncharacterized protein gbs1890
F: Putative uncharacterized protein gbs1890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,03917
Polymers100,0266
Non-polymers1,01311
Water4,774265
1
A: Putative uncharacterized protein gbs1890
B: Putative uncharacterized protein gbs1890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7116
Polymers33,3422
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-26 kcal/mol
Surface area11340 Å2
MethodPISA
2
D: Putative uncharacterized protein gbs1890
hetero molecules

C: Putative uncharacterized protein gbs1890
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8037
Polymers33,3422
Non-polymers4605
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_645x+1,y-1,z1
Buried area3920 Å2
ΔGint-27 kcal/mol
Surface area11220 Å2
MethodPISA
3
E: Putative uncharacterized protein gbs1890
hetero molecules

F: Putative uncharacterized protein gbs1890


Theoretical massNumber of molelcules
Total (without water)33,5264
Polymers33,3422
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area3580 Å2
ΔGint-26 kcal/mol
Surface area11070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.293, 53.800, 94.887
Angle α, β, γ (deg.)91.14, 90.02, 60.97
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Putative uncharacterized protein gbs1890


Mass: 16671.076 Da / Num. of mol.: 6 / Mutation: R403E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus agalactiae NEM316 (bacteria)
Strain: NEM316 / Gene: gbs1890 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8E371, protein-Npi-phosphohistidine-sugar phosphotransferase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 265 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.9 / Details: sodium thiocyanate, PEG 3350

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 29, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 80444 / % possible obs: 96.1 % / Redundancy: 2.1 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 26.6
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 2 % / Rmerge(I) obs: 0.243 / Mean I/σ(I) obs: 3.25 / % possible all: 94.5

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PDO

1pdo


Resolution: 1.8→33.78 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 28.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2419 4012 5 %Random selection
Rwork0.2064 ---
obs0.2082 80171 95.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→33.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5964 0 66 265 6295
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066188
X-RAY DIFFRACTIONf_angle_d1.0628362
X-RAY DIFFRACTIONf_dihedral_angle_d13.6972245
X-RAY DIFFRACTIONf_chiral_restr0.0711033
X-RAY DIFFRACTIONf_plane_restr0.0041041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.82120.36791380.26422274X-RAY DIFFRACTION86
1.8212-1.84340.35291250.25812614X-RAY DIFFRACTION95
1.8434-1.86670.31071470.24262696X-RAY DIFFRACTION95
1.8667-1.89130.25841460.22912522X-RAY DIFFRACTION95
1.8913-1.91720.28971340.24672605X-RAY DIFFRACTION95
1.9172-1.94460.30091250.23372625X-RAY DIFFRACTION95
1.9446-1.97360.26751410.2282644X-RAY DIFFRACTION96
1.9736-2.00440.26531250.22212689X-RAY DIFFRACTION95
2.0044-2.03730.28291190.22242605X-RAY DIFFRACTION96
2.0373-2.07240.24321530.22262676X-RAY DIFFRACTION96
2.0724-2.11010.26691340.22132595X-RAY DIFFRACTION96
2.1101-2.15070.27361580.21792625X-RAY DIFFRACTION97
2.1507-2.19460.26931280.20182619X-RAY DIFFRACTION96
2.1946-2.24230.28231420.22212720X-RAY DIFFRACTION96
2.2423-2.29440.26551330.21092606X-RAY DIFFRACTION97
2.2944-2.35180.26541570.21622680X-RAY DIFFRACTION97
2.3518-2.41540.22531360.21032628X-RAY DIFFRACTION97
2.4154-2.48640.24761270.21832677X-RAY DIFFRACTION97
2.4864-2.56660.27751330.20832677X-RAY DIFFRACTION97
2.5666-2.65830.23811310.22722644X-RAY DIFFRACTION97
2.6583-2.76470.25471490.23132701X-RAY DIFFRACTION97
2.7647-2.89050.2641310.22152656X-RAY DIFFRACTION97
2.8905-3.04280.26911560.22942677X-RAY DIFFRACTION98
3.0428-3.23330.2651380.21812650X-RAY DIFFRACTION97
3.2333-3.48270.24711520.22082657X-RAY DIFFRACTION96
3.4827-3.83270.22841380.19432640X-RAY DIFFRACTION96
3.8327-4.38630.20311160.17152613X-RAY DIFFRACTION95
4.3863-5.52240.20631560.16062568X-RAY DIFFRACTION95
5.5224-33.78610.18031440.18872576X-RAY DIFFRACTION94

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