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- PDB-2hro: Structure of the full-lenght Enzyme I of the PTS system from Stap... -

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Basic information

Entry
Database: PDB / ID: 2hro
TitleStructure of the full-lenght Enzyme I of the PTS system from Staphylococcus carnosus
ComponentsPhosphoenolpyruvate-protein phosphotransferase
KeywordsTRANSFERASE / PTS / protein Phosphorylation / Sugar transport / Histidine phosphorylation
Function / homology
Function and homology information


phosphoenolpyruvate-protein phosphotransferase / phosphoenolpyruvate-protein phosphotransferase activity / phosphoenolpyruvate-dependent sugar phosphotransferase system / kinase activity / metal ion binding / cytoplasm
Similarity search - Function
PtsI, HPr-binding domain / Phosphotransferase system, enzyme I / : / Phosphotransferase system, enzyme I-like / Phosphotransferase system, enzyme I N-terminal / PtsI, HPr-binding domain superfamily / PEP-utilising enzyme, N-terminal / Phosphohistidine domain / PEP-utilising enzyme, active site / PEP-utilizing enzymes phosphorylation site signature. ...PtsI, HPr-binding domain / Phosphotransferase system, enzyme I / : / Phosphotransferase system, enzyme I-like / Phosphotransferase system, enzyme I N-terminal / PtsI, HPr-binding domain superfamily / PEP-utilising enzyme, N-terminal / Phosphohistidine domain / PEP-utilising enzyme, active site / PEP-utilizing enzymes phosphorylation site signature. / PEP-utilising enzyme, conserved site / PEP-utilizing enzymes signature 2. / PEP-utilising enzyme, C-terminal / PEP-utilising enzyme, PEP-binding domain / PEP-utilising enzyme, mobile domain / Phosphohistidine domain superfamily / PEP-utilising enzyme, mobile domain / Enzyme I; Chain A, domain 2 / Phosphoenolpyruvate-binding domains / Glucose Oxidase; domain 1 / Pyruvate kinase-like domain superfamily / Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily / 3-Layer(bba) Sandwich / TIM Barrel / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Phosphoenolpyruvate-protein phosphotransferase
Similarity search - Component
Biological speciesStaphylococcus carnosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsMarquez, J.A. / Reinelt, S. / Koch, B. / Engelman, R. / Hengstenberg, W. / Scheffzek, K.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structure of the full-length enzyme I of the phosphoenolpyruvate-dependent sugar phosphotransferase system
Authors: Reinelt, S. / Koch, B. / Engelmann, R. / Hengstenberg, W. / Scheffzek, K.
History
DepositionJul 20, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoenolpyruvate-protein phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,4582
Polymers63,3621
Non-polymers961
Water3,099172
1
A: Phosphoenolpyruvate-protein phosphotransferase
hetero molecules

A: Phosphoenolpyruvate-protein phosphotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,9154
Polymers126,7232
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4290 Å2
ΔGint-50 kcal/mol
Surface area49860 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)173.364, 46.852, 85.297
Angle α, β, γ (deg.)90.00, 101.46, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe As.u. contains a monomer but the Biological unit is a dimer. The second part of the biological assembly is generated by applying the symetry operation -x, y, -z and the translation 1 0 1

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Components

#1: Protein Phosphoenolpyruvate-protein phosphotransferase / E.C.2.7.3.9 / Phosphotransferase system / enzyme I / PEP-dependent HPr protein kinase phosphoryltransferase


Mass: 63361.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus carnosus (bacteria) / Gene: Pts1 / Plasmid: pUC-ptsO2.6X / Production host: Escherichia coli (E. coli) / Strain (production host): DH5a
References: UniProt: P23533, phosphoenolpyruvate-protein phosphotransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.6854.07
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, hanging drop8.530% PEG 4000, 0.2 M Li2SO4 and 0.1 M Tris-HCl pH8.5 and 0.2 l of additive solution (solution No 11 of Hampton Crystal Screen, Hampton Research, VAPOR DIFFUSION, HANGING DROP, temperature 293K
2932vapor diffusion, sitting drop8.530% PEG 4000, 0.2 sodium malonate and 0.1 M Tris-HCl at pH of 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-210.933
SYNCHROTRONESRF BM1421.71, 1.71, 0.976
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDDec 2, 2002
MAR CCD 130 mm2CCDApr 28, 2003
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Diamond 111SINGLE WAVELENGTHMx-ray1
2Si 111 channelMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.9331
21.711
30.9761
ReflectionResolution: 2.5→34.86 Å / Num. all: 23570 / Num. obs: 23570 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.5→2.6 Å / % possible all: 93.9

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Processing

Software
NameVersionClassification
XDSdata scaling
SOLVEphasing
CNS1refinement
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 2.5→34.86 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 239616.53 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1179 5 %RANDOM
Rwork0.215 ---
all0.2151 23570 --
obs0.2151 23570 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.0559 Å2 / ksol: 0.29959 e/Å3
Displacement parametersBiso mean: 67.9 Å2
Baniso -1Baniso -2Baniso -3
1--27.671 Å20 Å2-3.691 Å2
2--3.504 Å20 Å2
3---24.167 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.5→34.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4070 0 5 172 4247
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.18
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.461.5
X-RAY DIFFRACTIONc_mcangle_it2.52
X-RAY DIFFRACTIONc_scbond_it2.162
X-RAY DIFFRACTIONc_scangle_it3.22.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 194 5 %
Rwork0.296 3687 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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