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- PDB-3mtq: Crystal structure of a putative phosphoenolpyruvate-dependent sug... -

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Basic information

Entry
Database: PDB / ID: 3mtq
TitleCrystal structure of a putative phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) permease (KPN_04802) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.70 A resolution
Componentsputative phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) permease
KeywordsTRANSFERASE / PTS system fructose IIA component / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
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
Putative PTS permease
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a putative phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) permease (KPN_04802) from Klebsiella pneumoniae subsp. pneumoniae MGH 78578 at 1.70 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Category: database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: putative phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) permease
B: putative phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) permease


Theoretical massNumber of molelcules
Total (without water)36,3042
Polymers36,3042
Non-polymers00
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-25 kcal/mol
Surface area12920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.753, 58.370, 62.725
Angle α, β, γ (deg.)90.000, 119.370, 90.000
Int Tables number5
Space group name H-MC121
DetailsCRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE.

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Components

#1: Protein putative phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) permease / Putative PTS permease


Mass: 18151.918 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: ATCC 700721 / MGH 78578 / Gene: KPN78578_47240, KPN_04802 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A6THW4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG.

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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: 1.97 Å3/Da / Density % sol: 37.63 %
Description: THE STATISTICS REPORTED IN REMARK 200 WERE COMPUTED WITH XSCALE WITH FRIEDEL PAIRS KEPT SEPARATE.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1700M ammonium acetate, 15.0000% Glycerol, 25.5000% polyethylene glycol 4000, 0.1M sodium citrate pH 5.6, Additive: 0.005 M mannose, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162,0.97934,0.97920
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 11, 2010 / Details: Flat collimating mirror, toroid focusing mirror
RadiationMonochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.911621
20.979341
30.97921
ReflectionResolution: 1.7→27.351 Å / Num. obs: 30169 / % possible obs: 90.6 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.768 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 9.75
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
1.7-1.760.4171.910386533188.3
1.76-1.830.3282.511324569393.5
1.83-1.910.2263.511058556292.9
1.91-2.020.1485.212089608492.6
2.02-2.140.1116.810681538891.8
2.14-2.310.0818.911429575491.6
2.31-2.540.0621110844545490.2
2.54-2.90.0461410493530088.5
2.9-3.660.03319.810811545687.5
3.66-27.3510.02524.910723543988.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PHENIXrefinement
SHELXphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→27.351 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 3.84 / SU ML: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.126
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION.
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1528 5.1 %RANDOM
Rwork0.205 ---
obs0.207 30168 97.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 68.79 Å2 / Biso mean: 29.377 Å2 / Biso min: 12.2 Å2
Baniso -1Baniso -2Baniso -3
1-5.4 Å20 Å22.9 Å2
2---2.62 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27.351 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2158 0 0 235 2393
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222348
X-RAY DIFFRACTIONr_bond_other_d0.0010.021522
X-RAY DIFFRACTIONr_angle_refined_deg1.6171.9563226
X-RAY DIFFRACTIONr_angle_other_deg1.03633769
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6435318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.23225.254118
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.19615403
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9061510
X-RAY DIFFRACTIONr_chiral_restr0.0940.2381
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022677
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02469
X-RAY DIFFRACTIONr_mcbond_it0.9861.51445
X-RAY DIFFRACTIONr_mcbond_other0.2621.5578
X-RAY DIFFRACTIONr_mcangle_it1.63922356
X-RAY DIFFRACTIONr_scbond_it2.1633903
X-RAY DIFFRACTIONr_scangle_it3.2034.5848
LS refinement shellResolution: 1.703→1.747 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.407 119 -
Rwork0.375 2130 -
all-2249 -
obs--98.34 %

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