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- PDB-4xeu: Crystal structure of a transketolase from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 4xeu
TitleCrystal structure of a transketolase from Pseudomonas aeruginosa
ComponentsTransketolase
KeywordsTRANSFERASE / structural genomics / National Institute for Allergy and Infectious Diseases / NIAID / thiamine pyrophosphate / TPP / calcium / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


transketolase / transketolase activity / pentose-phosphate shunt / metal ion binding / cytosol
Similarity search - Function
Transketolase, bacterial-like / Transketolase family / Transketolase-like TK C-terminal domain / : / Transketolase signature 1. / Transketolase, N-terminal / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. / Transketolase, C-terminal domain ...Transketolase, bacterial-like / Transketolase family / Transketolase-like TK C-terminal domain / : / Transketolase signature 1. / Transketolase, N-terminal / Transketolase, thiamine diphosphate binding domain / Transketolase binding site / Transketolase signature 2. / Transketolase, C-terminal domain / Rossmann fold - #920 / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / Thiamin diphosphate-binding fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To Be Published
Title: Crystal structure of a transketolase from Pseudomonas aeruginosa
Authors: Edwards, T.E. / Dranow, D.M. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionDec 24, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,4724
Polymers73,3291
Non-polymers1423
Water7,296405
1
A: Transketolase
hetero molecules

A: Transketolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,9438
Polymers146,6592
Non-polymers2846
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+1/31
Buried area8190 Å2
ΔGint-49 kcal/mol
Surface area39380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.150, 76.150, 193.610
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11A-830-

HOH

21A-865-

HOH

31A-870-

HOH

41A-884-

HOH

51A-887-

HOH

61A-895-

HOH

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Components

#1: Protein Transketolase


Mass: 73329.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: tktA / Plasmid: BG1861 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I5Y8, transketolase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 405 / 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: 2.21 Å3/Da / Density % sol: 44.34 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PsaeA.01294.a.B1 at 20 mg/mL against MCSG 1 screen condition E9, 0.2 M CaCl2, 25% PEG 3350 supplemented with 20% EG as cryo-protected

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 17, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 48109 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 6.2 % / Biso Wilson estimate: 31.517 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.076 / Χ2: 0.965 / Net I/σ(I): 18.55 / Num. measured all: 296240
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.95-26.20.8680.563.4721893353835370.61100
2-2.060.9130.4464.3821266342834260.48699.9
2.06-2.120.9470.3415.6320654333233290.37299.9
2.12-2.180.9610.2796.6620139324832470.304100
2.18-2.250.9750.2258.2319586315931580.245100
2.25-2.330.980.1879.6218785303030290.204100
2.33-2.420.9870.15811.4218327295529490.17299.8
2.42-2.520.9910.13213.1117768286428570.14499.8
2.52-2.630.9930.11415.1717024275327450.12499.7
2.63-2.760.9950.09418.0216122260825950.10299.5
2.76-2.910.9960.07721.3815276247924680.08499.6
2.91-3.080.9970.06524.7114647238523670.07199.2
3.08-3.30.9980.05328.9613750225122350.05899.3
3.3-3.560.9990.04434.9112556206720480.04899.1
3.56-3.90.9990.03739.6211539193119050.04198.7
3.9-4.360.9990.03344.3610535176217370.03698.6
4.36-5.040.9990.0346.859290157615460.03398.1
5.04-6.170.9990.03144.597837134513050.03497
6.17-8.720.9990.02847.976086107310330.0396.3
8.720.9990.02550.8531606555930.02790.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
REFMACrefinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2R8O
Resolution: 1.95→50 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / WRfactor Rfree: 0.1852 / WRfactor Rwork: 0.1533 / FOM work R set: 0.8663 / SU B: 6.535 / SU ML: 0.094 / SU R Cruickshank DPI: 0.1484 / SU Rfree: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1987 2363 4.9 %RANDOM
Rwork0.164 45738 --
obs0.1657 45738 99.43 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.15 Å2 / Biso mean: 29.27 Å2 / Biso min: 14.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20.15 Å2-0 Å2
2--0.3 Å20 Å2
3----0.96 Å2
Refinement stepCycle: final / Resolution: 1.95→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4765 0 6 405 5176
Biso mean--37.74 35.19 -
Num. residues----632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0194890
X-RAY DIFFRACTIONr_bond_other_d0.0010.024508
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.9416653
X-RAY DIFFRACTIONr_angle_other_deg0.843310310
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7025632
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.39723.911225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.24415721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3251531
X-RAY DIFFRACTIONr_chiral_restr0.0910.2724
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215726
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021165
X-RAY DIFFRACTIONr_mcbond_it1.4862.1152528
X-RAY DIFFRACTIONr_mcbond_other1.4832.1142527
X-RAY DIFFRACTIONr_mcangle_it2.2223.1593154
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 194 -
Rwork0.223 3341 -
all-3535 -
obs--99.97 %
Refinement TLS params.Method: refined / Origin x: 5.8298 Å / Origin y: 18.1743 Å / Origin z: 30.0821 Å
111213212223313233
T0.0147 Å2-0.0311 Å2-0.0037 Å2-0.0881 Å20.0083 Å2--0.0493 Å2
L0.2873 °20.0484 °20.2226 °2-0.2298 °2-0.0552 °2--0.2813 °2
S-0 Å °0.0478 Å °0.0622 Å °0.0036 Å °0.0074 Å °0.0716 Å °-0.0115 Å °0.0887 Å °-0.0074 Å °

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