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- PDB-4wpt: Crystal Structure of Mtb PEPCK in complex with PEP -

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Basic information

Entry
Database: PDB / ID: 4wpt
TitleCrystal Structure of Mtb PEPCK in complex with PEP
ComponentsPhosphoenolpyruvate carboxykinase [GTP]
KeywordsLYASE / TRANSFERASE / GTP-dependent PEPCK / Anaplerotic reaction / P-loop / omega-loop / R-loop
Function / homology
Function and homology information


glycerol biosynthetic process from pyruvate / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / propionate catabolic process / response to starvation / cellular response to dexamethasone stimulus / gluconeogenesis / cellular response to glucose stimulus / cellular response to insulin stimulus / manganese ion binding ...glycerol biosynthetic process from pyruvate / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / propionate catabolic process / response to starvation / cellular response to dexamethasone stimulus / gluconeogenesis / cellular response to glucose stimulus / cellular response to insulin stimulus / manganese ion binding / GTP binding / cytosol
Similarity search - Function
Phosphoenolpyruvate carboxykinase, GTP-utilising / Phosphoenolpyruvate carboxykinase, GTP-utilising, conserved site / Phosphoenolpyruvate carboxykinase, C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase, GTP-utilising, N-terminal / Phosphoenolpyruvate carboxykinase C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase N-terminal domain / Phosphoenolpyruvate carboxykinase (GTP) signature. / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 1 ...Phosphoenolpyruvate carboxykinase, GTP-utilising / Phosphoenolpyruvate carboxykinase, GTP-utilising, conserved site / Phosphoenolpyruvate carboxykinase, C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase, GTP-utilising, N-terminal / Phosphoenolpyruvate carboxykinase C-terminal P-loop domain / Phosphoenolpyruvate carboxykinase N-terminal domain / Phosphoenolpyruvate carboxykinase (GTP) signature. / Phosphoenolpyruvate Carboxykinase; domain 2 / Phosphoenolpyruvate Carboxykinase, domain 2 / Phosphoenolpyruvate Carboxykinase; domain 1 / Phosphoenolpyruvate Carboxykinase, domain 1 / Phosphoenolpyruvate Carboxykinase; domain 3 - #20 / Phosphoenolpyruvate carboxykinase, C-terminal / Phosphoenolpyruvate carboxykinase, N-terminal / Phosphoenolpyruvate Carboxykinase; domain 3 / Beta Complex / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOENOLPYRUVATE / PHOSPHATE ION / Phosphoenolpyruvate carboxykinase [GTP]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsKim, H.L. / Krieger, I.V. / Sacchettini, J.C.
CitationJournal: To Be Published
Title: Crystal Structure of Mtb PEPCK in complex with PEP
Authors: Kim, H.L. / Krieger, I.V. / Sacchettini, J.C.
History
DepositionOct 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Derived calculations / Refinement description / Category: pdbx_struct_oper_list / software
Item: _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.2Sep 27, 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
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: Phosphoenolpyruvate carboxykinase [GTP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,4024
Polymers69,0471
Non-polymers3553
Water13,763764
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.574, 122.813, 64.556
Angle α, β, γ (deg.)90.000, 116.660, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-949-

HOH

21A-986-

HOH

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Components

#1: Protein Phosphoenolpyruvate carboxykinase [GTP] / PEPCK


Mass: 69046.734 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: ATCC 25177 / H37Ra / Gene: pckG, MRA_0219 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A5TYT6, phosphoenolpyruvate carboxykinase (GTP)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-PEP / PHOSPHOENOLPYRUVATE / Phosphoenolpyruvic acid


Mass: 168.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5O6P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 764 / 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: 2.72 Å3/Da / Density % sol: 54.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 10% -16% (w/v) PEG 3350, 0.2 M KH2PO4

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.94967 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94967 Å / Relative weight: 1
ReflectionResolution: 1.13→50 Å / Num. obs: 365421 / % possible obs: 68.8 % / Redundancy: 1.9 % / Biso Wilson estimate: 16.88 Å2 / Rmerge(I) obs: 0.087 / Χ2: 1.87 / Net I/av σ(I): 7.942 / Net I/σ(I): 6.2 / Num. measured all: 708883
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Num. unique allΧ2% possible allRmerge(I) obs
1.13-1.151.12450.5640.9
1.15-1.171.114920.7355.6
1.17-1.191.240530.64615.2
1.19-1.221.366680.78125.1
1.22-1.241.391401.42234.6
1.24-1.271.4114611.5343.1
1.27-1.31.5142131.61853.6
1.3-1.341.6173910.77165.4
1.34-1.381.7205032.13777.2
1.38-1.422248921.12993.9
1.42-1.472.1256022.63196.40.838
1.47-1.532254902.95795.70.717
1.53-1.62.1258851.27497.80.427
1.6-1.692.1261001.33598.30.313
1.69-1.792.1262481.61398.90.243
1.79-1.932250523.99294.40.285
1.93-2.132249812.9693.90.171
2.13-2.432.1248451.94593.60.119
2.43-3.072.1265190.99699.80.061
3.07-502.1246410.79992.80.045

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Processing

Software
NameVersionClassification
PHENIXrefinement
HKL-3000data reduction
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WIE

4wie


Resolution: 1.6→37.894 Å / FOM work R set: 0.8827 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1946 4505 5 %
Rwork0.1692 85616 -
obs0.1704 90121 95.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.25 Å2 / Biso mean: 20.11 Å2 / Biso min: 7.72 Å2
Refinement stepCycle: final / Resolution: 1.6→37.894 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4704 0 21 764 5489
Biso mean--26.53 30.63 -
Num. residues----600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064951
X-RAY DIFFRACTIONf_angle_d1.0876757
X-RAY DIFFRACTIONf_chiral_restr0.078714
X-RAY DIFFRACTIONf_plane_restr0.006885
X-RAY DIFFRACTIONf_dihedral_angle_d13.641826
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.61820.25211670.21772884305196
1.6182-1.63720.25661560.20652885304197
1.6372-1.65720.25521490.20672891304097
1.6572-1.67820.21861600.20182893305397
1.6782-1.70020.2571530.19692892304597
1.7002-1.72350.23451730.1972859303297
1.7235-1.74820.23661770.18762953313097
1.7482-1.77430.20281680.18452872304098
1.7743-1.8020.22091520.1772942309498
1.802-1.83150.20711630.17332952311599
1.8315-1.86310.21011500.1712945309599
1.8631-1.8970.23461380.20822874301295
1.897-1.93350.43441040.34962327243178
1.9335-1.97290.22841540.20352930308498
1.9729-2.01580.2071600.17323005316599
2.0158-2.06270.20961030.17062387249079
2.0627-2.11430.26171470.20032809295694
2.1143-2.17150.18681680.154429763144100
2.1715-2.23530.1891520.16552645279788
2.2353-2.30750.23461330.23932507264083
2.3075-2.38990.22571380.165629913129100
2.3899-2.48560.18771480.167530243172100
2.4856-2.59870.1791530.159229933146100
2.5987-2.73570.20451340.16082987312199
2.7357-2.9070.17711660.154530033169100
2.907-3.13140.16781500.148830213171100
3.1314-3.44630.17051530.13832632278588
3.4463-3.94460.17281350.14422742287791
3.9446-4.9680.11711450.12672760290593
4.968-37.90430.18031560.16783035319199

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