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- PDB-4wl8: Crystal Structure of Mtb PEPCK in complex with non-hydrolyzable a... -

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Basic information

Entry
Database: PDB / ID: 4wl8
TitleCrystal Structure of Mtb PEPCK in complex with non-hydrolyzable analog of GTP
ComponentsPhosphoenolpyruvate carboxykinase [GTP]
KeywordsLYASE / TRANSFERASE / GTP-dependent PEPCK / P-loop / R-loop / omega-loop / Rate-limiting gluconeogenic enzyme / kinase / phosphoryl transfer / metal binding
Function / homology
Function and homology information


phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / gluconeogenesis / manganese ion binding / GTP binding / cytoplasm
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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / : / Phosphoenolpyruvate carboxykinase [GTP]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.61 Å
AuthorsKim, H.L. / Sacchettini, J.C.
CitationJournal: to be published
Title: Crystal Structure of Mtb PEPCK in complex with non-hydrolyzable analog of GTP
Authors: Kim, H.L.
History
DepositionOct 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoenolpyruvate carboxykinase [GTP]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,7164
Polymers69,0471
Non-polymers6693
Water14,484804
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)105.616, 123.009, 64.035
Angle α, β, γ (deg.)90.000, 116.970, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-841-

HOH

21A-928-

HOH

31A-974-

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 / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A5TYT6, phosphoenolpyruvate carboxykinase (GTP)
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: 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
#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 804 / 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: 2.74 Å3/Da / Density % sol: 55.18 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 10% (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: 1.0076 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 22, 2012 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0076 Å / Relative weight: 1
ReflectionResolution: 1.61→50 Å / Num. all: 92621 / Num. obs: 92621 / % possible obs: 98.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.128 / Χ2: 3.032 / Net I/av σ(I): 20.966 / Net I/σ(I): 8 / Num. measured all: 368099
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.61-1.642.30.7739551.5284.6
1.64-1.672.80.81142971.25192
1.67-1.73.40.78144951.26496.4
1.7-1.733.80.73946871.1598.8
1.73-1.7740.65146601.211100
1.77-1.814.10.57646941.23100
1.81-1.864.20.48646851.407100
1.86-1.914.20.41746791.54100
1.91-1.974.20.34146751.745100
1.97-2.034.20.32247652.405100
2.03-2.14.20.25346202.301100
2.1-2.194.20.21247062.696100
2.19-2.284.20.19147193.043100
2.28-2.44.20.17546943.378100
2.4-2.564.20.15947123.724100
2.56-2.754.20.14646804.442100
2.75-3.034.20.13547325.412100
3.03-3.474.20.11847036.917100
3.47-4.374.20.09447356.877100
4.37-504.10.06647284.26298.9

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Processing

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

4wie


Resolution: 1.61→38.204 Å / FOM work R set: 0.8919 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 18.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1804 4652 5.03 %
Rwork0.16 87870 -
obs0.161 92522 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.03 Å2 / Biso mean: 23.62 Å2 / Biso min: 10.44 Å2
Refinement stepCycle: final / Resolution: 1.61→38.204 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4697 0 39 804 5540
Biso mean--28.59 35.59 -
Num. residues----599
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064953
X-RAY DIFFRACTIONf_angle_d1.0986762
X-RAY DIFFRACTIONf_chiral_restr0.077713
X-RAY DIFFRACTIONf_plane_restr0.005881
X-RAY DIFFRACTIONf_dihedral_angle_d16.5621847
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 (%)
1.61-1.62570.2858990.2812089218870
1.6257-1.64480.34611270.2662658278588
1.6448-1.66490.29231370.26212723286092
1.6649-1.6860.27621530.24992878303195
1.686-1.70810.2881520.22962893304597
1.7081-1.73150.24871670.22342969313699
1.7315-1.75630.28071630.221529263089100
1.7563-1.78250.24681580.204529973155100
1.7825-1.81030.20691830.189329473130100
1.8103-1.840.20011360.181630073143100
1.84-1.87170.23631770.182629563133100
1.8717-1.90580.20241610.183629643125100
1.9058-1.94240.20551500.179530133163100
1.9424-1.98210.21791480.184229873135100
1.9821-2.02520.21451560.176730073163100
2.0252-2.07230.17431750.163729593134100
2.0723-2.12410.19461450.157230013146100
2.1241-2.18150.1741480.157429783126100
2.1815-2.24570.17641730.155829743147100
2.2457-2.31820.17741720.157929673139100
2.3182-2.4010.17921420.152930163158100
2.401-2.49710.1771590.15529753134100
2.4971-2.61080.20331610.154329873148100
2.6108-2.74840.18091640.153529753139100
2.7484-2.92050.1841640.151729953159100
2.9205-3.14590.17021760.154929813157100
3.1459-3.46230.16691480.139629943142100
3.4623-3.96290.14311610.139830223183100
3.9629-4.99110.13731530.126930183171100
4.9911-38.21480.15751440.16113014315898

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