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- PDB-4wou: Crystal Structure of Mtb PEPCK in complex with GDP and metals -

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Basic information

Entry
Database: PDB / ID: 4wou
TitleCrystal Structure of Mtb PEPCK in complex with GDP and metals
ComponentsPhosphoenolpyruvate carboxykinase [GTP]
KeywordsLYASE / TRANSFERASE / GTP-dependent PEPCK / Kinase / P-loop / Omega-loop / R-loop / metal binding protein
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
GUANOSINE-5'-DIPHOSPHATE / : / PHOSPHATE ION / Phosphoenolpyruvate carboxykinase [GTP]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.122 Å
AuthorsKim, H.L. / Sacchettini, J.C.
CitationJournal: To Be Published
Title: Crystal Structure of Mtb PEPCK in complex with GDP and metals
Authors: Kim, H.L. / Kriger, I.V. / Sacchettini, J.C.
History
DepositionOct 16, 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
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id

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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)69,7976
Polymers69,0471
Non-polymers7515
Water5,693316
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.316, 125.172, 122.147
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 1 types, 1 molecules A

#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)
References: UniProt: A5TYT6, phosphoenolpyruvate carboxykinase (GTP)

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Non-polymers , 6 types, 321 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 316 / 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: 2.98 Å3/Da / Density % sol: 58.74 %
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: 0.91993 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91993 Å / Relative weight: 1
ReflectionResolution: 2.122→50 Å / Num. obs: 44852 / % possible obs: 99.8 % / Redundancy: 8.5 % / Biso Wilson estimate: 35.35 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 27.75

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.2_1309)refinement
PDB_EXTRACT3.11data extraction
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
DENZOdata reduction
SCALEPACKdata scaling
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.122→47.578 Å / Occupancy max: 1 / Occupancy min: 0.67 / FOM work R set: 0.8152 / SU ML: 0.22 / Cross valid method: NONE / σ(F): 0.4 / Phase error: 25.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2112 4316 5.07 %
Rwork0.1773 80737 -
obs0.179 85053 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 88.81 Å2 / Biso mean: 41.5272 Å2 / Biso min: 24.93 Å2
Refinement stepCycle: LAST / Resolution: 2.122→47.578 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4661 0 41 316 5018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074829
X-RAY DIFFRACTIONf_angle_d1.1056570
X-RAY DIFFRACTIONf_chiral_restr0.074685
X-RAY DIFFRACTIONf_plane_restr0.005857
X-RAY DIFFRACTIONf_dihedral_angle_d14.0641747
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 (%)
2.122-2.14590.2921370.27542288242584
2.1459-2.17120.30671320.26822596272896
2.1712-2.19770.31761590.25462698285796
2.1977-2.22550.24721220.24562664278697
2.2255-2.25480.28861530.24482693284697
2.2548-2.28560.23591290.2292625275497
2.2856-2.31830.291160.23382725284198
2.3183-2.35290.27831070.22832708281598
2.3529-2.38970.2741470.20922712285999
2.3897-2.42880.30931340.19982657279199
2.4288-2.47070.24471470.20492722286999
2.4707-2.51570.26821710.19312703287498
2.5157-2.5640.2531370.19152670280799
2.564-2.61640.21151420.19332762290499
2.6164-2.67330.20531270.18262682280999
2.6733-2.73540.24291310.18112732286399
2.7354-2.80380.21591830.18632691287499
2.8038-2.87960.23311430.18642714285799
2.8796-2.96440.2021650.18132679284499
2.9644-3.060.21151700.17872719288999
3.06-3.16940.22061470.17982679282699
3.1694-3.29620.25711610.189627392900100
3.2962-3.44620.221620.185527172879100
3.4462-3.62780.20791410.174327412882100
3.6278-3.8550.20331320.158127572889100
3.855-4.15250.16871550.155227122867100
4.1525-4.57010.18071620.135427162878100
4.5701-5.23070.18381390.147327362875100
5.2307-6.58740.15861250.172427552880100
6.5874-47.590.15681400.156227452885100

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