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- PDB-4wie: Crystal structure of apo-PEPCK from Mycobacterium tuberculosis wi... -

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Basic information

Entry
Database: PDB / ID: 4wie
TitleCrystal structure of apo-PEPCK from Mycobacterium tuberculosis with glycerol
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
: / Phosphoenolpyruvate carboxykinase [GTP]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.18 Å
AuthorsKim, H.L. / Sacchettini, J.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Crystal structure of apo-PEPCK from Mycobacterium tuberculosis with glycerol
Authors: Kim, H.L. / Sacchettini, J.C.
History
DepositionSep 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Other
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _software.name
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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)69,1943
Polymers69,0471
Non-polymers1472
Water11,007611
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.958, 122.564, 64.555
Angle α, β, γ (deg.)90.000, 117.000, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-851-

HOH

21A-936-

HOH

31A-965-

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)
References: UniProt: A5TYT6, phosphoenolpyruvate carboxykinase (GTP)
#2: Chemical ChemComp-MN / MANGANESE (II) ION


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


Mass: 18.015 Da / Num. of mol.: 611 / 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: 2.71 Å3/Da / Density % sol: 54.69 %
Crystal growTemperature: 287 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: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Mar 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 37534 / % possible obs: 100 % / Redundancy: 4.2 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.127 / Rpim(I) all: 0.07 / Rrim(I) all: 0.146 / Χ2: 3.89 / Net I/av σ(I): 24.826 / Net I/σ(I): 11 / Num. measured all: 157035
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.18-2.224.10.318620.9120.170.3461.08799.9
2.22-2.264.10.26718730.9110.150.3071.254100
2.26-2.34.10.27118980.9280.1510.3111.29100
2.3-2.354.10.24618400.9310.1370.2821.382100
2.35-2.44.10.21618610.9430.120.2481.475100
2.4-2.464.10.20418740.9520.1140.2341.496100
2.46-2.524.20.19718760.9520.110.2261.71100
2.52-2.584.20.18318960.9530.1020.212.005100
2.58-2.664.20.1718450.9620.0940.1952.15100
2.66-2.754.20.1618710.9620.0890.1842.429100
2.75-2.844.20.15218750.9670.0850.1752.678100
2.84-2.964.20.1418770.9720.0780.163.067100
2.96-3.094.20.13518990.9760.0750.1553.823100
3.09-3.264.20.12718580.970.070.1464.962100
3.26-3.464.20.12518820.9710.0690.1436.393100
3.46-3.734.20.11618630.9720.0640.1336.814100
3.73-4.14.30.1118840.9770.0610.1267.77100
4.1-4.74.30.10818920.9780.060.1248.991100
4.7-5.914.30.10718940.9810.0590.1228.1100
5.91-504.20.09219140.9860.0510.1067.87299.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-3000data reduction
PHENIX(phenix.refine: 1.8.2_1309)refinement
PDB_EXTRACT3.15data extraction
HKL-3000data scaling
HKL-3000phasing
PHENIXphasing
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1KHG

1khg


Resolution: 2.18→33.213 Å / FOM work R set: 0.886 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1911 1877 5 %
Rwork0.1381 35652 -
obs0.1407 37529 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 90.98 Å2 / Biso mean: 23.96 Å2 / Biso min: 10.46 Å2
Refinement stepCycle: final / Resolution: 2.18→33.213 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4704 0 7 611 5322
Biso mean--28.02 31.32 -
Num. residues----600
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074942
X-RAY DIFFRACTIONf_angle_d1.0496743
X-RAY DIFFRACTIONf_chiral_restr0.071714
X-RAY DIFFRACTIONf_plane_restr0.005885
X-RAY DIFFRACTIONf_dihedral_angle_d12.4311818
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.18-2.23880.26071390.157827432882
2.2388-2.30470.22351470.155127432890
2.3047-2.3790.20581350.141127032838
2.379-2.4640.21291440.141427362880
2.464-2.56260.22871290.135727532882
2.5626-2.67920.18531470.132427472894
2.6792-2.82040.2011410.140127182859
2.8204-2.9970.21431480.144627492897
2.997-3.22820.2171630.140227432906
3.2282-3.55280.17931400.141227222862
3.5528-4.06610.19171420.131827602902
4.0661-5.11980.15051510.11627522903
5.1198-33.21710.16111510.151427832934

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