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- PDB-4wpv: Crystal Structure of E83A mutant of Mtb PEPCK in complex with Zn2... -

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Basic information

Entry
Database: PDB / ID: 4wpv
TitleCrystal Structure of E83A mutant of Mtb PEPCK in complex with Zn2+ and phosphate ion
ComponentsPhosphoenolpyruvate carboxykinase [GTP]
KeywordsLYASE / TRANSFERASE / GTP-dependent PEPCK / 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
PHOSPHATE ION / Phosphoenolpyruvate carboxykinase [GTP]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.672 Å
AuthorsKim, H.L. / Sacchettini, J.C.
CitationJournal: To Be Published
Title: Crystal Structure of E83A from Mtb PEPCK in complex with Zn2+ and phosphate ion
Authors: Kim, H.L. / Sacchettini, J.C.
History
DepositionOct 21, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 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_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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _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_label_asym_id / _struct_conn.ptnr2_label_atom_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)69,78110
Polymers68,9891
Non-polymers7939
Water14,880826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)102.762, 122.281, 63.984
Angle α, β, γ (deg.)90.000, 116.880, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-925-

HOH

21A-952-

HOH

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Components

#1: Protein Phosphoenolpyruvate carboxykinase [GTP] / PEPCK


Mass: 68988.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: E83A mutant / 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-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 826 / 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: 54.65 %
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: 1.2835 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 28, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2835 Å / Relative weight: 1
ReflectionResolution: 1.67→50 Å / Num. obs: 81050 / % possible obs: 99.5 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.043 / Χ2: 1.463 / Net I/av σ(I): 40.776 / Net I/σ(I): 17.6 / Num. measured all: 329340
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.67-1.73.40.1437540.77291.5
1.7-1.733.80.13640630.907100
1.73-1.7640.11440130.91100
1.76-1.84.10.10140460.922100
1.8-1.844.10.09140670.988100
1.84-1.884.10.08340901.044100
1.88-1.934.10.08840391.437100
1.93-1.984.10.06540451.189100
1.98-2.044.10.05840831.172100
2.04-2.14.10.06540511.606100
2.1-2.184.10.04740741.221100
2.18-2.274.10.05340701.548100
2.27-2.374.10.04340761.283100
2.37-2.494.20.04340531.395100
2.49-2.654.20.04640991.721100
2.65-2.864.20.05140682.427100
2.86-3.144.20.05340613.095100
3.14-3.64.10.04241092.489100
3.6-4.534.10.0340771.482100
4.53-504.20.02941121.29799.1

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Processing

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

4wie


Resolution: 1.672→47.814 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1766 4060 5.01 %
Rwork0.1551 --
obs0.1562 81047 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.62 Å2 / Biso mean: 18.8394 Å2 / Biso min: 7.62 Å2
Refinement stepCycle: final / Resolution: 1.672→47.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4604 0 38 826 5468
Biso mean--17.11 29.83 -
Num. residues----586

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