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- PDB-4r43: Crystal Structure Analysis of MTB PEPCK -

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Basic information

Entry
Database: PDB / ID: 4r43
TitleCrystal Structure Analysis of MTB PEPCK
ComponentsPhosphoenolpyruvate carboxykinase [GTP]
KeywordsLYASE / kinase / GDP Binding
Function / homology
Function and homology information


glycerol biosynthetic process from pyruvate / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / cellular response to iron ion starvation / propionate catabolic process / response to host immune response / oxaloacetate metabolic process / response to lipid / response to starvation / peptidoglycan-based cell wall ...glycerol biosynthetic process from pyruvate / phosphoenolpyruvate carboxykinase (GTP) / phosphoenolpyruvate carboxykinase (GTP) activity / cellular response to iron ion starvation / propionate catabolic process / response to host immune response / oxaloacetate metabolic process / response to lipid / response to starvation / peptidoglycan-based cell wall / gluconeogenesis / cellular response to glucose stimulus / manganese ion binding / GTP binding / extracellular region / plasma membrane / 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
GUANOSINE-5'-DIPHOSPHATE / : / DI(HYDROXYETHYL)ETHER / PHOSPHATE ION / : / Phosphoenolpyruvate carboxykinase [GTP]
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsBrynda, J. / Dostal, J. / Pichova, I. / Snasel, J. / Fanfrlik, J. / Machova, I.
CitationJournal: Plos One / Year: 2015
Title: Structural and Functional Studies of Phosphoenolpyruvate Carboxykinase from Mycobacterium tuberculosis.
Authors: Machova, I. / Snasel, J. / Dostal, J. / Brynda, J. / Fanfrlik, J. / Singh, M. / Tarabek, J. / Vanek, O. / Bednarova, L. / Pichova, I.
History
DepositionAug 19, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_comp_id / _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.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_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.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_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)70,5138
Polymers69,4951
Non-polymers1,0187
Water1,72996
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.358, 124.696, 121.466
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] / PEP carboxykinase / PEPCK


Mass: 69495.258 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: BCGT_4014, P425_00220, pckG, RVBD_0211 / Production host: Escherichia coli (E. coli)
References: UniProt: I6Y334, UniProt: P9WIH3*PLUS, phosphoenolpyruvate carboxykinase (GTP)

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Non-polymers , 5 types, 103 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


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


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.82 Å3/Da / Density % sol: 56.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M sodium acetate pH 4.6,30% PEG 300 , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.979402 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979402 Å / Relative weight: 1
ReflectionResolution: 1.8→47.55 Å / Num. obs: 72592 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 43.447 Å2 / Rmerge(I) obs: 0.053 / Χ2: 1.003 / Net I/σ(I): 24.24
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.16-2.290.32610.0552599672799
2.29-2.440.1913.0851388640499.9
2.44-2.640.12116.6646721599799.9
2.64-2.890.0821.1341067551999.9
2.89-3.230.05528.6439622500799.8
3.23-3.730.04435.9633001441799.8
3.73-4.560.03941.0526979379299.8
4.56-6.410.03843.9321971295999.7
6.410.03843.6711881173499.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation47.91 Å3.8 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREP11.0.02phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DTB

3dtb


Resolution: 1.8→47.55 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.2436 / WRfactor Rwork: 0.2085 / FOM work R set: 0.743 / SU B: 4.1 / SU ML: 0.115 / SU R Cruickshank DPI: 0.118 / SU Rfree: 0.1177 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2431 3632 5 %RANDOM
Rwork0.207 ---
obs0.2088 68999 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 99.81 Å2 / Biso mean: 36.15 Å2 / Biso min: 20.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å20 Å20 Å2
2--0.26 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4644 0 62 96 4802
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0194848
X-RAY DIFFRACTIONr_bond_other_d0.0060.023249
X-RAY DIFFRACTIONr_angle_refined_deg1.9461.9556604
X-RAY DIFFRACTIONr_angle_other_deg1.16837868
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0365608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.97723.929224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.63715714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1651531
X-RAY DIFFRACTIONr_chiral_restr0.1170.2690
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215492
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021035
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.532 253 -
Rwork0.492 4786 -
all-5039 -
obs--99.51 %

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