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- PDB-4wiu: Crystal Structure of PEPCK (Rv0211) from Mycobacterium tuberculos... -

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Basic information

Entry
Database: PDB / ID: 4wiu
TitleCrystal Structure of PEPCK (Rv0211) from Mycobacterium tuberculosis in complex with oxalate and Mn2+
ComponentsPhosphoenolpyruvate carboxykinase [GTP]
KeywordsLYASE / TRANSFERASE / GTP-dependent PEPCK / P-loop / R-loop / omega-loop
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
: / OXALATE ION / Phosphoenolpyruvate carboxykinase [GTP]
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.02 Å
AuthorsKim, H.L. / Sacchettini, J.C.
CitationJournal: to be published
Title: Crystal Structure of PEPCK (Rv0211) from Mycobacterium tuberculosis in complex with oxalate and Mn2+
Authors: Kim, H.L.
History
DepositionSep 26, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 22, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Other / Structure summary
Revision 1.2Feb 4, 2015Group: Derived calculations
Revision 1.3Feb 25, 2015Group: Derived calculations
Revision 1.4Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / software / struct_keywords
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 / _struct_keywords.text
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)67,7844
Polymers67,5491
Non-polymers2353
Water10,395577
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.969, 122.739, 64.697
Angle α, β, γ (deg.)90.00, 116.98, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-839-

HOH

21A-907-

HOH

31A-914-

HOH

41A-938-

HOH

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Components

#1: Protein Phosphoenolpyruvate carboxykinase [GTP] / PEPCK


Mass: 67549.102 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-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2O4
#4: 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
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 577 / 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: 2.73 Å3/Da / Density % sol: 54.89 %
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: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jan 31, 2012 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. obs: 45100 / % possible obs: 95.2 % / Redundancy: 3.9 % / Biso Wilson estimate: 23.81 Å2 / Rmerge(I) obs: 0.107 / Χ2: 6.494 / Net I/av σ(I): 35.262 / Net I/σ(I): 17.2 / Num. measured all: 173856
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.02-2.053.90.21521621.73392.6
2.05-2.093.90.20722072.27593
2.09-2.133.90.18622032.48493.5
2.13-2.183.90.16922502.53393.6
2.18-2.223.90.16921722.90493.8
2.22-2.273.30.19221484.77791.6
2.27-2.333.90.1522263.39794.4
2.33-2.393.90.14522634.39394.8
2.39-2.473.90.1422374.63194.8
2.47-2.543.90.13622435.56295.2
2.54-2.643.90.12622455.83195.5
2.64-2.743.90.12522726.10495.9
2.74-2.873.90.12222747.61996.1
2.87-3.023.90.11622878.66496.6
3.02-3.213.90.1122969.6396.8
3.21-3.453.90.105230910.95997.3
3.45-3.83.70.102230411.92596.2
3.8-4.353.60.094227511.72696
4.35-5.483.90.089233810.54698.6
5.48-503.80.079238911.85798.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.7.2_869)refinement
HKL-2000data reduction
PDB_EXTRACT3.15data extraction
HKL-2000data scaling
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2.02→31.784 Å / SU ML: 0.54 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 18.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1953 4465 5.08 %
Rwork0.1551 --
obs0.1571 87872 93.71 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.375 Å2 / ksol: 0.328 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.7229 Å2-0 Å2-2.209 Å2
2---2.3623 Å2-0 Å2
3----1.3606 Å2
Refinement stepCycle: LAST / Resolution: 2.02→31.784 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4704 0 13 577 5294
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074942
X-RAY DIFFRACTIONf_angle_d1.0156744
X-RAY DIFFRACTIONf_dihedral_angle_d12.881819
X-RAY DIFFRACTIONf_chiral_restr0.073715
X-RAY DIFFRACTIONf_plane_restr0.005884
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.02-2.04070.21951270.18892407X-RAY DIFFRACTION83
2.0407-2.06470.24581460.19922780X-RAY DIFFRACTION92
2.0647-2.08990.23641450.18052719X-RAY DIFFRACTION92
2.0899-2.11640.24911400.16272779X-RAY DIFFRACTION92
2.1164-2.14420.20531600.15322697X-RAY DIFFRACTION92
2.1442-2.17360.21961650.14772805X-RAY DIFFRACTION93
2.1736-2.20460.2031380.15942691X-RAY DIFFRACTION93
2.2046-2.23750.24621520.18032610X-RAY DIFFRACTION86
2.2375-2.27250.3121170.20572401X-RAY DIFFRACTION85
2.2725-2.30970.20271090.17132894X-RAY DIFFRACTION93
2.3097-2.34950.24131480.16292732X-RAY DIFFRACTION94
2.3495-2.39230.23511580.15532820X-RAY DIFFRACTION94
2.3923-2.43820.22341400.16112793X-RAY DIFFRACTION94
2.4382-2.4880.2171570.16192814X-RAY DIFFRACTION94
2.488-2.54210.20551170.16352809X-RAY DIFFRACTION95
2.5421-2.60120.2411460.15962828X-RAY DIFFRACTION95
2.6012-2.66620.17771440.15412844X-RAY DIFFRACTION95
2.6662-2.73830.20911670.15912761X-RAY DIFFRACTION95
2.7383-2.81880.21651670.16242832X-RAY DIFFRACTION96
2.8188-2.90970.18441840.16142841X-RAY DIFFRACTION96
2.9097-3.01360.22221530.15892838X-RAY DIFFRACTION96
3.0136-3.13420.19651360.15622859X-RAY DIFFRACTION96
3.1342-3.27670.19791550.15522849X-RAY DIFFRACTION97
3.2767-3.44920.19021660.15452909X-RAY DIFFRACTION97
3.4492-3.66510.18381510.15682782X-RAY DIFFRACTION93
3.6651-3.94760.17441690.1462725X-RAY DIFFRACTION94
3.9476-4.34390.15541370.12522826X-RAY DIFFRACTION94
4.3439-4.97040.14871540.11522901X-RAY DIFFRACTION98
4.9704-6.25440.15291420.15632954X-RAY DIFFRACTION99
6.2544-31.78830.17931750.16732907X-RAY DIFFRACTION99

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