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- PDB-1j3b: Crystal structure of ATP-dependent phosphoenolpyruvate carboxykin... -

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Basic information

Entry
Database: PDB / ID: 1j3b
TitleCrystal structure of ATP-dependent phosphoenolpyruvate carboxykinase from Thermus thermophilus HB8
ComponentsATP-dependent phosphoenolpyruvate carboxykinase
KeywordsTRANSFERASE / phosphoenolpyruvate carboxykinase / adenosine triphosphate / Thermus thermophilus / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


phosphoenolpyruvate carboxykinase (ATP) / phosphoenolpyruvate carboxykinase (ATP) activity / gluconeogenesis / ATP binding / metal ion binding / cytosol
Similarity search - Function
Phosphoenolpyruvate carboxykinase, ATP-utilising / Phosphoenolpyruvate carboxykinase (ATP), conserved site / Phosphoenolpyruvate carboxykinase / Phosphoenolpyruvate carboxykinase (ATP) 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, ATP-utilising / Phosphoenolpyruvate carboxykinase (ATP), conserved site / Phosphoenolpyruvate carboxykinase / Phosphoenolpyruvate carboxykinase (ATP) 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 (ATP) / Phosphoenolpyruvate carboxykinase (ATP)
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsSugahara, M. / Miyano, M. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of ATP-dependent phosphoenolpyruvate carboxykinase from Thermus thermophilus HB8 showing the structural basis of induced fit and thermostability.
Authors: Sugahara, M. / Ohshima, N. / Ukita, Y. / Sugahara, M. / Kunishima, N.
History
DepositionJan 21, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 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_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_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_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.ptnr1_label_seq_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_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: ATP-dependent phosphoenolpyruvate carboxykinase
B: ATP-dependent phosphoenolpyruvate carboxykinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,89315
Polymers118,7742
Non-polymers1,11913
Water12,773709
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.702, 129.910, 173.391
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a dimer in the asymmetric unit.

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Components

#1: Protein ATP-dependent phosphoenolpyruvate carboxykinase


Mass: 59387.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / References: UniProt: Q7SIC6, UniProt: Q5SLL5*PLUS
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 709 / 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: 2.9 Å3/Da / Density % sol: 57.25 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 6.3
Details: potassium phosphate, sodium phosphate, pH 6.3, MICROBATCH, temperature 291K
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
113.3 mg/mlprotein1drop
21.3 Mpotassium phosphate1reservoir
30.91 Msodium phosphate1reservoirpH6.3

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 2, 2002 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 99163 / Num. obs: 99163 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.32 % / Biso Wilson estimate: 33.1 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.07 / Net I/σ(I): 8
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.13 % / Rmerge(I) obs: 0.713 / Mean I/σ(I) obs: 4.19 / Num. unique all: 9804 / Rsym value: 0.675 / % possible all: 100
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 726185
Reflection shell
*PLUS
Highest resolution: 2 Å / % possible obs: 100 % / Mean I/σ(I) obs: 4.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1OEN

1oen


Resolution: 2→36.1 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.226 4873 -RANDOM
Rwork0.207 ---
all0.208 98995 --
obs0.208 98995 99.6 %-
Displacement parametersBiso mean: 36.6 Å2
Baniso -1Baniso -2Baniso -3
1-8.87 Å20 Å20 Å2
2---6.38 Å20 Å2
3----2.48 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.27 Å
Refinement stepCycle: LAST / Resolution: 2→36.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8201 0 59 709 8969
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.44
X-RAY DIFFRACTIONc_bond_d0.0054
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.307 447 -
Rwork0.291 --
obs-9051 96.9 %
Refinement
*PLUS
Lowest resolution: 40 Å / Num. reflection obs: 98955 / % reflection Rfree: 5 % / Rfactor Rfree: 0.23 / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
LS refinement shell
*PLUS
Rfactor Rfree: 0.31 / Rfactor Rwork: 0.29

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