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- PDB-1kf0: Crystal Structure of Pig Muscle Phosphoglycerate Kinase Ternary C... -

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Basic information

Entry
Database: PDB / ID: 1kf0
TitleCrystal Structure of Pig Muscle Phosphoglycerate Kinase Ternary Complex with AMP-PCP and 3PG
ComponentsPhosphoglycerate Kinase
KeywordsTRANSFERASE / ATP analogue
Function / homology
Function and homology information


phosphoglycerate kinase / phosphoglycerate kinase activity / ADP binding / gluconeogenesis / glycolytic process / phosphorylation / ATP binding / cytosol
Similarity search - Function
Phosphoglycerate kinase, N-terminal domain / Phosphoglycerate kinase / Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-PHOSPHOGLYCERIC ACID / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Phosphoglycerate kinase 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKovari, Z. / Flachner, B. / Naray-Szabo, G. / Vas, M.
CitationJournal: Biochemistry / Year: 2002
Title: Crystallographic and thiol-reactivity studies on the complex of pig muscle phosphoglycerate kinase with ATP analogues: correlation between nucleotide binding mode and helix flexibility.
Authors: Kovari, Z. / Flachner, B. / Naray-Szabo, G. / Vas, M.
History
DepositionNov 19, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_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_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Remark 999SEQUENCE SEQUENCE AUTHOR REMARK STATES THAT THE PIG PHOSPHOGLYCERATE KINASE (PGK) HAS NOT YET BEEN ...SEQUENCE SEQUENCE AUTHOR REMARK STATES THAT THE PIG PHOSPHOGLYCERATE KINASE (PGK) HAS NOT YET BEEN SEQUENCED. THEREFORE THE SEQUENCE OF THE STRUCTURE IS BASED ON THE SEQUENCE OF THE HORSE MUSCLE PGK AND ON THE INTERPRETATION OF THE ELECTRON DENSITY MAPS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoglycerate Kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2424
Polymers44,5261
Non-polymers7163
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.6, 110.3, 48.0
Angle α, β, γ (deg.)90, 93.9, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Phosphoglycerate Kinase /


Mass: 44526.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: muscle / Source: (natural) Sus scrofa (pig) / References: UniProt: Q7SIB7, phosphoglycerate kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID / 3-Phosphoglyceric acid


Mass: 186.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O7P
#4: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.17 Å3/Da / Density % sol: 43.32 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7
Details: magnesium chloride, PEG 8000, PH 7.0, 288K, VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 15 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110 mMAMP-PCP1reservoir
212 mM1reservoirMgCl2
310 mM3PG1reservoir
427-28 %(w/w)PEG80001reservoirpH7.0

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Data collection

DiffractionMean temperature: 297 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 3, 1996
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 12274 / Num. obs: 12274 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.081
Reflection shellResolution: 2.5→2.6 Å / Rmerge(I) obs: 0.252 / % possible all: 79.3
Reflection
*PLUS
% possible obs: 90.88 % / Rmerge(I) obs: 0.081
Reflection shell
*PLUS
% possible obs: 63.18 % / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pig muscle PGK ternary complex with MnAMP-PNP and 3-PG May et al., Proteins, 24:292-303, 1996)

Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2524 609 RANDOM
Rwork0.173 --
all0.2476 11956 -
obs0.2 10666 -
Displacement parametersBiso mean: 24.16 Å2
Baniso -1Baniso -2Baniso -3
1--5.075 Å20 Å20.88 Å2
2---5.437 Å20 Å2
3----4.459 Å2
Refinement stepCycle: LAST / Resolution: 2.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3032 0 43 81 3156
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_angle_deg0.842
X-RAY DIFFRACTIONx_dihedral_angle_d27.05
X-RAY DIFFRACTIONx_improper_angle_d0.5
LS refinement shellResolution: 2.5→2.61 Å
RfactorNum. reflection% reflection
Rfree0.3722 36 -
Rwork0.1249 --
obs-790 48.08 %
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor all: 0.2476 / Rfactor obs: 0.2 / Rfactor Rfree: 0.2524 / Rfactor Rwork: 0.173
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.05
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.3722 / Rfactor Rwork: 0.1249

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