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- PDB-1hdi: Pig muscle 3-PHOSPHOGLYCERATE KINASE complexed with 3-PG and MgADP. -

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Basic information

Entry
Database: PDB / ID: 1hdi
TitlePig muscle 3-PHOSPHOGLYCERATE KINASE complexed with 3-PG and MgADP.
ComponentsPHOSPHOGLYCERATE KINASE
KeywordsPHOSPHOTRANSFERASE / KINASE / PHOSPHOGLYCERATE / TERNARY COMPLEX / GLYCOLYSIS
Function / homology
Function and homology information


phosphoglycerate kinase / phosphoglycerate kinase activity / gluconeogenesis / ADP binding / 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 / ADENOSINE MONOPHOSPHATE / Phosphoglycerate kinase 1
Similarity search - Component
Biological speciesSUS SCROFA (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSzilagyi, A.N. / Ghosh, M. / Garman, E. / Vas, M.
CitationJournal: J. Mol. Biol. / Year: 2001
Title: A 1.8 A resolution structure of pig muscle 3-phosphoglycerate kinase with bound MgADP and 3-phosphoglycerate in open conformation: new insight into the role of the nucleotide in domain closure.
Authors: Szilagyi, A.N. / Ghosh, M. / Garman, E. / Vas, M.
History
DepositionNov 16, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Other
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_biol
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4May 1, 2024Group: 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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOGLYCERATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,9624
Polymers43,4041
Non-polymers5583
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)50.500, 105.200, 35.900
Angle α, β, γ (deg.)90.00, 98.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PHOSPHOGLYCERATE KINASE / / PGK


Mass: 43404.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) SUS SCROFA (pig) / Tissue: MUSCLESkeletal muscle / References: UniProt: Q7SIB7*PLUS, phosphoglycerate kinase
#2: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE / Adenosine monophosphate


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Comment: AMP*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 186.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O7P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.1 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.7
Details: THE ENZYME WAS DIALYSED IN 30 MM NAK-PHOSPHATE BUFFER, PH=8.0. SINGLE CRYSTALS WERE GROWN AT 15C WITHIN A FEW WEEKS IN HANGING DROPS (10-15 ML EACH) INITIALLY CONTAINING 1.25 M NAK-PHOSPHATE ...Details: THE ENZYME WAS DIALYSED IN 30 MM NAK-PHOSPHATE BUFFER, PH=8.0. SINGLE CRYSTALS WERE GROWN AT 15C WITHIN A FEW WEEKS IN HANGING DROPS (10-15 ML EACH) INITIALLY CONTAINING 1.25 M NAK-PHOSPHATE (PH=8.0), 100 MM 3-PG, 25 MM MGCL2, 20 MM ADP, 10 MM DITHIOTHREITOL, 0.02% NAN3 AND 15 MG/ML PGK. RESERVOIR SOLUTIONS CONTAINED 2.4-2.75 M NAK-PHOSPHATE(PH=8.0)., pH 7.70
Crystal grow
*PLUS
Temperature: 15 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11.25 Msodium potassium phosphate1drop
2100 mM3-PG1drop
325 mM1dropMgCl2
420 mMADP1drop
510 mMdithiothreitol1drop
60.02 %(w/v)1dropNaN3
715 mg/mlPGK1drop
82.4-2.75 Msodium potassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1997
RadiationMonochromator: GE111 BENT AASYMMETRIC / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.8→20 Å / Num. obs: 34292 / % possible obs: 95.6 % / Redundancy: 2.4 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 17
Reflection shellResolution: 1.8→1.88 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 3 / Rsym value: 0.244 / % possible all: 98.1
Reflection
*PLUS
Num. measured all: 125740
Reflection shell
*PLUS
% possible obs: 98.1 %

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Processing

Software
NameVersionClassification
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: THE STARTING MODEL WAS CHOSEN AS THE STRUCTURE OF THE MNADP BINARY COMPLEX OF PIG MUSCLE PGK CRYSTALLISED IN THE PRESENCE OF AMMONIUM SULPHATE (MAY ET AL., PERSONAL COMM.).

Resolution: 1.8→20 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1662 5 %RANDOM
Rwork0.207 ---
obs0.207 32755 95.5 %-
Displacement parametersBiso mean: 16.5 Å2
Refinement stepCycle: LAST / Resolution: 1.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3037 0 35 208 3280
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.011
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.62
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.7
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d2.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 1.8→1.86 Å / Total num. of bins used: 10 /
RfactorNum. reflection
Rfree0.299 -
Rwork0.237 3086
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.7
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg2.4

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