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- PDB-1php: STRUCTURE OF THE ADP COMPLEX OF THE 3-PHOSPHOGLYCERATE KINASE FRO... -

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Basic information

Entry
Database: PDB / ID: 1php
TitleSTRUCTURE OF THE ADP COMPLEX OF THE 3-PHOSPHOGLYCERATE KINASE FROM BACILLUS STEAROTHERMOPHILUS AT 1.65 ANGSTROMS
Components3-PHOSPHOGLYCERATE KINASE
KeywordsKINASE
Function / homology
Function and homology information


phosphoglycerate kinase / phosphoglycerate kinase activity / glycolytic process / ATP binding / cytoplasm
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
ADENOSINE-5'-DIPHOSPHATE / Phosphoglycerate kinase
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.65 Å
AuthorsDavies, G.J. / Watson, H.C.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 1994
Title: Structure of the ADP complex of the 3-phosphoglycerate kinase from Bacillus stearothermophilus at 1.65 A.
Authors: Davies, G.J. / Gamblin, S.J. / Littlechild, J.A. / Dauter, Z. / Wilson, K.S. / Watson, H.C.
#1: Journal: Proteins / Year: 1993
Title: The Structure of a Thermally Stable 3-Phosphoglycerate Kinase and a Comparison with its Mesophilic Equivalent
Authors: Davies, G.J. / Gamblin, S.J. / Littlechild, J.A. / Watson, H.C.
#2: Journal: J.Mol.Biol. / Year: 1992
Title: Purification, Crystallisation and Preliminary X-Ray Analysis of the 3-Phosphoglycerate Kinase from Bacillus Stearothermophilus
Authors: Davies, G.J. / Gamblin, S.J. / Littlechild, J.A. / Watson, H.C.
#3: Journal: Gene / Year: 1991
Title: Sequence and Expression of the Gene Encoding 3-Phosphoglycerate Kinase from Bacillus Stearothermophilus
Authors: Davies, G.J. / Littlechild, J.A. / Watson, H.C. / Hall, L.
History
DepositionApr 12, 1994Processing site: BNL
Revision 1.0Jun 22, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Other / Refinement description / Category: pdbx_database_status / software
Item: _pdbx_database_status.process_site / _software.classification
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Feb 14, 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 / _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: 3-PHOSPHOGLYCERATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2423
Polymers42,7901
Non-polymers4522
Water11,422634
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.410, 73.930, 68.570
Angle α, β, γ (deg.)90.00, 99.80, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO 188

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Components

#1: Protein 3-PHOSPHOGLYCERATE KINASE


Mass: 42790.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
References: UniProt: P18912, 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-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 634 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.84 %
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
28 mMTris-HCl1drop
31 mMMg-ATP1drop
40.1 mM1dropNaN3
510 %(w/v)PEG6001drop
640 %(w/v)PEG6001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 10 Å / Num. obs: 44754 / % possible obs: 94 % / Num. measured all: 119169 / Rmerge(I) obs: 0.056 / Biso Wilson estimate: 19 Å2
Reflection shell
*PLUS
Highest resolution: 1.65 Å / Lowest resolution: 1.7 Å / Rmerge(I) obs: 0.156

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 1.65→10 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.156 -
obs0.156 44754
Refinement stepCycle: LAST / Resolution: 1.65→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3008 0 28 634 3670
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.019
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_deg
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.33
X-RAY DIFFRACTIONx_mcangle_it3.1564
X-RAY DIFFRACTIONx_scbond_it5.9075
X-RAY DIFFRACTIONx_scangle_it8.8266
Refinement
*PLUS
Num. reflection all: 44754 / Rfactor all: 0.156 / Rfactor Rwork: 0.156
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONx_bond_d0.02
X-RAY DIFFRACTIONx_angle_d0.040.049
X-RAY DIFFRACTIONx_planar_d0.060.054
X-RAY DIFFRACTIONx_plane_restr0.020.014
X-RAY DIFFRACTIONx_chiral_restr0.060.035

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