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- PDB-13pk: TERNARY COMPLEX OF PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI -

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Basic information

Entry
Database: PDB / ID: 13pk
TitleTERNARY COMPLEX OF PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI
Components3-PHOSPHOGLYCERATE KINASEPhosphoglycerate kinase
KeywordsKINASE / PHOSPHOGLYCERATE / TERNARY COMPLEX / GLYCOLYSIS / TRANSFERASE
Function / homology
Function and homology information


phosphoglycerate kinase / phosphoglycerate kinase activity / glycosome / glycolytic process / phosphorylation / ATP binding
Similarity search - Function
Phosphoglycerate kinase, euglenozoa / 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-5'-DIPHOSPHATE / PHOSPHATE ION / Phosphoglycerate kinase, glycosomal
Similarity search - Component
Biological speciesTrypanosoma brucei (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBernstein, B.E. / Michels, P.A.M. / Hol, W.G.J.
CitationJournal: Nature / Year: 1997
Title: Synergistic effects of substrate-induced conformational changes in phosphoglycerate kinase activation.
Authors: Bernstein, B.E. / Michels, P.A. / Hol, W.G.
History
DepositionNov 23, 1996Processing site: BNL
Revision 1.0Dec 24, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_asym_id / _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_asym_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_ref_seq_dif.details / _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: 3-PHOSPHOGLYCERATE KINASE
B: 3-PHOSPHOGLYCERATE KINASE
C: 3-PHOSPHOGLYCERATE KINASE
D: 3-PHOSPHOGLYCERATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,54820
Polymers178,8004
Non-polymers2,74816
Water10,791599
1
A: 3-PHOSPHOGLYCERATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,5276
Polymers44,7001
Non-polymers8285
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: 3-PHOSPHOGLYCERATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3384
Polymers44,7001
Non-polymers6383
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: 3-PHOSPHOGLYCERATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4366
Polymers44,7001
Non-polymers7365
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: 3-PHOSPHOGLYCERATE KINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2464
Polymers44,7001
Non-polymers5463
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)113.213, 115.959, 171.327
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
3-PHOSPHOGLYCERATE KINASE / Phosphoglycerate kinase / PGK


Mass: 44699.984 Da / Num. of mol.: 4
Mutation: TRUNCATION OF T. BRUCEI SPECIFIC C-TERMINAL SEQUENCE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trypanosoma brucei (eukaryote) / Organelle: GLYCOSOME / Variant: GLYCOSOMAL VERSION / Plasmid: PET21A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P07378, phosphoglycerate kinase

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Non-polymers , 5 types, 615 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID / 3-Phosphoglyceric acid


Mass: 186.057 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H7O7P
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 599 / 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: 60.87 % / Description: MR SOLUTION USED INDIVIDUAL DOMAINS SEPARATELY
Crystal growMethod: vapor diffusion / pH: 8
Details: VAPOR DIFFUSION BY MIXING EQUAL VOLUMES OF: PROTEIN: 6MG/ML PGK/25MM TRIS PH 7.5/10MM DTT/10MM MGADP/ 10MM 3- PGA WELL SOLUTION: 2.5 M SODIUM POTASSIUM PHOSPHATE PH 8.0, vapor diffusion
PH range: 7.5-8.0
Crystal grow
*PLUS
Temperature: 10 ℃ / Method: vapor diffusion
Details: drop solution was mixed with an equal volume of reservoir solution
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
16 mg/mlprotein1drop
210 mM3-PGA1drop
310 mMMgADP1drop
425 mMTris-HCl1drop
550 mM1dropNaCl
610 mMdithiothreitol1drop
72.5 Mpotassium sodium phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 1, 1996
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 73223 / % possible obs: 98.5 % / Observed criterion σ(I): 2 / Rsym value: 0.061
Reflection shellResolution: 2.5→2.53 Å / Rsym value: 0.328
Reflection
*PLUS
Rmerge(I) obs: 0.061
Reflection shell
*PLUS
Rmerge(I) obs: 0.328

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PHP

1php


Resolution: 2.5→8 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.291 2549 6.6 %RANDOM
Rwork0.2206 ---
obs0.2206 73223 98.5 %-
Displacement parametersBiso mean: 47 Å2
Baniso -1Baniso -2Baniso -3
1-16.65 Å20 Å20 Å2
2---5.29 Å20 Å2
3----11.36 Å2
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12484 0 168 599 13251
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.55
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.5
X-RAY DIFFRACTIONx_mcangle_it2
X-RAY DIFFRACTIONx_scbond_it2
X-RAY DIFFRACTIONx_scangle_it2.5
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDRms dev position (Å)
11RESTRAINTSX-RAY DIFFRACTION100
22X-RAY DIFFRACTION50
LS refinement shellResolution: 2.5→2.53 Å / Total num. of bins used: 25 /
RfactorNum. reflection
Rfree0.362 185
Rwork0.338 2497
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.55
LS refinement shell
*PLUS
Rfactor obs: 0.338

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