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- PDB-2ybe: The structure of the fully closed conformation of human PGK in co... -

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Basic information

Entry
Database: PDB / ID: 2ybe
TitleThe structure of the fully closed conformation of human PGK in complex with L-ADP, 3PG and the TSA aluminium tetrafluoride at 2.0 A resolution
ComponentsPHOSPHOGLYCERATE KINASE 1
KeywordsTRANSFERASE / L-NUCLEOSIDE ANALOGUES / GLYCOLYSIS / NUCLEOTIDE BINDING
Function / homology
Function and homology information


Manipulation of host energy metabolism / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase (NAD(P)H) activity / Gluconeogenesis / canonical glycolysis / Glycolysis / plasminogen activation / epithelial cell differentiation / negative regulation of angiogenesis ...Manipulation of host energy metabolism / phosphoglycerate kinase / phosphoglycerate kinase activity / protein-disulfide reductase (NAD(P)H) activity / Gluconeogenesis / canonical glycolysis / Glycolysis / plasminogen activation / epithelial cell differentiation / negative regulation of angiogenesis / ADP binding / gluconeogenesis / glycolytic process / cellular response to hypoxia / membrane raft / phosphorylation / extracellular space / extracellular exosome / ATP binding / membrane / 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 / TETRAFLUOROALUMINATE ION / L-ADENOSINE-5'-DIPHOSPHATE / Phosphoglycerate kinase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBowler, M.W. / Chaloin, L. / Lionne, C.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Interaction of Human 3-Phosphoglycerate Kinase with its Two Substrates: Is Substrate Antagonism a Kinetic Advantage?
Authors: Lallemand, P. / Chaloin, L. / Roy, B. / Barman, T. / Bowler, M.W. / Lionne, C.
History
DepositionMar 7, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 23, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4496
Polymers44,6731
Non-polymers7765
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.202, 91.030, 108.807
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PHOSPHOGLYCERATE KINASE 1 / / PHOSPHOGLYCERATE KINASE / CELL MIGRATION-INDUCING GENE 10 PROTEIN / PRIMER RECOGNITION PROTEIN 2 / PRP 2


Mass: 44672.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P00558, phosphoglycerate kinase

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Non-polymers , 6 types, 121 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-LA8 / L-ADENOSINE-5'-DIPHOSPHATE / L-ADP / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2
#5: Chemical ChemComp-ALF / TETRAFLUOROALUMINATE ION


Mass: 102.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF4
#6: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID / 3-Phosphoglyceric acid


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


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsADENOSINE-5'-DIPHOSPHATE (ADP): THIS IS THE L-ENANTIOMER OF ADP

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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: 2.29 Å3/Da / Density % sol: 46.33 % / Description: NONE
Crystal growpH: 6.5 / Details: 29% PEG 2000MME, 0.1 M BIS/TRIS PH 6.25 .

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.932
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 31, 2011 / Details: GE 221
RadiationMonochromator: DIAMOND 001 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.932 Å / Relative weight: 1
ReflectionResolution: 2→46.7 Å / Num. obs: 25350 / % possible obs: 93.6 % / Observed criterion σ(I): 3 / Redundancy: 3.8 % / Biso Wilson estimate: 27 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 11.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.47 / Mean I/σ(I) obs: 2.2 / % possible all: 83.5

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Processing

Software
NameVersionClassification
REFMAC5.6.0107refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WZC

2wzc


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.939 / SU B: 11.603 / SU ML: 0.172 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24329 1287 5.1 %RANDOM
Rwork0.19316 ---
obs0.19582 24020 93.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.468 Å2
Baniso -1Baniso -2Baniso -3
1--0.61 Å20 Å20 Å2
2--3.08 Å20 Å2
3----2.46 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3079 0 45 116 3240
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223171
X-RAY DIFFRACTIONr_bond_other_d0.0010.022155
X-RAY DIFFRACTIONr_angle_refined_deg1.8661.9964280
X-RAY DIFFRACTIONr_angle_other_deg1.03935307
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3875408
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.52225.641117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.81615578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6231511
X-RAY DIFFRACTIONr_chiral_restr0.1110.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213465
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02561
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.436 75 -
Rwork0.328 1419 -
obs--81.59 %
Refinement TLS params.Method: refined / Origin x: 1.406 Å / Origin y: -7.207 Å / Origin z: -19.412 Å
111213212223313233
T1.0909 Å2-0.2032 Å2-0.0527 Å2-0.9225 Å2-0.1268 Å2--0.028 Å2
L2.0711 °20.466 °2-0.7515 °2-1.7213 °2-0.8805 °2--4.8596 °2
S-0.2872 Å °1.2534 Å °-0.146 Å °-1.3017 Å °0.347 Å °0.0395 Å °0.7461 Å °-0.5992 Å °-0.0597 Å °

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