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- PDB-2x13: The catalytically active fully closed conformation of human phosp... -

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Basic information

Entry
Database: PDB / ID: 2x13
TitleThe catalytically active fully closed conformation of human phosphoglycerate kinase in complex with ADP and 3phosphoglycerate
ComponentsPHOSPHOGLYCERATE KINASE 1
KeywordsTRANSFERASE / TRANSITION STATE ANALOGUE / HEREDITARY HEMOLYTIC ANEMIA / ATP-BINDING / KINASE / GLYCOLYSIS / DISEASE MUTATION
Function / homology
Function and homology information


negative regulation of pyruvate decarboxylation to acetyl-CoA / 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 pyruvate decarboxylation to acetyl-CoA / 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 / gluconeogenesis / glycolytic process / ADP binding / cellular response to hypoxia / non-specific serine/threonine protein kinase / mitochondrial matrix / membrane raft / protein serine kinase activity / protein serine/threonine kinase activity / extracellular space / extracellular exosome / ATP binding / metal ion 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 / ADENOSINE-5'-DIPHOSPHATE / Phosphoglycerate kinase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.74 Å
AuthorsBowler, M.W. / Cliff, M.J. / Marston, J.P.M. / Baxter, N.J. / Hownslow, A.M.H. / Varga, A.V. / Szabo, J. / Vas, M. / Blackburn, G.M. / Waltho, J.P.
CitationJournal: Structure / Year: 2024
Title: Metal fluorides-multi-functional tools for the study of phosphoryl transfer enzymes, a practical guide.
Authors: Pellegrini, E. / Juyoux, P. / von Velsen, J. / Baxter, N.J. / Dannatt, H.R.W. / Jin, Y. / Cliff, M.J. / Waltho, J.P. / Bowler, M.W.
History
DepositionDec 21, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 29, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 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
Revision 1.4Aug 21, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)45,1794
Polymers44,5411
Non-polymers6383
Water4,990277
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.940, 91.440, 108.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 44541.426 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
#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


Mass: 186.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O7P
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 277 / 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: 2.03 Å3/Da / Density % sol: 43.28 % / Description: NONE
Crystal growpH: 6.5 / Details: 0.1M BIS/TRIS PH 6.5 21% P2000MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 26, 2009 / Details: GE 211
RadiationMonochromator: DIAMOND 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.74→20 Å / Num. obs: 40002 / % possible obs: 98.4 % / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Biso Wilson estimate: 18.7 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.1
Reflection shellResolution: 1.74→1.83 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 3 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MIR
Starting model: PDB ENTRY 2WZB

2wzb


Resolution: 1.74→28.36 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 4.948 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2181 2014 5 %RANDOM
Rwork0.1853 ---
obs0.18695 37940 98.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.135 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2--1.3 Å20 Å2
3----2.04 Å2
Refinement stepCycle: LAST / Resolution: 1.74→28.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3063 0 39 277 3379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223176
X-RAY DIFFRACTIONr_bond_other_d0.0010.022161
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.9944293
X-RAY DIFFRACTIONr_angle_other_deg0.86535339
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9315414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.15125.714119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1315581
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0321511
X-RAY DIFFRACTIONr_chiral_restr0.0780.2492
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213489
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02569
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_it0.571.52029
X-RAY DIFFRACTIONr_mcbond_other0.1611.5840
X-RAY DIFFRACTIONr_mcangle_it1.01823252
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.7531147
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8614.51037
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: 1.739→1.784 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 148 -
Rwork0.258 2676 -
obs--94.64 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1888-0.97670.88983.4287-0.73213.0901-0.2373-0.28250.14840.57760.2038-0.0185-0.2843-0.2320.03350.12470.0282-0.00520.0655-0.01970.01133.3773.526-5.312
21.1674-0.46530.31411.3721-0.48611.37110.00950.0080.016-0.0902-0.02580.0724-0.0088-0.07380.01630.0106-0.00130.00030.0472-0.01350.046-5.65210.299-31.767
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 189
2X-RAY DIFFRACTION2A190 - 416

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