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- PDB-2x15: The catalytically active fully closed conformation of human phosp... -

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Basic information

Entry
Database: PDB / ID: 2x15
TitleThe catalytically active fully closed conformation of human phosphoglycerate kinase in complex with ADP and 1,3- bisphosphoglycerate
ComponentsPHOSPHOGLYCERATE KINASE 1
KeywordsTRANSFERASE / TRANSITION STATE ANALOGUE / HEREDITARY HEMOLYTIC ANEMIA / PHOSPHOPROTEIN / KINASE / GLYCOLYSIS / PHOSPHORYL TRANSFER / 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 / ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / 1,3-BISPHOSPHOGLYCERIC ACID / Phosphoglycerate kinase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBowler, M.W. / Cliff, M.J. / Marston, J.P.M. / Baxter, N.J. / Hounslow, A.M.H. / Varga, A.V. / Szabo, J. / Vas, M. / Blackburn, G.M. / Waltho, J.P.
CitationJournal: To be Published
Title: The Structure of Human Phosphoglycerate Kinase in its Fully Active Conformation in Complex with Ground State Analoges
Authors: Bowler, M.W. / Cliff, M.J. / Marston, J.P.M. / Baxter, N.J. / Hounslow, A.M.H. / Varga, A.V. / Szabo, J. / Vas, M. / Blackburn, G.M. / Waltho, J.P.
History
DepositionDec 21, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2011Provider: 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 / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.pdbx_ptnr2_label_alt_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_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)45,9526
Polymers44,5411
Non-polymers1,4115
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.730, 91.750, 108.310
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 / / PRIMER RECOGNITION PROTEIN 2 / CELL MIGRATION-INDUCING GENE 10 PROTEIN / PRP 2


Mass: 44541.426 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH ADP AND 1,3-BPG / 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, 85 molecules

#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 / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-X15 / 1,3-BISPHOSPHOGLYCERIC ACID / 1,3-Bisphosphoglyceric acid


Mass: 266.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O10P2
#5: Chemical ChemComp-3PG / 3-PHOSPHOGLYCERIC ACID / 3-Phosphoglyceric acid


Mass: 186.057 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7O7P
#6: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 80 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details1,3-BISPHOSPHOGLYCERATE (X15): 1,3-BISPHOSPHOGLYCERATE WAS FORMED IN CRYSTALLO BY SOAKING CRYSTALS ...1,3-BISPHOSPHOGLYCERATE (X15): 1,3-BISPHOSPHOGLYCERATE WAS FORMED IN CRYSTALLO BY SOAKING CRYSTALS CONTAINING ADP AND 3PG IN ATP

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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: 2.16 Å3/Da / Density % sol: 43 % / 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: May 6, 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: 2.1→20 Å / Num. obs: 22995 / % possible obs: 99.1 % / Observed criterion σ(I): 3 / Redundancy: 2.8 % / Biso Wilson estimate: 25.2 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 10.2
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 3 / % possible all: 99.8

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Processing

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

2wzb


Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 10.756 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 1,3-BISPHOSPHOGLYCERATE WAS FORMED IN THE CRYSTALS BY SOAKING ATP INTO CRYSTALS OF THE ADP 3PG COMPLEX.
RfactorNum. reflection% reflectionSelection details
Rfree0.23795 1184 5.2 %RANDOM
Rwork0.19249 ---
obs0.19488 21765 98.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.736 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20 Å2
2--1.73 Å20 Å2
3----1.57 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3063 0 85 80 3228
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0223155
X-RAY DIFFRACTIONr_bond_other_d0.0010.022145
X-RAY DIFFRACTIONr_angle_refined_deg1.4011.9954260
X-RAY DIFFRACTIONr_angle_other_deg0.84535286
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4535406
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.43125.641117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.06515573
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9781511
X-RAY DIFFRACTIONr_chiral_restr0.0780.2490
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213449
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02565
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_it0.481.52017
X-RAY DIFFRACTIONr_mcbond_other0.1261.5836
X-RAY DIFFRACTIONr_mcangle_it0.87323228
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.59931138
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.5534.51032
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: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.27 82 -
Rwork0.239 1605 -
obs--99.76 %
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)
12.0214-0.3871-0.32523.44010.65633.70090.0031-0.32910.23250.34960.1829-0.4912-0.44160.6348-0.1860.155-0.0759-0.03810.1852-0.0550.08993.4183.667-5.455
22.0887-0.535-0.4051.78310.59141.65340.2240.24820.5701-0.4649-0.16730.0434-0.5824-0.235-0.05670.31080.09830.00910.09720.07270.2026-5.67510.404-31.915
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 189
2X-RAY DIFFRACTION2A190 - 416

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