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

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Basic information

Entry
Database: PDB / ID: 2wzd
TitleThe catalytically active fully closed conformation of human phosphoglycerate kinase K219A mutant in complex with ADP, 3PG and aluminium trifluoride
ComponentsPHOSPHOGLYCERATE KINASE 1
KeywordsTRANSFERASE / HEREDITARY HEMOLYTIC ANEMIA / PHOSPHOPROTEIN / KINASE / 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 / ADENOSINE-5'-DIPHOSPHATE / ALUMINUM FLUORIDE / Phosphoglycerate kinase 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 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: J.Am.Chem.Soc. / Year: 2010
Title: Transition State Analogue Structures of Human Phosphoglycerate Kinase Establish the Importance of Charge Balance in Catalysis.
Authors: Cliff, M.J. / Bowler, M.W. / Szabo, J. / Marston, J.P.M. / Varga, A.V. / Hownslow, A.M.H. / Baxter, N.J. / Blackburn, G.M. / Vas, M. / Waltho, J.P.
History
DepositionNov 27, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 7, 2011Group: Database references
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_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_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.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

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOGLYCERATE KINASE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3726
Polymers44,6151
Non-polymers7575
Water8,395466
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.380, 91.590, 108.480
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 / PRP 2 / CELL MIGRATION-INDUCING GENE 10 PROTEIN


Mass: 44614.520 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-417 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: COMPLEXED WITH ADP, 3PG AND ALUMINIUM TRIFLUORIDE / 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, 471 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-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3
#5: 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
#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.: 466 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsENGINEERED RESIDUE IN CHAIN A, LYS 220 TO ALA

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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: 2.19 Å3/Da / Density % sol: 50 % / Description: NONE
Crystal growpH: 6.5 / Details: 22% PEG2000MME, 0.1M BIS/TRIS PH 6.5

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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: Jan 22, 2009 / Details: GE211
RadiationMonochromator: C111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.56→20 Å / Num. obs: 55495 / % possible obs: 98 % / Observed criterion σ(I): 3 / Redundancy: 2.7 % / Biso Wilson estimate: 14.5 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.9
Reflection shellResolution: 1.56→1.64 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.7 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C39

3c39


Resolution: 1.56→20 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 2.787 / SU ML: 0.053 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE METAL FLUORIDE IS MODELED AS AF33 WITH A COORDINATING WATER MOLECULE (A3000)AS THIS IS THE OBSERVED SPECIES IN 19F-NMR EXPERIEMNTS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20181 2800 5 %RANDOM
Rwork0.16634 ---
obs0.16815 52652 97.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 5.368 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2--0.95 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 1.56→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3036 0 44 466 3546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223161
X-RAY DIFFRACTIONr_bond_other_d0.0010.022141
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.9934276
X-RAY DIFFRACTIONr_angle_other_deg0.94235291
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3845415
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.54325.714119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27415574
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.5551511
X-RAY DIFFRACTIONr_chiral_restr0.0910.2489
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0213482
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02568
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_it0.8111.52019
X-RAY DIFFRACTIONr_mcbond_other0.2671.5837
X-RAY DIFFRACTIONr_mcangle_it1.35223238
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.27931142
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6444.51032
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: 1.56→1.6 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 177 -
Rwork0.222 3608 -
obs--92.32 %
Refinement TLS params.

S33: -0.0238 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.446-1.39570.74574.2064-0.90312.4891-0.3254-0.34980.13340.71020.3492-0.0421-0.2366-0.19070.1460.0723-0.01030.0764-0.020.01023.4183.6669-5.4552
21.2674-0.63810.28971.7941-0.69581.1430.05770.0773-0.0025-0.1597-0.03390.08240.0364-0.02260.0422-0.0035-0.00160.0528-0.00910.0248-5.674610.4044-31.9151
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 189
2X-RAY DIFFRACTION2A190 - 416

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