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- PDB-4gpz: Crystal structure of human B type phosphoglycerate mutase H11 pho... -

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Basic information

Entry
Database: PDB / ID: 4gpz
TitleCrystal structure of human B type phosphoglycerate mutase H11 phosphorylated form
ComponentsPhosphoglycerate mutase 1
KeywordsISOMERASE / HYDROLASE / ALPHA/BETA
Function / homology
Function and homology information


bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase activity / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / Gluconeogenesis / canonical glycolysis / Glycolysis / gluconeogenesis / secretory granule lumen ...bisphosphoglycerate mutase / bisphosphoglycerate mutase activity / phosphoglycerate mutase activity / 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase activity / phosphoglycerate mutase (2,3-diphosphoglycerate-dependent) / Gluconeogenesis / canonical glycolysis / Glycolysis / gluconeogenesis / secretory granule lumen / ficolin-1-rich granule lumen / hydrolase activity / Neutrophil degranulation / protein kinase binding / extracellular exosome / extracellular region / membrane / cytoplasm / cytosol
Similarity search - Function
Phosphoglycerate mutase 1 / Phosphoglycerate/bisphosphoglycerate mutase, active site / Phosphoglycerate mutase family phosphohistidine signature. / Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoglycerate mutase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsHe, C. / Zhou, L. / Zhang, L.
CitationJournal: Nat Commun / Year: 2013
Title: Tyr26 phosphorylation of PGAM1 provides a metabolic advantage to tumours by stabilizing the active conformation.
Authors: Hitosugi, T. / Zhou, L. / Fan, J. / Elf, S. / Zhang, L. / Xie, J. / Wang, Y. / Gu, T.L. / Aleckovic, M. / Leroy, G. / Kang, Y. / Kang, H.B. / Seo, J.H. / Shan, C. / Jin, P. / Gong, W. / ...Authors: Hitosugi, T. / Zhou, L. / Fan, J. / Elf, S. / Zhang, L. / Xie, J. / Wang, Y. / Gu, T.L. / Aleckovic, M. / Leroy, G. / Kang, Y. / Kang, H.B. / Seo, J.H. / Shan, C. / Jin, P. / Gong, W. / Lonial, S. / Arellano, M.L. / Khoury, H.J. / Chen, G.Z. / Shin, D.M. / Khuri, F.R. / Boggon, T.J. / Kang, S. / He, C. / Chen, J.
History
DepositionAug 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _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

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Assembly

Deposited unit
A: Phosphoglycerate mutase 1
B: Phosphoglycerate mutase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4185
Polymers59,9922
Non-polymers4263
Water6,954386
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2870 Å2
ΔGint-6 kcal/mol
Surface area20840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.360, 81.174, 90.381
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 mutase 1 / BPG-dependent PGAM 1 / Phosphoglycerate mutase isozyme B / PGAM-B


Mass: 29996.076 Da / Num. of mol.: 2 / Fragment: Human type B phosphoglycerate mutase
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGAM1, PGAMA, CDABP0006 / Production host: Escherichia coli (E. coli)
References: UniProt: P18669, EC: 3.1.3.13, EC: 5.4.2.1, bisphosphoglycerate mutase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.38 Å3/Da / Density % sol: 48.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG3350, MES, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 180 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.65→60.478 Å / Num. all: 72475 / Num. obs: 72475 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shell
Resolution (Å)Diffraction-ID% possible all
1.65-1.711100
1.71-1.781100
1.78-1.861100
1.86-1.961100
1.96-2.081100
2.08-2.241100

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
PHASESphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YFK

1yfk


Resolution: 1.65→60.39 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.829 / SU ML: 0.061 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21382 3493 5.1 %RANDOM
Rwork0.18502 ---
obs0.18647 65490 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.291 Å2
Baniso -1Baniso -2Baniso -3
1-2.29 Å20 Å2-0 Å2
2---0.44 Å20 Å2
3----1.86 Å2
Refinement stepCycle: LAST / Resolution: 1.65→60.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3844 0 25 386 4255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0193966
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.4711.9745384
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9515475
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.92423.617188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63415676
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.9371533
X-RAY DIFFRACTIONr_chiral_restr0.3030.2569
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0213027
X-RAY DIFFRACTIONr_gen_planes_other
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_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 243 -
Rwork0.276 4495 -
obs--99.71 %

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