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- PDB-5y64: Phosphoglycerate mutase 1 H11 phosphorylated form complexed with KH1 -

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Basic information

Entry
Database: PDB / ID: 5y64
TitlePhosphoglycerate mutase 1 H11 phosphorylated form complexed with KH1
Components(Phosphoglycerate mutase ...) x 2
KeywordsISOMERASE/INHIBITOR / ISOMERASE / ISOMERASE-INHIBITOR complex
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
Chem-8LF / Phosphoglycerate mutase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.149 Å
AuthorsZhou, L. / Jiang, L.L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China21472026 China
CitationJournal: To Be Published
Title: Phosphoglycerate mutase 1 H11 phosphorylated form complexed with KH1
Authors: Zhou, L. / Jiang, L.L.
History
DepositionAug 10, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 5, 2018Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)60,5535
Polymers59,9132
Non-polymers6403
Water2,774154
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-8 kcal/mol
Surface area20460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.527, 82.736, 104.361
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain B
21chain C

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain BB3 - 235
211chain CC2 - 235

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Components

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Phosphoglycerate mutase ... , 2 types, 2 molecules BC

#1: Protein Phosphoglycerate mutase 1 / BPG-dependent PGAM 1 / Phosphoglycerate mutase isozyme B / PGAM-B


Mass: 29917.104 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGAM1, PGAMA, CDABP0006 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P18669, phosphoglycerate mutase (2,3-diphosphoglycerate-dependent), bisphosphoglycerate mutase
#2: Protein Phosphoglycerate mutase 1 / BPG-dependent PGAM 1 / Phosphoglycerate mutase isozyme B / PGAM-B


Mass: 29996.076 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGAM1, PGAMA, CDABP0006 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P18669, phosphoglycerate mutase (2,3-diphosphoglycerate-dependent), bisphosphoglycerate mutase

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Non-polymers , 4 types, 157 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#5: Chemical ChemComp-8LF / ~{N}-[3,4-bis(oxidanyl)-9,10-bis(oxidanylidene)anthracen-2-yl]-4-methyl-benzenesulfonamide


Mass: 409.412 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H15NO6S / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.97 Å3/Da / Density % sol: 58.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: MES, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.149→50 Å / Num. obs: 39535 / % possible obs: 99.9 % / Redundancy: 7.1 % / Biso Wilson estimate: 45.5 Å2 / Rmerge(I) obs: 0.065 / Rpim(I) all: 0.026 / Rrim(I) all: 0.071 / Χ2: 1.033 / Net I/σ(I): 11.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.237.30.74438890.8250.2950.8011.073100
2.23-2.327.30.53538840.9060.2120.5761.096100
2.32-2.427.30.37839290.9510.150.4071.096100
2.42-2.557.30.26638930.9760.1050.2861.074100
2.55-2.717.30.19239060.9850.0760.2071.014100
2.71-2.927.30.12739310.9930.050.1371.068100
2.92-3.217.20.09539490.9950.0380.1031.024100
3.21-3.686.90.0739740.9970.0290.0760.94699.9
3.68-4.636.70.05140110.9980.0210.0550.9699.9
4.63-506.90.03241690.9990.0130.0350.96499.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
PHENIXphenix.refine: 1.8.2_1309refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.149→38.373 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 25.1
RfactorNum. reflection% reflection
Rfree0.2362 1982 5.02 %
Rwork0.2033 --
obs0.205 39473 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 86.29 Å2 / Biso mean: 47.21 Å2 / Biso min: 27.7 Å2
Refinement stepCycle: final / Resolution: 2.149→38.373 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3761 0 42 154 3957
Biso mean--66.09 46.49 -
Num. residues----467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093903
X-RAY DIFFRACTIONf_angle_d1.1635304
X-RAY DIFFRACTIONf_chiral_restr0.047554
X-RAY DIFFRACTIONf_plane_restr0.006683
X-RAY DIFFRACTIONf_dihedral_angle_d14.4831461
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11B2174X-RAY DIFFRACTION6.651TORSIONAL
12C2174X-RAY DIFFRACTION6.651TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1494-2.20320.291400.25912561270197
2.2032-2.26270.30671520.244126292781100
2.2627-2.32930.29591250.233526762801100
2.3293-2.40450.25051480.229426242772100
2.4045-2.49040.27271290.221827012830100
2.4904-2.59010.26731320.230126412773100
2.5901-2.70790.2561280.22226652793100
2.7079-2.85070.26021420.219826882830100
2.8507-3.02920.31911440.237826662810100
3.0292-3.2630.2151410.222126852826100
3.263-3.59110.2521760.218526602836100
3.5911-4.11030.21071330.183527032836100
4.1103-5.17650.19751540.162327382892100
5.1765-38.3790.22071380.19872854299299

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