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- PDB-3dcy: Crystal Structure a TP53-induced glycolysis and apoptosis regulat... -

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Basic information

Entry
Database: PDB / ID: 3dcy
TitleCrystal Structure a TP53-induced glycolysis and apoptosis regulator protein from Homo sapiens.
ComponentsREGULATOR PROTEIN
Keywordsapoptosis regulator / OMIM 610775 / C12orf5 / TIGAR / TP53-induced glycolysis and apoptosis regulator / CASP Target / Structural Genomics Medical Relevance / Protein Structure Initiative / PSI / Center for Eukaryotic Structural Genomics / CESG / Isomerase / Phosphoprotein
Function / homology
Function and homology information


: / regulation of response to DNA damage checkpoint signaling / regulation of pentose-phosphate shunt / intracellular anatomical structure / : / cellular response to cobalt ion / fructose 2,6-bisphosphate metabolic process / fructose-2,6-bisphosphate 2-phosphatase / fructose-2,6-bisphosphate 2-phosphatase activity / positive regulation of hexokinase activity ...: / regulation of response to DNA damage checkpoint signaling / regulation of pentose-phosphate shunt / intracellular anatomical structure / : / cellular response to cobalt ion / fructose 2,6-bisphosphate metabolic process / fructose-2,6-bisphosphate 2-phosphatase / fructose-2,6-bisphosphate 2-phosphatase activity / positive regulation of hexokinase activity / intestinal epithelial cell development / fructose 1,6-bisphosphate metabolic process / negative regulation of programmed cell death / negative regulation of glucose catabolic process to lactate via pyruvate / negative regulation of glycolytic process / negative regulation of mitophagy / positive regulation of cardiac muscle cell apoptotic process / negative regulation of reactive oxygen species metabolic process / positive regulation of DNA repair / response to ischemia / response to gamma radiation / TP53 Regulates Metabolic Genes / autophagy / cellular response to hypoxia / mitochondrial outer membrane / response to xenobiotic stimulus / apoptotic process / DNA damage response / nucleus / cytosol / cytoplasm
Similarity search - Function
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
PHOSPHATE ION / Fructose-2,6-bisphosphatase TIGAR
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.748 Å
AuthorsMcCoy, J.G. / Bingman, C.A. / Wesenberg, G.E. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)
CitationJournal: To be Published
Title: Crystal Structure a TP53-induced glycolysis and apoptosis regulator protein from Homo sapiens.
Authors: McCoy, J.G. / Bingman, C.A. / Wesenberg, G.E. / Phillips Jr., G.N.
History
DepositionJun 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: REGULATOR PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2402
Polymers31,1451
Non-polymers951
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.983, 76.408, 79.536
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein REGULATOR PROTEIN


Mass: 31145.246 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: C12orf5 / Plasmid: PVP 16 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q9NQ88
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS STRUCTURE WAS SUBMITTED AS CASP8 ID T0394.

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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: 2.1 Å3/Da / Density % sol: 40.6 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PROTEIN SOLUTION (10 MG/ML SEMET PROTEIN, 0.050 M NACL, 0.0003 M TCEP, 0.005 M MES PH 6.0) MIXED IN A 1:1 RATIO WITH WELL SOLUTION (20% PEG 3350, 0.10 M MES PH 6.0) CRYOPROTECTED WITH 20% ...Details: PROTEIN SOLUTION (10 MG/ML SEMET PROTEIN, 0.050 M NACL, 0.0003 M TCEP, 0.005 M MES PH 6.0) MIXED IN A 1:1 RATIO WITH WELL SOLUTION (20% PEG 3350, 0.10 M MES PH 6.0) CRYOPROTECTED WITH 20% ETHYLENE GLYCOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.97942 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 4, 2008 / Details: Adjustable focusing mirrors in K-B geometry
RadiationMonochromator: Si(111) Double Crystal Monochromater / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.748→50 Å / Num. obs: 25927 / % possible obs: 99.8 % / Redundancy: 13.9 % / Rmerge(I) obs: 0.109 / Χ2: 2.108 / Net I/σ(I): 16.223
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.75-1.819.70.542.36925140.94698.4
1.81-1.89130.4425330.97599.8
1.89-1.9714.30.31825651.123100
1.97-2.0714.60.24725561.157100
2.07-2.214.60.18825551.308100
2.2-2.3814.70.15625701.451100
2.38-2.6114.60.13226051.645100
2.61-2.9914.60.10926102.31100
2.99-3.7714.50.08326382.663100
3.77-5013.80.06827816.78699.9

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Phasing

PhasingMethod: SAD
Phasing MAD set

R cullis centric: 0 / Highest resolution: 1.75 Å / Lowest resolution: 36.43 Å / Power centric: 0

IDR cullis acentricPower acentricReflection acentricReflection centric
ISO_100227293113
ANO_10.443.003226260
Phasing MAD set shell

R cullis centric: 0 / Power centric: 0

IDResolution (Å)R cullis acentricPower acentricReflection acentricReflection centric
ISO_17.66-36.4300215150
ISO_15.48-7.6600423154
ISO_14.49-5.4800569155
ISO_13.9-4.4900695162
ISO_13.49-3.900788149
ISO_13.19-3.4900869154
ISO_12.95-3.1900962159
ISO_12.76-2.95001051158
ISO_12.61-2.76001103161
ISO_12.47-2.61001182160
ISO_12.36-2.47001236156
ISO_12.26-2.36001307156
ISO_12.17-2.26001360155
ISO_12.09-2.17001423160
ISO_12.02-2.09001470162
ISO_11.96-2.02001506154
ISO_11.9-1.96001584159
ISO_11.84-1.9001633160
ISO_11.8-1.84001673149
ISO_11.75-1.8001680140
ANO_17.66-36.430.1578.8412150
ANO_15.48-7.660.1599.1234230
ANO_14.49-5.480.1738.1535690
ANO_13.9-4.490.1997.0176950
ANO_13.49-3.90.2525.6867880
ANO_13.19-3.490.2695.4018690
ANO_12.95-3.190.2635.3599620
ANO_12.76-2.950.2815.06410510
ANO_12.61-2.760.314.56311030
ANO_12.47-2.610.3593.79511820
ANO_12.36-2.470.3773.51912360
ANO_12.26-2.360.4342.93713070
ANO_12.17-2.260.4732.66713600
ANO_12.09-2.170.5292.36714230
ANO_12.02-2.090.5861.99414700
ANO_11.96-2.020.6371.72615060
ANO_11.9-1.960.6911.55115840
ANO_11.84-1.90.7661.36516330
ANO_11.8-1.840.8431.15916620
ANO_11.75-1.80.9071.01915880
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
1-9.508-43.389-30.512SE18.062.79
2-3.922-37.232-39.334SE15.192.34
3-4.411-61.117-8.823SE18.892.36
4-3.863-48.1-39.159SE23.822.26
5-1.071-3.339-44.033SE19.182.12
6-6.683-46.528-24.71SE31.831.97
7-4.386-0.724-75.575SE25.621.59
8-10.437-16.046-49.611SE26.621.48
9-28.627-45.478-7.317SE22.260.42
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 25842
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.81-100670.713503
5.35-6.8159.80.818509
4.64-5.3554.40.88508
4.17-4.6454.90.886544
3.82-4.1756.80.898599
3.54-3.8258.50.888653
3.32-3.5456.40.886687
3.13-3.3258.60.88727
2.97-3.13600.871763
2.84-2.9756.70.901808
2.72-2.8453.30.882824
2.61-2.7257.10.904874
2.52-2.6155.10.886919
2.43-2.5253.80.896919
2.36-2.4356.10.899958
2.29-2.3653.20.898973
2.22-2.2954.90.911044
2.17-2.22550.9051028
2.11-2.1756.50.8831086
2.06-2.1158.50.8971086
2.01-2.0659.30.8841126
1.97-2.0158.80.8891137
1.93-1.97600.8851163
1.89-1.9363.20.8851216
1.85-1.8967.90.8591189
1.82-1.8571.50.8521256
1.79-1.8271.90.8191234
1.75-1.7974.60.7751509

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
DM5phasing
REFMAC5.2.0019refinement
PDB_EXTRACT3data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.748→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.229 / WRfactor Rwork: 0.185 / SU B: 2.29 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Additional Fo-Fc density surrounding the loop containing residues 226-230 suggested some structural ambiguity in this region.
RfactorNum. reflection% reflectionSelection details
Rfree0.229 1313 5.075 %RANDOM
Rwork0.18 ---
obs0.182 25870 99.511 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.653 Å2
Baniso -1Baniso -2Baniso -3
1--0.357 Å20 Å20 Å2
2--0.22 Å20 Å2
3---0.137 Å2
Refinement stepCycle: LAST / Resolution: 1.748→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2007 0 5 266 2278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222056
X-RAY DIFFRACTIONr_angle_refined_deg1.4791.9772782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9795267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.42623.80492
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.25715388
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9071515
X-RAY DIFFRACTIONr_chiral_restr0.1050.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021532
X-RAY DIFFRACTIONr_nbd_refined0.2080.21029
X-RAY DIFFRACTIONr_nbtor_refined0.3040.21437
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2211
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.170.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.222
X-RAY DIFFRACTIONr_mcbond_it1.0791.51319
X-RAY DIFFRACTIONr_mcangle_it1.69622056
X-RAY DIFFRACTIONr_scbond_it2.6863825
X-RAY DIFFRACTIONr_scangle_it4.0224.5716
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.748-1.7930.388940.2531673188193.939
1.793-1.8420.248990.2281739184699.567
1.842-1.8960.2771040.1961683178899.944
1.896-1.9540.248900.1816621752100
1.954-2.0180.229730.1771597167199.94
2.018-2.0890.213830.1851556164099.939
2.089-2.1670.225910.17215051596100
2.167-2.2560.246700.17514531523100
2.256-2.3560.207610.17214061467100
2.356-2.4710.216730.17613261399100
2.471-2.6040.2840.18612601344100
2.604-2.7610.245730.18311961269100
2.761-2.9520.244550.18611591214100
2.952-3.1870.248640.1910591123100
3.187-3.490.187430.1659811024100
3.49-3.90.227490.15895944100
3.9-4.50.147350.146821856100
4.5-5.5020.201300.175693723100
5.502-7.7430.272290.234550579100
7.743-55.1320.329130.234335899.441

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