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- PDB-3e9d: Structure of full-length TIGAR from Danio rerio -

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Basic information

Entry
Database: PDB / ID: 3e9d
TitleStructure of full-length TIGAR from Danio rerio
ComponentsZgc:56074
KeywordsHYDROLASE / histidine phosphatase
Function / homology
Function and homology information


regulation of pentose-phosphate shunt / fructose-2,6-bisphosphate 2-phosphatase / fructose-2,6-bisphosphate 2-phosphatase activity / negative regulation of glycolytic process / catalytic activity / autophagy / mitochondrial outer membrane / apoptotic process / mitochondrion / nucleus ...regulation of pentose-phosphate shunt / fructose-2,6-bisphosphate 2-phosphatase / fructose-2,6-bisphosphate 2-phosphatase activity / negative regulation of glycolytic process / catalytic activity / autophagy / mitochondrial outer membrane / apoptotic process / mitochondrion / 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 B
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsLi, H. / Jogl, G.
CitationJournal: To be Published
Title: TIGAR (TP53 induced glycolysis and apoptosis regulator) is a fructose-2,6- and fructose-1,6-bisphosphatase
Authors: Li, H. / Jogl, G.
History
DepositionAug 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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: Zgc:56074
B: Zgc:56074
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6798
Polymers59,2212
Non-polymers4586
Water12,574698
1
A: Zgc:56074
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8404
Polymers29,6111
Non-polymers2293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Zgc:56074
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8404
Polymers29,6111
Non-polymers2293
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)127.661, 115.541, 61.311
Angle α, β, γ (deg.)90.000, 104.660, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-538-

HOH

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Components

#1: Protein Zgc:56074


Mass: 29610.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: zgc:56074 / Plasmid: pET26b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21Star / References: UniProt: Q7ZVE3
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 698 / 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: 3.69 Å3/Da / Density % sol: 66.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 1 M sodium phosphate, pH 6.5, vapor diffusion, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorDetector: CCD / Date: Mar 14, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 57061 / % possible obs: 96.1 % / Redundancy: 3 % / Rmerge(I) obs: 0.076 / Χ2: 0.974
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.072.20.42547000.858179.3
2.07-2.152.50.3452630.884189.4
2.15-2.252.80.3257180.896196.8
2.25-2.3730.26359000.919199.4
2.37-2.523.10.20658970.9671100
2.52-2.713.10.15859230.962199.9
2.71-2.993.20.1159341.042199.8
2.99-3.423.20.06559281.051199.5
3.42-4.313.20.04358791.049199.1
4.31-303.20.03359190.994198.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
COMOphasing
REFMAC5.5.0044refinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.939 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 6.363 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 2835 5 %RANDOM
Rwork0.171 ---
obs0.173 56186 96.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 74.88 Å2 / Biso mean: 28.07 Å2 / Biso min: 12.82 Å2
Baniso -1Baniso -2Baniso -3
1-1.63 Å20 Å2-0.32 Å2
2---0.7 Å20 Å2
3----1.09 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3826 0 22 698 4546
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213915
X-RAY DIFFRACTIONr_angle_refined_deg1.141.9555287
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5265487
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.78623.545189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.79615678
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.381534
X-RAY DIFFRACTIONr_chiral_restr0.0760.2588
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212968
X-RAY DIFFRACTIONr_mcbond_it0.7361.52430
X-RAY DIFFRACTIONr_mcangle_it1.40623905
X-RAY DIFFRACTIONr_scbond_it2.16331485
X-RAY DIFFRACTIONr_scangle_it3.6134.51382
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 198 -
Rwork0.243 3289 -
all-3487 -
obs--81.78 %
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)
10.7514-0.2627-0.13950.57510.04290.4831-0.0168-0.01840.0387-0.02530.0376-0.02210.0107-0.0001-0.02080.0381-0.002-0.00860.01250.00020.004621.7608-17.821914.2836
20.56070.30010.18960.83530.0990.89540.03350.01750.00820.07750.02910.05380.03280.0094-0.06260.0226-0.0050.01010.0054-0.00230.012122.813918.495412.2484
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2501 - 250
2X-RAY DIFFRACTION2BB1 - 1481 - 148
3X-RAY DIFFRACTION2BB160 - 250160 - 250

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