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- PDB-3e9c: Structure of a tryptic core fragment of TIGAR from Danio rerio -

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Basic information

Entry
Database: PDB / ID: 3e9c
TitleStructure of a tryptic core fragment of 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
: / Fructose-2,6-bisphosphatase TIGAR B
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / 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

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Assembly

Deposited unit
A: Zgc:56074
B: Zgc:56074
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2994
Polymers59,2212
Non-polymers782
Water8,701483
1
A: Zgc:56074
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6893
Polymers29,6111
Non-polymers782
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Zgc:56074


Theoretical massNumber of molelcules
Total (without water)29,6111
Polymers29,6111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)136.672, 136.672, 66.753
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Zgc:56074


Mass: 29610.650 Da / Num. of mol.: 2 / Fragment: tryptic core fragment
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-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 483 / 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: 3.04 Å3/Da / Density % sol: 59.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.5
Details: 1 M potassium sodium tartrate, 100 mM MES, 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: Feb 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 47347 / % possible obs: 99.6 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.058 / Χ2: 0.97
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.075.80.43993530.884199.3
2.07-2.155.80.32293060.909199
2.15-2.255.80.23593570.942199.6
2.25-2.375.80.18493990.959199.7
2.37-2.525.90.13794051.001199.6
2.52-2.715.90.10493781.032199.8
2.71-2.995.90.0794111.012199.9
2.99-3.425.90.04893900.978199.9
3.42-4.315.90.03793911.0291100
4.31-505.90.0393770.946199.3

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Phasing

PhasingMethod: SAD
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se42.4150.8970.4920.1670.309
2Se33.4930.0410.5520.0360.323
3Se38.0960.5680.530.0370.278
4Se48.1980.1580.6670.0510.317
5Se47.1270.3250.6890.0040.292
6Se37.8970.2640.7480.0120.294
7Se35.3050.7120.4880.0270.248
8Se45.5440.10.6650.0820.338
9Se600.3780.8980.0250.384
10Se26.2560.5320.4120.1170.206
11Se600.6430.0710.1540.214
12Se600.4980.7020.0230.119
13Se24.6940.8660.4690.0960.067
Phasing dmFOM : 0.55 / FOM acentric: 0.54 / FOM centric: 0.56 / Reflection: 47394 / Reflection acentric: 45438 / Reflection centric: 1956
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.7-37.1630.920.940.821061867239
3.6-5.70.910.920.8164396042397
2.9-3.60.790.790.7280197666353
2.5-2.90.580.580.4880417745296
2.1-2.50.380.380.321411013675435
2-2.10.20.20.286798443236

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVE2.13phasing
RESOLVE2.13phasing
REFMAC5.5.0044refinement
PDB_EXTRACT3.006data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2→19.92 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 1 / SU B: 6.183 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.209 2406 5.1 %RANDOM
Rwork0.17 ---
obs0.172 47347 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 92.19 Å2 / Biso mean: 29.33 Å2 / Biso min: 12.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å20 Å2
2---0.02 Å20 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3160 0 2 483 3645
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213219
X-RAY DIFFRACTIONr_angle_refined_deg1.1621.9494340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7145395
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.75423.203153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91415557
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.681528
X-RAY DIFFRACTIONr_chiral_restr0.0740.2499
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212414
X-RAY DIFFRACTIONr_mcbond_it0.7261.51998
X-RAY DIFFRACTIONr_mcangle_it1.38423216
X-RAY DIFFRACTIONr_scbond_it2.11731221
X-RAY DIFFRACTIONr_scangle_it3.5094.51124
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 202 -
Rwork0.263 3194 -
all-3396 -
obs--100 %
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)
10.88950.1462-0.31840.4833-0.01960.6760.0249-0.01660.0368-0.0334-0.00050.01540.05240.0466-0.02450.0178-0.0118-0.00070.0423-0.00020.0046-33.531861.87810.865
21.2579-0.0804-0.28840.6571-0.12090.7303-0.0065-0.0370.04370.01880.02250.0477-0.01910.0026-0.0160.0029-0.00020.00680.0088-0.00090.0228-67.160160.581511.6442
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 141 - 14
2X-RAY DIFFRACTION1AA29 - 9229 - 92
3X-RAY DIFFRACTION1AA122 - 153122 - 153
4X-RAY DIFFRACTION1AA158 - 250158 - 250
5X-RAY DIFFRACTION2BB2 - 142 - 14
6X-RAY DIFFRACTION2BB29 - 9229 - 92
7X-RAY DIFFRACTION2BB119 - 148119 - 148
8X-RAY DIFFRACTION2BB160 - 250160 - 250

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