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- PDB-3e9e: Structure of full-length H11A mutant form of TIGAR from Danio rerio -

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Basic information

Entry
Database: PDB / ID: 3e9e
TitleStructure of full-length H11A mutant form 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
PHOSPHATE ION / Fructose-2,6-bisphosphatase TIGAR B
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 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
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,2774
Polymers59,0872
Non-polymers1902
Water5,945330
1
A: Zgc:56074
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6392
Polymers29,5441
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Zgc:56074
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6392
Polymers29,5441
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.358, 91.358, 155.875
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: 29543.584 Da / Num. of mol.: 2 / Mutation: H11A
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.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 3.18 Å3/Da / Density % sol: 61.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 3% PEG 8000, 100 mM calcium acetate, 100mM imidazole, pH 7.5, 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: Jul 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 42544 / % possible obs: 99.1 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.079 / Χ2: 0.974
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.183.50.44641850.775197.5
2.18-2.263.80.3642130.833199
2.26-2.373.90.29642450.885199.2
2.37-2.493.90.22242290.932199.3
2.49-2.653.90.17742731.016199.4
2.65-2.853.90.13142831.047199.6
2.85-3.143.90.09242591.049199.6
3.14-3.593.90.06842731.07199.7
3.59-4.523.80.05743101.022199.6
4.52-303.80.05342741.08198.1

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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: 2.1→30 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 1 / SU B: 9.188 / SU ML: 0.112 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.159 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.234 2151 5.1 %RANDOM
Rwork0.192 ---
obs0.194 42534 99.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.68 Å2 / Biso mean: 29.925 Å2 / Biso min: 15.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å2-0.14 Å20 Å2
2---0.28 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3743 0 10 330 4083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0213820
X-RAY DIFFRACTIONr_angle_refined_deg1.2481.9545155
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5325476
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.86523.478184
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.35915663
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4261534
X-RAY DIFFRACTIONr_chiral_restr0.0820.2576
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212896
X-RAY DIFFRACTIONr_mcbond_it0.7421.52378
X-RAY DIFFRACTIONr_mcangle_it1.3623817
X-RAY DIFFRACTIONr_scbond_it2.08731442
X-RAY DIFFRACTIONr_scangle_it3.3954.51338
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 151 -
Rwork0.231 2887 -
all-3038 -
obs--97.06 %
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)
11.2020.4060.58891.3920.05961.1141-0.1192-0.00920.0582-0.1114-0.0517-0.0442-0.1936-0.02250.17090.1229-0.0377-0.04580.02820.01240.078791.718925.8821-0.2847
22.19590.21860.20160.52850.21920.725-0.1048-0.1301-0.0856-0.00190.0284-0.0255-0.0868-0.11730.07640.01590.0207-0.01020.1254-0.05760.062366.64518.585725.9225
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1491 - 149
2X-RAY DIFFRACTION1AA160 - 250160 - 250
3X-RAY DIFFRACTION2BB2 - 1482 - 148
4X-RAY DIFFRACTION2BB160 - 250160 - 250

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