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- PDB-2dfu: Crystal structure of the 2-hydroxyhepta-2,4-diene-1,7-dioate isom... -

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Basic information

Entry
Database: PDB / ID: 2dfu
TitleCrystal structure of the 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase from Thermus Thermophilus HB8
Componentsprobable 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase
KeywordsISOMERASE / 2-hydroxyhepta-2 / 4-diene-1 / 7-dioate isomerase / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


acetylpyruvate hydrolase activity / carboxylic acid metabolic process / isomerase activity / metal ion binding
Similarity search - Function
Rv2993c-like, N-terminal / Rv2993c-like, N-terminal / FAH / Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase C-terminal / SH3 type barrels. / Roll ...Rv2993c-like, N-terminal / Rv2993c-like, N-terminal / FAH / Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase C-terminal / SH3 type barrels. / Roll / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Probable 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMizutani, H. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of the 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase from Thermus Thermophilus HB8
Authors: Mizutani, H. / Kunishima, N.
History
DepositionMar 3, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 3, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: probable 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase
B: probable 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase
C: probable 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase
D: probable 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase


Theoretical massNumber of molelcules
Total (without water)117,6944
Polymers117,6944
Non-polymers00
Water11,584643
1
A: probable 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase
B: probable 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase


Theoretical massNumber of molelcules
Total (without water)58,8472
Polymers58,8472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3070 Å2
ΔGint-20 kcal/mol
Surface area19310 Å2
MethodPISA
2
C: probable 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase
D: probable 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase


Theoretical massNumber of molelcules
Total (without water)58,8472
Polymers58,8472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-20 kcal/mol
Surface area19140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.340, 73.412, 122.632
Angle α, β, γ (deg.)90.00, 111.78, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimmer. There are two dimmers in the asymmetric unit,which is chain A & B and chain C & D, respectively.

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Components

#1: Protein
probable 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase


Mass: 29423.447 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q5SK43, 5-carboxymethyl-2-hydroxymuconate Delta-isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 643 / 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: 3.31 Å3/Da / Density % sol: 62.87 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 5.4
Details: sodium chloride, lithium sulfate, sodium citrate, pH 5.4, microbatch, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 4, 2005
RadiationMonochromator: Bending magnet / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 78745 / Num. obs: 78745 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 24.7 Å2 / Rmerge(I) obs: 0.083 / Rsym value: 0.075 / Net I/σ(I): 11.8
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 4.29 / Num. unique all: 7869 / Rsym value: 0.29 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WZO

1wzo


Resolution: 2.2→30 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1853439.85 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.224 3956 5 %RANDOM
Rwork0.197 ---
all0.198 78392 --
obs0.197 78392 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.0233 Å2 / ksol: 0.333487 e/Å3
Displacement parametersBiso mean: 41.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.36 Å20 Å24.45 Å2
2--5.54 Å20 Å2
3----4.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7795 0 0 643 8438
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.321.5
X-RAY DIFFRACTIONc_mcangle_it2.132
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it3.122.5
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.264 635 4.9 %
Rwork0.241 12329 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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