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- PDB-1vdk: Crystal structure of fumarase from thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 1vdk
TitleCrystal structure of fumarase from thermus thermophilus HB8
ComponentsFumarate hydratase class II
KeywordsLYASE / fumarase / TCA cycle / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


tricarboxylic acid cycle heteromeric enzyme complex / fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / tricarboxylic acid cycle
Similarity search - Function
Fumarate hydratase, class II / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 ...Fumarate hydratase, class II / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) / Fumarase C; Chain A, domain 2 / Fumarase C; Chain B, domain 1 / Fumarase/histidase, N-terminal / L-Aspartase-like / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Fumarate hydratase class II
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMizutani, H. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of fumarase from thermus thermophilus HB8
Authors: Mizutani, H. / Kunishima, N.
History
DepositionMar 23, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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: Fumarate hydratase class II
B: Fumarate hydratase class II


Theoretical massNumber of molelcules
Total (without water)101,8782
Polymers101,8782
Non-polymers00
Water11,674648
1
A: Fumarate hydratase class II
B: Fumarate hydratase class II

A: Fumarate hydratase class II
B: Fumarate hydratase class II


Theoretical massNumber of molelcules
Total (without water)203,7574
Polymers203,7574
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area26620 Å2
ΔGint-167 kcal/mol
Surface area56920 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)125.336, 140.122, 135.372
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsThe biological assembly is tetramer generated from the dimer in the asymmetric unit by the operations: -x+1, y, -z+1/2.

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Components

#1: Protein Fumarate hydratase class II / Fumarase C


Mass: 50939.238 Da / Num. of mol.: 2 / Mutation: V128A/H401Y
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: P84127, fumarate hydratase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 648 / 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: 2.92 Å3/Da / Density % sol: 57.82 %
Crystal growTemperature: 295 K / Method: microbatch / pH: 7.4
Details: 30% PEG3000, 0.1M HEPES, 0.2M NaCl, pH 7.4, microbatch, temperature 295.0K

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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: Nov 4, 2003 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 110091 / Num. obs: 110091 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.56 % / Biso Wilson estimate: 22.5 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.045 / Net I/σ(I): 17.5
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.341 / Mean I/σ(I) obs: 5.33 / Num. unique all: 10916 / Rsym value: 0.305 / % 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 1FUO

1fuo


Resolution: 1.8→30 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3409617.19 / 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
Rfree0.201 5515 5 %RANDOM
Rwork0.185 ---
all0.186 110091 --
obs0.186 109925 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.0649 Å2 / ksol: 0.362433 e/Å3
Displacement parametersBiso mean: 32.1 Å2
Baniso -1Baniso -2Baniso -3
1--2.59 Å20 Å20 Å2
2--0.25 Å20 Å2
3---2.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7032 0 0 648 7680
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d19.9
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 1.8→1.86 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.226 524 4.8 %
Rwork0.222 10388 -
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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