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- PDB-1yfe: Crystal structure of apo fumarase C from Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 1yfe
TitleCrystal structure of apo fumarase C from Escherichia coli
ComponentsFumarate hydratase class II
KeywordsLYASE / fumarase / kreb's cycle / apo / allosteric
Function / homology
Function and homology information


tricarboxylic acid cycle heteromeric enzyme complex / fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / malate metabolic process / tricarboxylic acid cycle / response to oxidative stress / identical protein binding
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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.19 Å
AuthorsWeaver, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Structure of free fumarase C from Escherichia coli.
Authors: Weaver, T.
History
DepositionDec 31, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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


Theoretical massNumber of molelcules
Total (without water)50,5491
Polymers50,5491
Non-polymers00
Water2,018112
1
A: Fumarate hydratase class II

A: Fumarate hydratase class II

A: Fumarate hydratase class II

A: Fumarate hydratase class II


Theoretical massNumber of molelcules
Total (without water)202,1954
Polymers202,1954
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_775-x+2,-y+2,z1
crystal symmetry operation3_756-x+2,y,-z+11
crystal symmetry operation4_576x,-y+2,-z+11
Buried area28650 Å2
ΔGint-205 kcal/mol
Surface area53900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)121.570, 127.960, 62.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Fumarate hydratase class II / Fumarase C


Mass: 50548.770 Da / Num. of mol.: 1 / Fragment: A-subunit / Mutation: none / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Strain: K12 / References: UniProt: P05042, fumarate hydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.38 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEg 3350, 100 mM MOPS, 50 mM LiSO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: XENTRONICS / Detector: AREA DETECTOR / Date: Dec 4, 1992
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.06→8 Å / Num. all: 30312 / Num. obs: 27639 / % possible obs: 91 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.63 % / Biso Wilson estimate: 18.4 Å2 / Rmerge(I) obs: 0.0705 / Rsym value: 0.0493 / Net I/σ(I): 12.963
Reflection shellResolution: 2.06→2.143 Å / Redundancy: 0.84 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 0.943 / Rsym value: 0.2897 / % possible all: 56

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Processing

Software
NameVersionClassification
X-GENdata scaling
X-GENdata reduction
X-PLORmodel building
CNS1.1refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1FUO (A subunit)

1fuo


Resolution: 2.19→8 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 106024.28 / 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
Rfree0.21 2272 9.9 %RANDOM
Rwork0.203 ---
obs0.203 22920 92.3 %-
all-27639 --
Displacement parametersBiso mean: 32.4 Å2
Baniso -1Baniso -2Baniso -3
1--2.29 Å20 Å20 Å2
2---2.67 Å20 Å2
3---4.96 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.27 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.19→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3463 0 0 112 3575
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.2
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.19→2.32 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.274 326 10.2 %
Rwork0.286 2872 -
obs--78 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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