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- PDB-8sbs: Fumarate C - R126A in (3-(N-morpholino)propanesulfonic acid) at pH 7.5 -

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Basic information

Entry
Database: PDB / ID: 8sbs
TitleFumarate C - R126A in (3-(N-morpholino)propanesulfonic acid) at pH 7.5
ComponentsFumarate hydratase class II
KeywordsLYASE / fumarate hydrates / fumarate / Krebs Cycle / metabolism
Function / homology
Function and homology information


fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / malate metabolic process / tricarboxylic acid cycle / response to oxidative stress / identical protein binding / cytoplasm
Similarity search - Function
Fumarate hydratase, class II / Fumarase C, C-terminal / Fumarase C C-terminus / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/histidase, N-terminal / L-Aspartase-like
Similarity search - Domain/homology
Fumarate hydratase class II
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsWeaver, T.M. / May, J. / Bhattacharyya, B.
Funding support United States, 1items
OrganizationGrant numberCountry
Other governmentUniversity Wisconsin - La Crosse Faculty Research Grant United States
CitationJournal: To Be Published
Title: Fumarate C - R126A in (3-(N-morpholino)propanesulfonic acid) at pH 7.5
Authors: Weaver, T.M. / May, J. / Bhattacharyya, B.
History
DepositionApr 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release

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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)51,1531
Polymers51,1531
Non-polymers00
Water4,324240
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)204,6144
Polymers204,6144
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area27050 Å2
ΔGint-195 kcal/mol
Surface area55350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.958, 120.778, 127.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-548-

HOH

21A-669-

HOH

31A-695-

HOH

41A-738-

HOH

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Components

#1: Protein Fumarate hydratase class II / Fumarase C / Aerobic fumarase / Iron-independent fumarase


Mass: 51153.379 Da / Num. of mol.: 1 / Mutation: R126A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DH5alpha / Gene: fumC, b1611, JW1603 / Plasmid: pASK40 / Production host: Escherichia coli (E. coli) / Strain (production host): DH5alpha / References: UniProt: P05042, fumarate hydratase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.34 Å3/Da / Density % sol: 47.4 % / Description: Rectangular
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: PEG 3350, 150 mM MOPS

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 24, 2019
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.909→87.809 Å / Num. obs: 37702 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.018 / Rrim(I) all: 0.069 / Net I/σ(I): 24.4
Reflection shellResolution: 1.909→1.94 Å / Redundancy: 14.9 % / Rmerge(I) obs: 0.722 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 1877 / CC1/2: 0.787 / Rpim(I) all: 0.193 / Rrim(I) all: 0.748 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→28.26 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 1916 5.09 %random
Rwork0.1879 ---
obs0.1899 37677 99.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.3 Å2
Refinement stepCycle: LAST / Resolution: 1.91→28.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3440 0 0 240 3680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083527
X-RAY DIFFRACTIONf_angle_d0.954785
X-RAY DIFFRACTIONf_dihedral_angle_d5.433484
X-RAY DIFFRACTIONf_chiral_restr0.054555
X-RAY DIFFRACTIONf_plane_restr0.007628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.960.34141440.32222511X-RAY DIFFRACTION100
1.96-2.010.34061310.28492503X-RAY DIFFRACTION100
2.01-2.070.30561380.2432564X-RAY DIFFRACTION100
2.07-2.140.29111360.23062501X-RAY DIFFRACTION100
2.14-2.210.29391410.23632522X-RAY DIFFRACTION100
2.21-2.30.28891260.24622530X-RAY DIFFRACTION100
2.3-2.40.28651020.22642570X-RAY DIFFRACTION100
2.4-2.530.26551330.21822531X-RAY DIFFRACTION100
2.53-2.690.25691430.20772547X-RAY DIFFRACTION100
2.69-2.90.23931310.2052557X-RAY DIFFRACTION100
2.9-3.190.21521290.19632576X-RAY DIFFRACTION100
3.19-3.650.22911340.18162584X-RAY DIFFRACTION100
3.65-4.590.2041540.14572581X-RAY DIFFRACTION100
4.6-28.260.16061740.14242684X-RAY DIFFRACTION100

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