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- PDB-7c18: Crystal structure of FumaraseC from Mannheimia succiniciproducens... -

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Basic information

Entry
Database: PDB / ID: 7c18
TitleCrystal structure of FumaraseC from Mannheimia succiniciproducens in complex with Fumarate
ComponentsFumarate hydratase class II
KeywordsLYASE / FumaraseC / Mannheimia succiniciproducens / succinate production / TCA cycle
Function / homology
Function and homology information


fumarate hydratase activity / fumarate hydratase / fumarate metabolic process / tricarboxylic acid cycle / 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
FUMARIC ACID / Fumarate hydratase class II
Similarity search - Component
Biological speciesMannheimia succiniciproducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsKim, B. / Lee, S.H. / Kim, K.-J.
CitationJournal: To Be Published
Title: Structural studies reveal the molecular mechanism of isocitrate lyase from Chloroflexus aurantiacus
Authors: Kim, B. / Lee, S.H. / Kim, K.-J.
History
DepositionMay 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 5, 2021Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Database references
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.1Nov 29, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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
C: Fumarate hydratase class II
D: Fumarate hydratase class II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,6268
Polymers201,1614
Non-polymers4644
Water5,441302
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Size-exclusive chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area33820 Å2
ΔGint-195 kcal/mol
Surface area51110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.089, 104.276, 125.333
Angle α, β, γ (deg.)90.000, 94.100, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 50290.328 Da / Num. of mol.: 4 / Mutation: S319C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mannheimia succiniciproducens (strain MBEL55E) (bacteria)
Strain: MBEL55E / Gene: fumC, MS0760 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: Q65UJ3, fumarate hydratase
#2: Chemical
ChemComp-FUM / FUMARIC ACID


Mass: 116.072 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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

Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 20% polyethylene glycol 3350, 0.2M Potassium fluoride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 83884 / % possible obs: 97.9 % / Redundancy: 4.8 % / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.055 / Rrim(I) all: 0.134 / Χ2: 4.204 / Net I/σ(I): 11.1 / Num. measured all: 403604
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.1-2.143.80.27340920.8460.150.3131.85696.3
2.14-2.1840.2641870.8570.1390.2971.96697.3
2.18-2.223.90.24841050.8660.1320.2822.01997.1
2.22-2.263.90.23241380.9020.1230.2642.14496.9
2.26-2.314.10.22641180.9050.1180.2572.29996.8
2.31-2.374.20.21341960.9270.1090.2412.4297.4
2.37-2.424.10.21141280.9280.1090.2382.62997.1
2.42-2.494.10.241240.9380.1030.2262.58297.1
2.49-2.564.30.18841890.9460.0960.2122.6497.4
2.56-2.654.40.17641730.9520.0870.1973.09397.1
2.65-2.744.50.16341250.960.0810.1833.28597.8
2.74-2.854.60.15541820.9660.0750.1733.597.9
2.85-2.984.90.14242000.9740.0680.1583.88698
2.98-3.1450.13242420.9790.0610.1464.19498.6
3.14-3.335.30.12142190.9830.0550.1334.77698.7
3.33-3.595.60.11242370.9870.0490.1235.66698.7
3.59-3.956.10.10942750.9880.0460.1197.25699.4
3.95-4.526.30.10342900.9890.0420.1118.00999.4
4.52-5.76.30.09242930.9920.0380.15.99699.5
5.7-506.50.08243710.9920.0340.0895.40599.3

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YFE

1yfe


Resolution: 2.12→32.57 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.898 / SU B: 6.758 / SU ML: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.321 / ESU R Free: 0.222
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.241 4190 5 %RANDOM
Rwork0.1846 ---
obs0.1874 79682 96.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 78.04 Å2 / Biso mean: 20.324 Å2 / Biso min: 10.91 Å2
Baniso -1Baniso -2Baniso -3
1-2.06 Å20 Å2-0.73 Å2
2---0.99 Å2-0 Å2
3----0.96 Å2
Refinement stepCycle: final / Resolution: 2.12→32.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13978 0 32 302 14312
Biso mean--24.57 22.14 -
Num. residues----1848
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01314266
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713396
X-RAY DIFFRACTIONr_angle_refined_deg1.6981.63919350
X-RAY DIFFRACTIONr_angle_other_deg1.3621.57231158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1851844
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.224.161644
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.902152418
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8031552
X-RAY DIFFRACTIONr_chiral_restr0.080.21969
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216032
X-RAY DIFFRACTIONr_gen_planes_other0.0030.022700
LS refinement shellResolution: 2.12→2.17 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.296 261 -
Rwork0.242 5050 -
obs--82.91 %

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