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- PDB-7c1a: Crystal structure of FumaraseC (S319C) from Mannheimia succinicip... -

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Basic information

Entry
Database: PDB / ID: 7c1a
TitleCrystal structure of FumaraseC (S319C) from Mannheimia succiniciproducens in complex with malate
ComponentsFumarate hydratase class II
KeywordsLYASE / FumaraseC / Mannheimia succiniciproducens / succinate production / TCA cycle
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
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
(2S)-2-hydroxybutanedioic acid / Fumarate hydratase class II
Similarity search - Component
Biological speciesMannheimia succiniciproducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.144 Å
AuthorsKim, B. / Lee, S.H. / Kim, K.-J.
CitationJournal: To Be Published
Title: Structural and Biochemical analysis of FumaraseC from Mannheimia succiniciproducens
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 1.1Nov 29, 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
C: Fumarate hydratase class II
D: Fumarate hydratase class II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)201,6988
Polymers201,1614
Non-polymers5364
Water10,719595
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, size-exclusive chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32420 Å2
ΔGint-206 kcal/mol
Surface area51470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.592, 106.238, 125.317
Angle α, β, γ (deg.)90.000, 94.980, 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-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 595 / 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

CrystalDensity Matthews: 2.06 Å3/Da / Density % sol: 40.39 %
Crystal growTemperature: 285 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: 2.14→50 Å / Num. obs: 86681 / % possible obs: 97.1 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.149 / Rpim(I) all: 0.101 / Rrim(I) all: 0.181 / Χ2: 2.714 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.192.50.30242120.6890.220.3751.56595.4
2.19-2.232.50.29842920.7130.2170.3711.67395.9
2.23-2.272.50.27642200.7560.2010.3431.795
2.27-2.322.50.2742690.5670.1960.3351.79796.1
2.32-2.372.60.25642780.8050.1840.3171.79996.1
2.37-2.422.50.2443010.8340.1730.2971.78196.2
2.42-2.482.60.23342060.8380.1680.2891.88695.8
2.48-2.552.60.22842820.6980.1610.282.02496.3
2.55-2.622.60.20142900.8840.1430.2482.02196
2.62-2.712.70.18643250.9120.130.2282.14197.2
2.71-2.812.70.17543150.9280.1220.2142.1596.6
2.81-2.922.70.16842870.8790.1170.2062.41997.1
2.92-3.052.80.1643290.9420.1090.1942.81697.1
3.05-3.212.90.14143610.9630.0950.1712.5798
3.21-3.413.10.1344000.9560.0850.1562.86398.7
3.41-3.683.10.11944570.9730.0770.1423.3298.9
3.68-4.053.20.11343930.9740.0720.1354.11399
4.05-4.633.30.10744580.9770.0670.1274.53799.4
4.63-5.833.20.10444800.9810.0660.1233.64399.2
5.83-503.30.09345260.9850.0590.1114.28798.9

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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: 2.144→33.12 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.87 / SU B: 6.111 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.313 / ESU R Free: 0.216
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2325 4281 4.9 %RANDOM
Rwork0.1821 ---
obs0.1847 82387 96.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 48.32 Å2 / Biso mean: 11.301 Å2 / Biso min: 1.37 Å2
Baniso -1Baniso -2Baniso -3
1-1.02 Å2-0 Å2-0.51 Å2
2---1.08 Å2-0 Å2
3---0.14 Å2
Refinement stepCycle: final / Resolution: 2.144→33.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13954 0 36 595 14585
Biso mean--18.26 12.19 -
Num. residues----1846
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01314246
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713362
X-RAY DIFFRACTIONr_angle_refined_deg1.4981.63719323
X-RAY DIFFRACTIONr_angle_other_deg1.3091.57131086
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.76951842
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27424.161644
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.919152411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0871552
X-RAY DIFFRACTIONr_chiral_restr0.0710.21967
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216002
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022682
LS refinement shellResolution: 2.144→2.2 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 291 -
Rwork0.215 5732 -
all-6023 -
obs--91.12 %

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