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- PDB-7c1c: Crystal structure of FumaraseC from Mannheimia succiniciproducens -

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Basic information

Entry
Database: PDB / ID: 7c1c
TitleCrystal structure of FumaraseC from Mannheimia succiniciproducens
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 / malate 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
Fumarate hydratase class II
Similarity search - Component
Biological speciesMannheimia succiniciproducens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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

Downloads & links

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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)202,84723
Polymers201,0974
Non-polymers1,75019
Water25,8701436
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, size-exclusive chromatography
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area37690 Å2
ΔGint-215 kcal/mol
Surface area50460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.618, 105.512, 125.487
Angle α, β, γ (deg.)90.000, 94.960, 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: 50274.266 Da / Num. of mol.: 4
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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1436 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.02 Å3/Da / Density % sol: 39.14 %
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: Nov 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 240435 / % possible obs: 94.3 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.036 / Rrim(I) all: 0.091 / Χ2: 2.703 / Net I/σ(I): 11.2 / Num. measured all: 1457116
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.5360.342117340.9520.1470.3731.88792.4
1.53-1.556.10.323116990.9570.1380.3521.9192.1
1.55-1.5860.291117080.9610.1250.3172.01992
1.58-1.626.10.272116820.9660.1160.2962.05991.7
1.62-1.6560.252116280.9680.1080.2752.10391.6
1.65-1.696.10.228116200.9740.0970.2482.18391.6
1.69-1.736.10.211116490.9780.090.2292.26691.4
1.73-1.786.10.19116780.9810.0810.2072.36691.9
1.78-1.8360.17117680.9840.0730.1852.49192.7
1.83-1.8960.152117940.9860.0650.1652.61392.4
1.89-1.9660.136118410.9870.0590.1492.75893.1
1.96-2.0460.119118940.9890.0510.132.96993.3
2.04-2.1360.108120290.9890.0470.1183.10494.4
2.13-2.2460.098120930.9890.0420.1073.30895.1
2.24-2.3860.091122340.9910.0390.0993.37895.7
2.38-2.5660.084123490.9920.0360.0913.26396.7
2.56-2.8260.075125550.9930.0330.0823.24898.4
2.82-3.236.10.068127980.9950.030.0743.19899.7
3.23-4.076.50.06128150.9960.0260.0663.369100
4.07-506.30.057128670.9950.0250.0623.21899.2

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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: 1.5→28.56 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.079 / SU ML: 0.04 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.067
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.165 12012 5 %RANDOM
Rwork0.1392 ---
obs0.1406 228063 94.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 65.26 Å2 / Biso mean: 13.441 Å2 / Biso min: 7.44 Å2
Baniso -1Baniso -2Baniso -3
1-1.42 Å20 Å2-0.4 Å2
2---1.17 Å20 Å2
3----0.17 Å2
Refinement stepCycle: final / Resolution: 1.5→28.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14014 0 114 1436 15564
Biso mean--28.11 23.49 -
Num. residues----1852
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01314393
X-RAY DIFFRACTIONr_bond_other_d0.0010.01713565
X-RAY DIFFRACTIONr_angle_refined_deg1.8031.63619493
X-RAY DIFFRACTIONr_angle_other_deg1.6361.57231559
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32551852
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.62124.149646
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.632152436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.6961552
X-RAY DIFFRACTIONr_chiral_restr0.10.21975
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216052
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022700
LS refinement shellResolution: 1.5→1.538 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.203 790 -
Rwork0.178 16416 -
obs--91.64 %

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