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- PDB-6nzc: Crystal structure of E. coli fumarase C N326A variant with closed... -

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Basic information

Entry
Database: PDB / ID: 6nzc
TitleCrystal structure of E. coli fumarase C N326A variant with closed SS Loop at 1.40 angstrom resolution
ComponentsFumarate hydratase class II
KeywordsLYASE / fumarase / metabolism / Krebs Cycle / citrate
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 / Fumarase/aspartase (C-terminal domain) / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/aspartase (N-terminal domain) ...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 / Fumarase/aspartase (N-terminal domain) / Ribonucleotide Reductase Protein R1; domain 1 / 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
CITRIC ACID / Fumarate hydratase class II
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.403 Å
AuthorsWeaver, T.M. / May, J.F. / Bhattacharyya, B.
CitationJournal: Febs Lett. / Year: 2020
Title: Closed fumarase C active-site structures reveal SS Loop residue contribution in catalysis.
Authors: Stuttgen, G.M. / Grosskopf, J.D. / Berger, C.R. / May, J.F. / Bhattacharyya, B. / Weaver, T.M.
History
DepositionFeb 13, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2Oct 11, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,7774
Polymers102,3932
Non-polymers3842
Water16,916939
1
A: Fumarate hydratase class II
B: Fumarate hydratase class II
hetero molecules

A: Fumarate hydratase class II
B: Fumarate hydratase class II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)205,5548
Polymers204,7864
Non-polymers7684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area29580 Å2
ΔGint-211 kcal/mol
Surface area55360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.819, 217.389, 86.109
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 51196.469 Da / Num. of mol.: 2 / Mutation: N326A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fumC, b1611, JW1603 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05042, fumarate hydratase
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 939 / 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: 2.43 Å3/Da / Density % sol: 49.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.9 / Details: PEG 3350, citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.9787 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jun 13, 2018
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9787 Å / Relative weight: 1
ReflectionResolution: 1.4→108.7 Å / Num. obs: 187757 / % possible obs: 99.2 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 14.3
Reflection shellResolution: 1.4→1.43 Å / Redundancy: 13.3 % / Rmerge(I) obs: 1.27 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 9382 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FUO

1fuo


Resolution: 1.403→59.42 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 14.13 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1613 9334 4.97 %
Rwork0.1356 178398 -
obs0.1369 187732 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.8 Å2 / Biso mean: 19.9713 Å2 / Biso min: 8.9 Å2
Refinement stepCycle: final / Resolution: 1.403→59.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6960 0 26 939 7925
Biso mean--20.82 30.91 -
Num. residues----919
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4029-1.41880.23293110.184959506261100
1.4188-1.43550.22783180.181859636281100
1.4355-1.4530.21053140.154959226236100
1.453-1.47140.18823010.145359236224100
1.4714-1.49080.18283150.140459606275100
1.4908-1.51120.1783220.132759566278100
1.5112-1.53280.16253040.124859816285100
1.5328-1.55570.14833040.121959456249100
1.5557-1.580.1693100.121659546264100
1.58-1.60590.16053030.119959686271100
1.6059-1.63360.16573240.118559196243100
1.6336-1.66330.15263400.114359576297100
1.6633-1.69530.16853210.118859486269100
1.6953-1.72990.16143250.124759546279100
1.7299-1.76750.17852970.126559796276100
1.7675-1.80870.15762980.127659576255100
1.8087-1.85390.18693110.136360236334100
1.8539-1.9040.17083260.134459446270100
1.904-1.960.1773010.134560006301100
1.96-2.02330.16672920.129759976289100
2.0233-2.09560.15323280.128959796307100
2.0956-2.17950.15843170.132160136330100
2.1795-2.27870.15232550.13074549480476
2.2787-2.39890.14723140.133459886302100
2.3989-2.54920.1553180.14260306348100
2.5492-2.7460.16963400.140360236363100
2.746-3.02230.14793350.145960246359100
3.0223-3.45960.16592910.14461216412100
3.4596-4.35860.14382980.124361426440100
4.3586-59.47380.15863010.146863296630100

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