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- PDB-6nza: Crystal structure of E. coli fumarase C K324A variant with closed... -

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Basic information

Entry
Database: PDB / ID: 6nza
TitleCrystal structure of E. coli fumarase C K324A variant with closed SS Loop at 1.41 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: 1.406 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)102,7474
Polymers102,3632
Non-polymers3842
Water16,646924
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)205,4948
Polymers204,7264
Non-polymers7684
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area29040 Å2
ΔGint-206 kcal/mol
Surface area55150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.232, 217.563, 86.383
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: 51181.391 Da / Num. of mol.: 2 / Mutation: K324A
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 (E. coli) / 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.: 924 / 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: 49.43 %
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: 1.406→93.27 Å / Num. obs: 187824 / % possible obs: 100 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.122 / Net I/σ(I): 0.129
Reflection shellResolution: 1.406→1.43 Å / Redundancy: 13.5 % / Rmerge(I) obs: 0.1177 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 9292 / % 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: 1.406→59.342 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.89
RfactorNum. reflection% reflection
Rfree0.17 9449 5.03 %
Rwork0.1448 --
obs0.1461 187804 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 72.26 Å2 / Biso mean: 20.2502 Å2 / Biso min: 8.23 Å2
Refinement stepCycle: final / Resolution: 1.406→59.342 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6956 0 26 924 7906
Biso mean--49.25 32.1 -
Num. residues----920
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.406-1.42170.24643120.209958636175
1.4217-1.43840.22513180.196259136231
1.4384-1.45590.23073190.177859066225
1.4559-1.47440.22063090.170958766185
1.4744-1.49380.21722840.165559386222
1.4938-1.51420.1942880.158159426230
1.5142-1.53590.21323280.14658516179
1.5359-1.55880.19493030.142759386241
1.5588-1.58320.17543170.136758956212
1.5832-1.60910.19133130.139159366249
1.6091-1.63690.19283100.134458686178
1.6369-1.66660.16073310.130159236254
1.6666-1.69870.18223330.133658746207
1.6987-1.73340.1673400.13259036243
1.7334-1.77110.17843220.134659136235
1.7711-1.81230.16783000.130759206220
1.8123-1.85760.19163010.140559616262
1.8576-1.90780.18253110.142459366247
1.9078-1.9640.18533100.146259026212
1.964-2.02740.16532950.144959686263
2.0274-2.09980.17513260.137359366262
2.0998-2.18390.16683170.139959386255
2.1839-2.28330.16142930.135960096302
2.2833-2.40370.15983360.138159476283
2.4037-2.55430.15793270.149559426269
2.5543-2.75150.17353240.148759876311
2.7515-3.02840.17983210.15559986319
3.0284-3.46650.16753360.149660276363
3.4665-4.36730.14753180.131460616379
4.3673-59.39450.14643070.150862846591

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