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- PDB-6nzb: Crystal structure of E. coli fumarase C S318A variant with closed... -

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Basic information

Entry
Database: PDB / ID: 6nzb
TitleCrystal structure of E. coli fumarase C S318A variant with closed SS Loop at 1.37 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: 1.37 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)103,2156
Polymers102,4472
Non-polymers7684
Water16,304905
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)206,43112
Polymers204,8944
Non-polymers1,5378
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area32540 Å2
ΔGint-202 kcal/mol
Surface area53790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.797, 216.577, 86.675
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: 51223.492 Da / Num. of mol.: 2 / Mutation: S318A
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 (bacteria) / References: UniProt: P05042, fumarate hydratase
#2: Chemical
ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H8O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 905 / 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: 2.41 Å3/Da / Density % sol: 49.02 %
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 18, 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: 1.37→92.87 Å / Num. obs: 198237 / % possible obs: 98.3 % / Redundancy: 14.5 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 19
Reflection shellResolution: 1.37→1.39 Å / Redundancy: 11.9 % / Rmerge(I) obs: 1.14 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 8866 / % possible all: 88.9

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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: 1.37→59.079 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1769 9772 4.93 %
Rwork0.147 188384 -
obs0.1485 198156 98.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 63.82 Å2 / Biso mean: 19.6898 Å2 / Biso min: 8.88 Å2
Refinement stepCycle: final / Resolution: 1.37→59.079 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6968 0 52 905 7925
Biso mean--26.53 30.65 -
Num. residues----921
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 (%)
1.37-1.38550.30052770.24485492576987
1.3855-1.40180.26632730.21666019629295
1.4018-1.41890.25933400.20946122646297
1.4189-1.43680.22582880.19156208649697
1.4368-1.45570.22692730.18266235650897
1.4557-1.47570.22553230.17546217654098
1.4757-1.49680.22943310.16946205653698
1.4968-1.51910.20113410.166176651798
1.5191-1.54290.20713060.15876235654198
1.5429-1.56810.20423470.16176181652898
1.5681-1.59520.21583160.15736290660698
1.5952-1.62420.19653100.14656272658298
1.6242-1.65540.17623510.14346201655298
1.6554-1.68920.19273170.13896287660498
1.6892-1.7260.19133090.14366308661799
1.726-1.76610.20673450.16136259660499
1.7661-1.81030.19523520.15576269662199
1.8103-1.85920.20333100.15356322663299
1.8592-1.91390.18583250.14836321664699
1.9139-1.97570.17823470.14376340668799
1.9757-2.04630.17973300.14136316664699
2.0463-2.12830.17773210.13896350667199
2.1283-2.22510.16983590.13966368672799
2.2251-2.34250.15833500.134963836733100
2.3425-2.48920.17983310.143263966727100
2.4892-2.68140.17113260.141964246750100
2.6814-2.95130.16793330.14364546787100
2.9513-3.37830.16463210.143164926813100
3.3783-4.25610.14393590.127965106869100
4.2561-59.13390.15483610.144967327093100

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