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- PDB-6nz9: Crystal structure of E. coli fumarase C bound to citrate at 1.53 ... -

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Basic information

Entry
Database: PDB / ID: 6nz9
TitleCrystal structure of E. coli fumarase C bound to citrate at 1.53 angstrom resolution
ComponentsFumarate hydratase class II
KeywordsLYASE / fumarase / inhibitor complex / metabolism / Krebs 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 / response to oxidative stress / identical protein binding
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 / Ribonucleotide Reductase Protein R1; domain 1 ...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 / Ribonucleotide Reductase Protein R1; domain 1 / Fumarase/aspartase (N-terminal domain) / 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: 1.528 Å
AuthorsStuttgen, G.M. / May, J.F. / Bhattcharyya, B. / Weaver, T.M.
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)103,2476
Polymers102,4792
Non-polymers7684
Water13,223734
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)206,49512
Polymers204,9584
Non-polymers1,5378
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area30490 Å2
ΔGint-186 kcal/mol
Surface area54560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.157, 216.679, 86.936
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: 51239.492 Da / Num. of mol.: 2
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 / Citric acid


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


Mass: 18.015 Da / Num. of mol.: 734 / 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: 2.45 Å3/Da / Density % sol: 49.71 %
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-D / Wavelength: 1.0781 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.528→63.553 Å / Num. obs: 146755 / % possible obs: 100 % / Redundancy: 10.9 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 14.7
Reflection shellResolution: 1.528→1.55 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.975 / Num. unique obs: 7249 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FUO

1fuo


Resolution: 1.528→45.975 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.08
RfactorNum. reflection% reflection
Rfree0.1734 7329 4.99 %
Rwork0.1565 --
obs0.1573 146741 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 91.27 Å2 / Biso mean: 21.655 Å2 / Biso min: 9.88 Å2
Refinement stepCycle: final / Resolution: 1.528→45.975 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6932 0 52 734 7718
Biso mean--31.36 27.64 -
Num. residues----915
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
1.5279-1.54530.21992380.20345634801
1.5453-1.56340.24172480.197846084856
1.5634-1.58250.25452430.198945954838
1.5825-1.60250.1982220.191146094831
1.6025-1.62360.20652210.176646534874
1.6236-1.64590.20662730.17246234896
1.6459-1.66940.17922310.167245964827
1.6694-1.69430.18322300.163945974827
1.6943-1.72080.1962670.16146204887
1.7208-1.7490.20632260.161346404866
1.749-1.77920.18042590.159345924851
1.7792-1.81150.18662260.155446354861
1.8115-1.84640.19182620.153545954857
1.8464-1.8840.17292330.155146154848
1.884-1.9250.19272530.167246414894
1.925-1.96980.19092160.163446624878
1.9698-2.01910.16942480.158946274875
2.0191-2.07360.18462350.150446474882
2.0736-2.13470.1752630.151846004863
2.1347-2.20360.13962540.148246424896
2.2036-2.28230.16252510.14946384889
2.2823-2.37370.17392830.150146104893
2.3737-2.48170.17662380.158546684906
2.4817-2.61250.19192390.160946474886
2.6125-2.77620.17672550.159446544909
2.7762-2.99050.18222500.16246994949
2.9905-3.29140.1652340.160847214955
3.2914-3.76750.15392230.149647384961
3.7675-4.74590.14462320.132647725004
4.7459-45.99590.16872760.161249055181

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