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- PDB-6p3c: E. coli fumarase mutant - T187A -

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Basic information

Entry
Database: PDB / ID: 6p3c
TitleE. coli fumarase mutant - T187A
ComponentsFumarate hydratase class II
KeywordsLYASE / fumarase / 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 / Fumarate lyase, conserved site / Fumarate lyases signature. / Fumarate lyase family / Fumarate lyase, N-terminal / Lyase / Fumarase/aspartase (N-terminal domain) / Fumarase/aspartase (Central domain) ...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/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
CITRATE ANION / Fumarate hydratase class II
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.459 Å
AuthorsMay, J.F. / Bhattcharyya, B. / Weaver, T.M.
CitationJournal: To Be Published
Title: Fumarase C variant at the active site
Authors: May, J.F. / Bhattcharyya, B. / Weaver, T.M.
History
DepositionMay 23, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,9914
Polymers102,6132
Non-polymers3782
Water15,529862
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)205,9838
Polymers205,2264
Non-polymers7564
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area29530 Å2
ΔGint-200 kcal/mol
Surface area55720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.065, 218.448, 86.649
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: 51306.582 Da / Num. of mol.: 2 / Mutation: T187A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: fumC, b1611, JW1603 / Plasmid: pASK40 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05042, fumarate hydratase
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 862 / 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: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.9 / Details: PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.9786 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 24, 2019
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.459→30 Å / Num. obs: 170661 / % possible obs: 99.96 % / Observed criterion σ(I): 2 / Redundancy: 14.3 % / Biso Wilson estimate: 15.86 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.023 / Rrim(I) all: 0.085 / Net I/σ(I): 17.8
Reflection shellResolution: 1.459→1.511 Å / Redundancy: 14.4 % / Rmerge(I) obs: 0.996 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 16898 / CC1/2: 0.861 / Rpim(I) all: 0.271 / Rrim(I) all: 1.033 / % possible all: 99.99

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
PDB_EXTRACT3.25data extraction
autoPROCdata scaling
PHASERphasing
HKL-2000data collection
PHENIXmodel building
autoPROCdata processing
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NZC

6nzc


Resolution: 1.459→29.501 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1821 8576 5.03 %
Rwork0.1624 162062 -
obs0.1634 170638 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.8 Å2 / Biso mean: 20.5761 Å2 / Biso min: 9.65 Å2
Refinement stepCycle: final / Resolution: 1.459→29.501 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6960 0 26 862 7848
Biso mean--31.06 30.12 -
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
1.4591-1.47570.25473190.222353485667
1.4757-1.4930.2333030.208453245627
1.493-1.51120.21432630.199653405603
1.5112-1.53040.22212960.191753885684
1.5304-1.55050.20252740.187853805654
1.5505-1.57180.22082830.181953285611
1.5718-1.59420.21352720.176853855657
1.5942-1.6180.17332690.174753585627
1.618-1.64330.21632860.1753385624
1.6433-1.67020.18133060.164653745680
1.6702-1.6990.18582630.170653825645
1.699-1.72990.19062950.167753685663
1.7299-1.76320.21163000.176653415641
1.7632-1.79920.21382860.173353615647
1.7992-1.83830.19833090.172153985707
1.8383-1.8810.1952750.16753895664
1.881-1.92810.1762640.168753835647
1.9281-1.98020.18142930.170453835676
1.9802-2.03840.18673030.170653595662
2.0384-2.10420.1793210.165953495670
2.1042-2.17940.18092520.164854655717
2.1794-2.26660.18183190.159653385657
2.2666-2.36970.16572590.159954625721
2.3697-2.49460.19952820.167254155697
2.4946-2.65080.18882980.16754285726
2.6508-2.85530.17912920.163254335725
2.8553-3.14240.19092550.165854985753
3.1424-3.59640.17132890.155154835772
3.5964-4.52850.15542870.135155345821
4.5285-29.50730.16022630.150757305993

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