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- PDB-6os7: E. coli fumarase mutant - R126A -

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Basic information

Entry
Database: PDB / ID: 6os7
TitleE. coli fumarase mutant - R126A
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 / 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
CITRATE ANION / Fumarate hydratase class II
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.36 Å
AuthorsStuttgen, G.M. / May, J.F. / Bhattcharyya, B. / Weaver, T.M.
Funding support United States, 1items
OrganizationGrant numberCountry
Other governmentWeaver FRG United States
CitationJournal: To Be Published
Title: Fumarase C variant that eliminates the B-site
Authors: Stuttgen, G.M. / May, J.F. / Bhattcharyya, B. / Weaver, T.M.
History
DepositionMay 1, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2020Provider: repository / Type: Initial release
Revision 2.0Aug 16, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_src_gen / pdbx_audit_support / pdbx_contact_author / pdbx_entity_instance_feature / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_conf / struct_mon_prot_cis / struct_site / struct_site_gen
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_number_of_molecules / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_contact_author.id / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.pdb_mon_id / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_high / _refine.ls_d_res_low / _refine.overall_SU_ML / _refine.pdbx_overall_phase_error / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_high / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.d_res_high / _refine_ls_shell.d_res_low / _refine_ls_shell.number_reflns_all / _refine_ls_shell.pdbx_total_number_of_bins_used / _software.name / _software.version / _struct_conf.beg_auth_comp_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_comp_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_mon_prot_cis.pdbx_omega_angle
Description: Model orientation/position
Details: Re-refined and rebuilt sections of model. In particular, the SS Loop and N-terminal b-strands (residue 3 - 18) from the A-subunit and domain 3 from the B-subunit. The SS Loop is missing ...Details: Re-refined and rebuilt sections of model. In particular, the SS Loop and N-terminal b-strands (residue 3 - 18) from the A-subunit and domain 3 from the B-subunit. The SS Loop is missing residues 317 - 323 and domain 3 is missing residues 417 - 424. The N-terminal b-strands from the A-subunit have localized disorder not witnessed in prior FumC structure A-subunits. The alteration of R126 to alanine has increased the disorder in these three areas.
Provider: author / Type: Coordinate replacement
Revision 2.1Oct 11, 2023Group: Refinement description / Category: pdbx_initial_refinement_model

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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)102,8696
Polymers102,3072
Non-polymers5624
Water10,539585
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)205,73812
Polymers204,6144
Non-polymers1,1258
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area29990 Å2
ΔGint-184 kcal/mol
Surface area54630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.521, 217.598, 86.266
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 51153.379 Da / Num. of mol.: 2 / Mutation: R126A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: fumC, b1611, JW1603 / Variant: K-12 / Plasmid: pASK40 / Production host: Escherichia coli K-12 (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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 585 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 49.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.9 / Details: PEG 3350, sodium citrate

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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: RAYONIX MX300HE / 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: 1.36→108.799 Å / Num. obs: 207186 / % possible obs: 100 % / Redundancy: 14.4 % / Biso Wilson estimate: 14.25 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.116 / Rpim(I) all: 0.032 / Net I/σ(I): 13
Reflection shellResolution: 1.361→1.384 Å / Redundancy: 14.6 % / Rmerge(I) obs: 1.47 / Num. unique obs: 10280 / CC1/2: 0.843 / Rpim(I) all: 0.401 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data collection
XDSdata reduction
autoPROCdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6NZ9

6nz9


Resolution: 1.36→46.74 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 15.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1693 10290 4.97 %
Rwork0.1448 --
obs0.146 207147 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.36→46.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6849 0 38 585 7472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067281
X-RAY DIFFRACTIONf_angle_d0.8379918
X-RAY DIFFRACTIONf_dihedral_angle_d6.0381031
X-RAY DIFFRACTIONf_chiral_restr0.0751148
X-RAY DIFFRACTIONf_plane_restr0.0071316
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.36-1.380.22293700.19996477X-RAY DIFFRACTION100
1.38-1.390.23133600.18226448X-RAY DIFFRACTION100
1.39-1.410.20593380.17476498X-RAY DIFFRACTION100
1.41-1.430.20683380.16626512X-RAY DIFFRACTION100
1.43-1.450.19123410.15546518X-RAY DIFFRACTION100
1.45-1.470.18243430.14416535X-RAY DIFFRACTION100
1.47-1.490.18143290.14086534X-RAY DIFFRACTION100
1.49-1.510.17023180.1356537X-RAY DIFFRACTION100
1.51-1.530.17653430.12886512X-RAY DIFFRACTION100
1.53-1.560.16733420.13196501X-RAY DIFFRACTION100
1.56-1.580.16543320.1296529X-RAY DIFFRACTION100
1.58-1.610.16293490.13176532X-RAY DIFFRACTION100
1.61-1.640.1643370.1316537X-RAY DIFFRACTION100
1.64-1.680.17023760.13946480X-RAY DIFFRACTION100
1.68-1.710.17563480.13856517X-RAY DIFFRACTION100
1.71-1.750.16723300.13986583X-RAY DIFFRACTION100
1.75-1.80.17063370.1386554X-RAY DIFFRACTION100
1.8-1.850.17083070.1336585X-RAY DIFFRACTION100
1.85-1.90.16543530.13446515X-RAY DIFFRACTION100
1.9-1.960.1683770.14256524X-RAY DIFFRACTION100
1.96-2.030.18333120.14666593X-RAY DIFFRACTION100
2.03-2.110.17433300.14586613X-RAY DIFFRACTION100
2.11-2.210.16363780.13886545X-RAY DIFFRACTION100
2.21-2.330.15373420.13926545X-RAY DIFFRACTION100
2.33-2.470.1753370.1466615X-RAY DIFFRACTION100
2.47-2.660.17323180.1516629X-RAY DIFFRACTION100
2.66-2.930.16683590.1526597X-RAY DIFFRACTION100
2.93-3.360.17183510.15446671X-RAY DIFFRACTION100
3.36-4.230.15573510.13776697X-RAY DIFFRACTION100
4.23-46.740.16263440.14856924X-RAY DIFFRACTION100

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