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- PDB-6j57: Crystal structure of fumarylpyruvate hydrolase from Corynebacteri... -

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Basic information

Entry
Database: PDB / ID: 6j57
TitleCrystal structure of fumarylpyruvate hydrolase from Corynebacterium glutamicum
ComponentsPredicted 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase
KeywordsHYDROLASE
Function / homology
Function and homology information


Lyases; Carbon-carbon lyases; Carboxy-lyases / Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / carboxylic acid metabolic process / catalytic activity / isomerase activity / lyase activity / metal ion binding
Similarity search - Function
Fumarylacetoacetate hydrolase; domain 2 / Fumarylacetoacetase-like, C-terminal domain / Fumarylacetoacetase-like, C-terminal / Fumarylacetoacetate (FAA) hydrolase C-terminal / Fumarylacetoacetase-like, C-terminal domain superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Predicted 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase / 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase (Catechol pathway)
Similarity search - Component
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsHong, H. / Seo, H. / Kim, K.-J. / Park, W.
CitationJournal: Environ.Microbiol. / Year: 2020
Title: Sequence, structure and function-based classification of the broadly conserved FAH superfamily reveals two distinct fumarylpyruvate hydrolase subfamilies.
Authors: Hong, H. / Seo, H. / Park, W. / Kim, K.J.
History
DepositionJan 10, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 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: Predicted 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase
B: Predicted 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,93616
Polymers63,3192
Non-polymers1,61714
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6380 Å2
ΔGint-135 kcal/mol
Surface area21170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.766, 72.173, 119.032
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Predicted 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase / beta-keto hydrolase


Mass: 31659.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: cg3350 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A1R4GQY2, UniProt: Q8NLC0*PLUS
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.26 Å3/Da / Density % sol: 45.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: Ammonium sulfate, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 4, 2016
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2→61.72 Å / Num. obs: 38656 / % possible obs: 98.5 % / Redundancy: 3.4 % / Rpim(I) all: 0.057 / Net I/σ(I): 19.04
Reflection shellResolution: 2→2.03 Å / Num. unique obs: 1864 / Rpim(I) all: 0.203

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RR6

3rr6


Resolution: 2.01→28.03 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.007 / SU ML: 0.109 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.174 / ESU R Free: 0.158
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2174 1888 4.9 %RANDOM
Rwork0.169 ---
obs0.1713 36748 98.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 86.75 Å2 / Biso mean: 22.14 Å2 / Biso min: 10.68 Å2
Baniso -1Baniso -2Baniso -3
1--1.72 Å2-0 Å2-0 Å2
2--0.49 Å2-0 Å2
3---1.23 Å2
Refinement stepCycle: final / Resolution: 2.01→28.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4328 0 93 192 4613
Biso mean--53.03 25.53 -
Num. residues----560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0134513
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174106
X-RAY DIFFRACTIONr_angle_refined_deg1.5951.6586139
X-RAY DIFFRACTIONr_angle_other_deg1.3621.5859542
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6935558
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3123.451226
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.1115702
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7831522
X-RAY DIFFRACTIONr_chiral_restr0.0740.2594
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025018
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02904
LS refinement shellResolution: 2.006→2.058 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 132 -
Rwork0.223 2535 -
all-2667 -
obs--93.94 %

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