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- PDB-6j5x: Crystal structure of fumarylpyruvate hydrolase from Corynebacteri... -

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Basic information

Entry
Database: PDB / ID: 6j5x
TitleCrystal structure of fumarylpyruvate hydrolase from Corynebacterium glutamicum in complex with Mn2+ and pyruvate
ComponentsPredicted 2-keto-4-pentenoate hydratase/2-oxohepta-3-ene-1,7-dioic acid hydratase
KeywordsHYDROLASE
Function / homology
Function and homology information


acetylpyruvate hydrolase activity / Lyases; Carbon-carbon lyases; Carboxy-lyases / Isomerases; Intramolecular oxidoreductases; Transposing C=C bonds / 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 / Fumarylacetoacetase-like, C-terminal domain superfamily / Fumarylacetoacetate (FAA) hydrolase family / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
: / PYRUVIC ACID / 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: 1.79 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 12, 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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Revision 2.1Nov 22, 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: 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)64,18912
Polymers63,3192
Non-polymers87010
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-119 kcal/mol
Surface area20830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.621, 71.296, 112.260
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.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H4O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / 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: 2.11 Å3/Da / Density % sol: 41.58 %
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: 1.785→60.19 Å / Num. obs: 51565 / % possible obs: 97.5 % / Redundancy: 4 % / Rpim(I) all: 0.035 / Net I/σ(I): 23.22
Reflection shellResolution: 1.79→1.82 Å / Num. unique obs: 4136 / Rpim(I) all: 0.193

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.24data extraction
HKL-2000data collection
HKL-2000data scaling
MOLREPphasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6J57

6j57


Resolution: 1.79→48.72 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.369 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.129
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 2479 4.9 %RANDOM
Rwork0.1862 ---
obs0.1882 51553 97.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 86.04 Å2 / Biso mean: 24.384 Å2 / Biso min: 13.65 Å2
Baniso -1Baniso -2Baniso -3
1--1.96 Å2-0 Å20 Å2
2--1.06 Å2-0 Å2
3---0.9 Å2
Refinement stepCycle: final / Resolution: 1.79→48.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4328 0 43 174 4545
Biso mean--49.61 25.52 -
Num. residues----560
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134473
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174072
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.656093
X-RAY DIFFRACTIONr_angle_other_deg1.3531.5739455
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0525560
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.73123.275229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.38415709
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3531523
X-RAY DIFFRACTIONr_chiral_restr0.0760.2589
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025046
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02911
LS refinement shellResolution: 1.785→1.832 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 166 -
Rwork0.278 3256 -
all-3422 -
obs--90.91 %

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