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- PDB-6jvv: Crystal structure of maleylpyruvate hydrolase from Sphingobium.sp... -

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Basic information

Entry
Database: PDB / ID: 6jvv
TitleCrystal structure of maleylpyruvate hydrolase from Sphingobium.sp SYK-6
Componentsmaleylpyruvate hydrolase
KeywordsHYDROLASE
Function / homology
Function and homology information


acetylpyruvate hydrolase 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 C-terminal / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Fumarylacetoacetase-like C-terminal domain-containing protein
Similarity search - Component
Biological speciesSphingobium sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsHong, H. / Kim, K.-J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2019
Title: Structural insights into a maleylpyruvate hydrolase from sphingobium sp. SYK-6, a bacterium degrading lignin-derived aryls.
Authors: Hong, H. / Seo, H. / Kim, K.J.
History
DepositionApr 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
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

Downloads & links

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Assembly

Deposited unit
A: maleylpyruvate hydrolase
B: maleylpyruvate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,58513
Polymers66,5542
Non-polymers1,03111
Water5,945330
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-32 kcal/mol
Surface area20010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.089, 74.519, 67.967
Angle α, β, γ (deg.)90.000, 118.560, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein maleylpyruvate hydrolase


Mass: 33277.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingobium sp. (strain NBRC 103272 / SYK-6) (bacteria)
Strain: NBRC 103272 / SYK-6 / Gene: SLG_11280 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: G2IPX5
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 2.24 Å3/Da / Density % sol: 45.14 % / Mosaicity: 0.473 °
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG3350, Lithium sulfate

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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 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 91240 / % possible obs: 97.4 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.023 / Rrim(I) all: 0.058 / Χ2: 1.62 / Net I/σ(I): 13 / Num. measured all: 562926
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.5340.3528650.8070.1850.3981.15861.1
1.53-1.5550.31844630.8810.1530.3541.17897
1.55-1.585.40.29346360.9160.1340.3241.29398.8
1.58-1.625.60.26146560.9460.1180.2871.33799.1
1.62-1.655.60.23945840.9580.1070.2621.37298.8
1.65-1.695.70.21346170.9660.0950.2341.41499.3
1.69-1.735.80.18846290.9780.0830.2061.46799.2
1.73-1.785.90.16546620.9810.0720.1811.54599.5
1.78-1.836.10.14146310.9870.060.1531.56899.6
1.83-1.896.20.12246410.9910.0520.1331.68199.7
1.89-1.966.40.09946700.9940.0420.1081.70399.7
1.96-2.046.50.08346690.9960.0340.091.75999.9
2.04-2.136.70.07346840.9970.030.0791.79399.9
2.13-2.246.80.06446840.9980.0260.0691.752100
2.24-2.386.80.05846820.9980.0230.0621.73999.9
2.38-2.566.80.05346800.9980.0210.0571.69699.9
2.56-2.826.90.04746910.9980.0190.0511.68199.9
2.82-3.2370.03947090.9990.0160.0421.597100
3.23-4.0770.03747150.9990.0150.041.79399.9
4.07-506.40.03946720.9980.0170.0432.17997.1

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Processing

Software
NameVersionClassificationNB
HKL-2000data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PFZ

4pfz


Resolution: 1.51→31.63 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.136 / SU ML: 0.041 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.061 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1737 4511 4.9 %RANDOM
Rwork0.1515 ---
obs0.1526 86720 98.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.13 Å2 / Biso mean: 19.236 Å2 / Biso min: 9.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.83 Å2-0 Å2-0.32 Å2
2---0.24 Å20 Å2
3---0.89 Å2
Refinement stepCycle: final / Resolution: 1.51→31.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3976 0 66 330 4372
Biso mean--40.57 29.47 -
Num. residues----525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0134211
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174057
X-RAY DIFFRACTIONr_angle_refined_deg1.9341.645740
X-RAY DIFFRACTIONr_angle_other_deg1.5061.5799365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7185539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.23821.005209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.83515656
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1591537
X-RAY DIFFRACTIONr_chiral_restr0.1030.2554
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024727
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02864
LS refinement shellResolution: 1.51→1.549 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 303 -
Rwork0.242 5975 -
all-6278 -
obs--92.09 %

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