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

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Basic information

Entry
Database: PDB / ID: 6jvw
TitleCrystal structure of maleylpyruvate hydrolase from Sphingobium sp. SYK-6 in complex with manganese (II) ion and pyruvate
Componentsmaleylpyruvate hydrolase
KeywordsHYDROLASE
Function / homology
Function and homology information


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 / FAA_hydrolase domain-containing protein
Similarity search - Component
Biological speciesSphingobium sp.
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,0747
Polymers66,6962
Non-polymers3785
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-24 kcal/mol
Surface area20060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.409, 74.181, 68.727
Angle α, β, γ (deg.)90.000, 119.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein maleylpyruvate hydrolase


Mass: 33348.172 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-PYR / PYRUVIC ACID


Mass: 88.062 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O3 / Feature type: SUBJECT OF INVESTIGATION
#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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.29 Å3/Da / Density % sol: 46.18 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / Details: PEG 3350, 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: 0.97935 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 27826 / % possible obs: 97.5 % / Redundancy: 3 % / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.041 / Rrim(I) all: 0.077 / Χ2: 2.581 / Net I/σ(I): 15.8 / Num. measured all: 84215
Reflection shellResolution: 2.25→2.29 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.233 / Num. unique obs: 1358 / CC1/2: 0.938 / Rpim(I) all: 0.163 / Rrim(I) all: 0.286 / Χ2: 1.515 / % possible all: 95.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JVV

6jvv


Resolution: 2.25→31.58 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.496 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.236 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2028 1481 5.3 %RANDOM
Rwork0.1534 ---
obs0.1559 26338 97.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 109.7 Å2 / Biso mean: 32.042 Å2 / Biso min: 14.82 Å2
Baniso -1Baniso -2Baniso -3
1--2.25 Å20 Å2-2.13 Å2
2--3.19 Å20 Å2
3---0.89 Å2
Refinement stepCycle: final / Resolution: 2.25→31.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3973 0 20 123 4116
Biso mean--41.94 31.7 -
Num. residues----524
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0134149
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173987
X-RAY DIFFRACTIONr_angle_refined_deg1.6191.6435664
X-RAY DIFFRACTIONr_angle_other_deg1.2561.5789197
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6085532
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.76620.798213
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.14515655
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7751538
X-RAY DIFFRACTIONr_chiral_restr0.0730.2550
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024699
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02863
LS refinement shellResolution: 2.252→2.31 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 109 -
Rwork0.221 1864 -
all-1973 -
obs--93.2 %

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