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- PDB-3nst: Crystal Structure of Salicylate 1,2-dioxygenase G106A mutant from... -

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Basic information

Entry
Database: PDB / ID: 3nst
TitleCrystal Structure of Salicylate 1,2-dioxygenase G106A mutant from Pseudoaminobacter salicylatoxidans
ComponentsGentisate 1,2-dioxygenase
KeywordsOXIDOREDUCTASE / Beta-barrel / cupins
Function / homology
Function and homology information


dioxygenase activity / metal ion binding
Similarity search - Function
: / Cupin 2, conserved barrel / Cupin domain / RmlC-like cupin domain superfamily / Jelly Rolls / RmlC-like jelly roll fold / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Gentisate 1,2-dioxygenase
Similarity search - Component
Biological speciesPseudaminobacter salicylatoxidans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.4 Å
AuthorsFerraroni, M. / Briganti, F. / Matera, I.
CitationJournal: FEBS J. / Year: 2013
Title: The salicylate 1,2-dioxygenase as a model for a conventional gentisate 1,2-dioxygenase: crystal structures of the G106A mutant and its adducts with gentisate and salicylate.
Authors: Ferraroni, M. / Matera, I. / Burger, S. / Reichert, S. / Steimer, L. / Scozzafava, A. / Stolz, A. / Briganti, F.
History
DepositionJul 2, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gentisate 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7678
Polymers41,1581
Non-polymers6087
Water6,179343
1
A: Gentisate 1,2-dioxygenase
hetero molecules

A: Gentisate 1,2-dioxygenase
hetero molecules

A: Gentisate 1,2-dioxygenase
hetero molecules

A: Gentisate 1,2-dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,06732
Polymers164,6344
Non-polymers2,43428
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)73.715, 87.046, 167.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-385-

HOH

21A-700-

HOH

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Components

#1: Protein Gentisate 1,2-dioxygenase


Mass: 41158.461 Da / Num. of mol.: 1 / Mutation: G106A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudaminobacter salicylatoxidans (bacteria)
Strain: BN12 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: Q67FT0, gentisate 1,2-dioxygenase
#2: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 343 / 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: 3.27 Å3/Da / Density % sol: 62.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8
Details: 8% PEG10000, pH 8.0, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8123 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jan 1, 2009
RadiationMonochromator: Si(111), horizontally focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 2.4→83.96 Å / Num. all: 21100 / Num. obs: 21100 / % possible obs: 98.4 % / Redundancy: 4.2 % / Biso Wilson estimate: 40.159 Å2 / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.4-2.534.20.5051.51302430800.50599.3
2.53-2.684.20.37721222828920.37799
2.68-2.874.20.2842.71148727220.28498.8
2.87-3.14.20.1794.31078725460.17998.7
3.1-3.394.20.116.6987123470.1198.5
3.39-3.794.30.0769895821020.07698.2
3.79-4.384.20.06110.6790418720.06197.6
4.38-5.374.20.05811.1671415900.05897.7
5.37-7.594.10.0698.6514912430.06997.5
7.59-47.0883.90.0569.727597060.05695.5

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.19data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
DNAdata collection
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2PHD

2phd


Resolution: 2.4→83.92 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.928 / WRfactor Rfree: 0.1942 / WRfactor Rwork: 0.1376 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8681 / SU B: 6.055 / SU ML: 0.141 / SU R Cruickshank DPI: 0.2418 / SU Rfree: 0.2135 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2192 1088 5.2 %RANDOM
Rwork0.1516 ---
obs0.155 21099 97.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 84.84 Å2 / Biso mean: 35.3052 Å2 / Biso min: 6.26 Å2
Baniso -1Baniso -2Baniso -3
1-1.39 Å20 Å20 Å2
2--1.72 Å20 Å2
3----3.11 Å2
Refinement stepCycle: LAST / Resolution: 2.4→83.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2735 0 37 343 3115
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0222868
X-RAY DIFFRACTIONr_angle_refined_deg1.9281.9543896
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2525353
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.94223.134134
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.79915442
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1951524
X-RAY DIFFRACTIONr_chiral_restr0.1330.2407
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212226
X-RAY DIFFRACTIONr_mcbond_it1.0331.51744
X-RAY DIFFRACTIONr_mcangle_it1.86622809
X-RAY DIFFRACTIONr_scbond_it2.98531124
X-RAY DIFFRACTIONr_scangle_it4.6294.51084
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 83 -
Rwork0.214 1486 -
all-1569 -
obs--98.74 %

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