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

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Basic information

Entry
Database: PDB / ID: 3nvc
TitleCrystal Structure of Salicylate 1,2-dioxygenase G106A mutant from Pseudoaminobacter salicylatoxidans in complex with salicylate
ComponentsGentisate 1,2-Dioxygenase
KeywordsOXIDOREDUCTASE / Beta-Barrel
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
: / 2-HYDROXYBENZOIC ACID / Gentisate 1,2-dioxygenase
Similarity search - Component
Biological speciesPseudaminobacter salicylatoxidans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.45 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 8, 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)41,6296
Polymers41,1581
Non-polymers4705
Water3,117173
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)166,51524
Polymers164,6344
Non-polymers1,88120
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
Buried area27850 Å2
ΔGint-219 kcal/mol
Surface area49440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.273, 86.977, 167.626
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-402-

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-SAL / 2-HYDROXYBENZOIC ACID / SALICYLIC ACID


Mass: 138.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H6O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 3.29 Å3/Da / Density % sol: 62.6 %
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, 2008
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: 2.45→83.918 Å / Num. all: 20120 / Num. obs: 20120 / % possible obs: 99.1 % / Redundancy: 3.4 % / Biso Wilson estimate: 52.1 Å2 / Rmerge(I) obs: 0.079 / Rsym value: 0.079 / Net I/σ(I): 11.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.45-2.582.90.4771.6850129130.47799.5
2.58-2.743.20.3822887127830.38299.7
2.74-2.933.40.291.3887625800.2999.6
2.93-3.163.60.1782.9870024310.17899.6
3.16-3.463.70.0967.7823522370.09699.4
3.46-3.873.70.06211.7749420270.06299.3
3.87-4.473.70.04315.8657317830.04398.9
4.47-5.483.70.03419.5562315310.03498.6
5.48-7.753.60.03817.1432511980.03898.5
7.75-19.64630.0465.418856370.04691

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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: 2.45→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.2382 / WRfactor Rwork: 0.1706 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7989 / SU B: 8.871 / SU ML: 0.202 / SU R Cruickshank DPI: 0.308 / SU Rfree: 0.2683 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2724 1022 5.1 %RANDOM
Rwork0.1933 ---
obs0.1972 20084 98.54 %-
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: 93.41 Å2 / Biso mean: 45.3088 Å2 / Biso min: 11.08 Å2
Baniso -1Baniso -2Baniso -3
1-2.48 Å20 Å20 Å2
2--2.7 Å20 Å2
3----5.17 Å2
Refinement stepCycle: LAST / Resolution: 2.45→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2735 0 29 173 2937
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222848
X-RAY DIFFRACTIONr_angle_refined_deg1.8771.9533870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2835349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.91423.03132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.98815439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7161524
X-RAY DIFFRACTIONr_chiral_restr0.1210.2405
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212222
X-RAY DIFFRACTIONr_mcbond_it0.8891.51738
X-RAY DIFFRACTIONr_mcangle_it1.63122797
X-RAY DIFFRACTIONr_scbond_it2.42431110
X-RAY DIFFRACTIONr_scangle_it3.7614.51072
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 58 -
Rwork0.269 1394 -
all-1452 -
obs--98.71 %

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