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- PDB-3njz: Crystal Structure of Salicylate 1,2-dioxygenase from Pseudoaminob... -

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Basic information

Entry
Database: PDB / ID: 3njz
TitleCrystal Structure of Salicylate 1,2-dioxygenase from Pseudoaminobacter salicylatoxidans Adducts with salicylate
ComponentsGentisate 1,2-dioxygenase
KeywordsOXIDOREDUCTASE / BETA-SANDWICH
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: 2.1 Å
AuthorsFerraroni, M. / Briganti, F. / Matera, I.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: Crystal structures of salicylate 1,2-dioxygenase-substrates adducts: A step towards the comprehension of the structural basis for substrate selection in class III ring cleaving dioxygenases.
Authors: Ferraroni, M. / Matera, I. / Steimer, L. / Burger, S. / Scozzafava, A. / Stolz, A. / Briganti, F.
History
DepositionJun 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 21, 2012Group: Database references
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,5235
Polymers41,1441
Non-polymers3784
Water5,837324
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)166,09020
Polymers164,5784
Non-polymers1,51316
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area28110 Å2
ΔGint-240 kcal/mol
Surface area48780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.652, 86.961, 166.465
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein Gentisate 1,2-dioxygenase /


Mass: 41144.438 Da / Num. of mol.: 1
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 / 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 / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 3.37 Å3/Da / Density % sol: 63.51 %
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: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 4, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→83.333 Å / Num. all: 32880 / Num. obs: 32880 / % possible obs: 99.9 % / Redundancy: 4.3 % / Biso Wilson estimate: 25.632 Å2 / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 11.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.1-2.214.30.4231.72029247580.42399.9
2.21-2.3540.4610.51782444910.46199.9
2.35-2.514.40.2253.21850642210.225100
2.51-2.714.30.2191.61703239320.21999.9
2.71-2.974.40.125.71625536700.12100
2.97-3.324.40.0847.71461032920.084100
3.32-3.834.20.1113.31220629250.111100
3.83-4.74.30.0714.91062424920.071100
4.7-6.644.30.0414.1855819760.04100
6.64-47.2984.10.03615.7459211230.03698.9

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.19data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→30 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.889 / WRfactor Rfree: 0.2106 / WRfactor Rwork: 0.1746 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8187 / SU B: 4.038 / SU ML: 0.106 / SU R Cruickshank DPI: 0.1742 / SU Rfree: 0.1604 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2309 1644 5.1 %RANDOM
Rwork0.1913 ---
obs0.1933 32423 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: 62.99 Å2 / Biso mean: 25.8136 Å2 / Biso min: 10.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20 Å20 Å2
2--1.22 Å20 Å2
3----1.7 Å2
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2845 0 23 324 3192
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222978
X-RAY DIFFRACTIONr_angle_refined_deg1.481.9514053
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6685371
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.41523.165139
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.19415467
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8411525
X-RAY DIFFRACTIONr_chiral_restr0.0980.2427
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0212329
X-RAY DIFFRACTIONr_mcbond_it0.6731.51822
X-RAY DIFFRACTIONr_mcangle_it1.25622940
X-RAY DIFFRACTIONr_scbond_it2.19631156
X-RAY DIFFRACTIONr_scangle_it3.4624.51109
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 129 -
Rwork0.226 2288 -
all-2417 -
obs--99.83 %

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