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- PDB-4fbf: Crystal Structure of the Salicylate 1,2-dioxygenase from Pseudoam... -

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Basic information

Entry
Database: PDB / ID: 4fbf
TitleCrystal Structure of the Salicylate 1,2-dioxygenase from Pseudoaminobacter salicylatoxidans W104Y mutant
ComponentsGentisate 1,2-dioxygenase
KeywordsOXIDOREDUCTASE / BETA-SANDWICH / METALLOPROTEIN / DIOXYGENASE / AROMATIC COMPOUND DEGRADATION
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 / FOURIER SYNTHESIS / Resolution: 2.7 Å
AuthorsFerraroni, M. / Briganti, F. / Matera, I.
CitationJournal: J.Struct.Biol. / Year: 2012
Title: The generation of a 1-hydroxy-2-naphthoate 1,2-dioxygenase by single point mutations of salicylate 1,2-dioxygenase - Rational design of mutants and the crystal structures of the A85H and W104Y variants.
Authors: Ferraroni, M. / Steimer, L. / Matera, I. / Burger, S. / Scozzafava, A. / Stolz, A. / Briganti, F.
History
DepositionMay 23, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 26, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2012Group: Database references
Revision 1.2Feb 28, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,0482
Polymers40,9921
Non-polymers561
Water2,792155
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)164,1928
Polymers163,9694
Non-polymers2234
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 area20580 Å2
ΔGint-175 kcal/mol
Surface area49590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.570, 87.970, 167.274
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-543-

HOH

21A-594-

HOH

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Components

#1: Protein Gentisate 1,2-dioxygenase / Salicylate 1 / 2-Dioxygenase


Mass: 40992.223 Da / Num. of mol.: 1 / Mutation: W104Y
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-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 3.35 Å3/Da / Density % sol: 63.24 %
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: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.542 Å
DetectorType: OXFORD ONYX CCD / Detector: CCD / Date: Apr 22, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.7→83.637 Å / Num. all: 15486 / Num. obs: 15486 / % possible obs: 99.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.134 / Rsym value: 0.134 / Net I/σ(I): 15.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.7-2.855.20.4221.81145122150.422100
2.85-3.025.20.2952.51087621040.295100
3.02-3.234.90.2672.5986919950.267100
3.23-3.495.10.1534.6952418780.153100
3.49-3.824.90.1285.2832217030.128100
3.82-4.274.60.1025.9718815530.10299.6
4.27-4.935.10.06110.8706413840.061100
4.93-6.045.10.06210.9600711820.062100
6.04-8.544.90.05911.546249390.059100
8.54-29.2354.30.03617.823175330.03697

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.19data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.7→30 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.867 / WRfactor Rfree: 0.2026 / WRfactor Rwork: 0.1568 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7816 / SU B: 11.964 / SU ML: 0.246 / SU R Cruickshank DPI: 0.4991 / SU Rfree: 0.3273 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.499 / ESU R Free: 0.327 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.272 776 5 %RANDOM
Rwork0.2003 ---
obs0.2039 15485 99.88 %-
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: 68.52 Å2 / Biso mean: 33.419 Å2 / Biso min: 5.59 Å2
Baniso -1Baniso -2Baniso -3
1-2.31 Å20 Å20 Å2
2---0.24 Å20 Å2
3----2.07 Å2
Refinement stepCycle: LAST / Resolution: 2.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2664 0 1 155 2820
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222740
X-RAY DIFFRACTIONr_angle_refined_deg1.7681.9463728
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1495336
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.90623.228127
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.29615421
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0011521
X-RAY DIFFRACTIONr_chiral_restr0.1110.2396
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212137
X-RAY DIFFRACTIONr_mcbond_it0.7321.51690
X-RAY DIFFRACTIONr_mcangle_it1.39322722
X-RAY DIFFRACTIONr_scbond_it2.00331050
X-RAY DIFFRACTIONr_scangle_it3.3154.51006
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 59 -
Rwork0.264 1081 -
all-1140 -
obs--100 %

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