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

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Basic information

Entry
Database: PDB / ID: 4fah
TitleCrystal Structure of the Salicylate 1,2-dioxygenase from Pseudoaminobacter salicylatoxidans A85H 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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 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 22, 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 / diffrn_source / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_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)41,1382
Polymers41,0821
Non-polymers561
Water6,017334
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)164,5538
Polymers164,3294
Non-polymers2234
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 area21580 Å2
ΔGint-158 kcal/mol
Surface area52430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.185, 90.010, 169.058
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-749-

HOH

21A-817-

HOH

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Components

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


Mass: 41082.328 Da / Num. of mol.: 1 / Mutation: A85H
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 / Iron


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


Mass: 18.015 Da / Num. of mol.: 334 / 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: 3.34 Å3/Da / Density % sol: 63.2 %
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: Jun 16, 2009
RadiationMonochromator: Si(111), horizontally focussing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8123 Å / Relative weight: 1
ReflectionResolution: 2.5→84.529 Å / Num. all: 18577 / Num. obs: 18577 / % possible obs: 96.3 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.5-2.643.80.5181.51010726890.51897.1
2.64-2.83.80.4251.7958525390.42596.8
2.8-2.993.70.2792.7897424060.27996.8
2.99-3.233.80.1824.2834922250.18296.4
3.23-3.543.80.1126.7783120820.11296.5
3.54-3.953.80.098697218550.0996.1
3.95-4.563.70.0739.1613616420.07395.5
4.56-5.593.70.0758.5525314150.07596.4
5.59-7.913.60.0817.9396910930.08194.8
7.91-56.3443.50.069.922266310.0693.8

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.19data scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.2221 / WRfactor Rwork: 0.1432 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8542 / SU B: 7.501 / SU ML: 0.169 / SU R Cruickshank DPI: 0.309 / SU Rfree: 0.2603 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.309 / ESU R Free: 0.26 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 958 5.2 %RANDOM
Rwork0.1567 ---
obs0.1609 18567 95.47 %-
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: 77.53 Å2 / Biso mean: 40.3652 Å2 / Biso min: 21.26 Å2
Baniso -1Baniso -2Baniso -3
1-1.71 Å20 Å20 Å2
2--1.58 Å20 Å2
3----3.3 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2744 0 1 334 3079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0222824
X-RAY DIFFRACTIONr_angle_refined_deg1.7751.9433842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8485348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.35223.106132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.3815437
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4321523
X-RAY DIFFRACTIONr_chiral_restr0.1260.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212211
X-RAY DIFFRACTIONr_mcbond_it0.8441.51739
X-RAY DIFFRACTIONr_mcangle_it1.57722798
X-RAY DIFFRACTIONr_scbond_it2.48131085
X-RAY DIFFRACTIONr_scangle_it3.9254.51044
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 60 -
Rwork0.191 1296 -
all-1356 -
obs--96.86 %

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