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- PDB-4dn9: CRYSTAL STRUCTURE OF putative Antibiotic biosynthesis monooxygena... -

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Basic information

Entry
Database: PDB / ID: 4dn9
TitleCRYSTAL STRUCTURE OF putative Antibiotic biosynthesis monooxygenase from Chloroflexus aurantiacus J-10-fl
ComponentsAntibiotic biosynthesis monooxygenase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGRC / PSI-Biology / New York Structural Genomics Research Consortium
Function / homology
Function and homology information


catalytic activity / monooxygenase activity
Similarity search - Function
ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / Antibiotic biosynthesis monooxygenase
Similarity search - Component
Biological speciesChloroflexus aurantiacus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsMalashkevich, V.N. / Bhosle, R. / Toro, R. / Seidel, R. / Almo, S.C. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: CRYSTAL STRUCTURE OF putative Antibiotic biosynthesis monooxygenase from Chloroflexus aurantiacus J-10-fl
Authors: Malashkevich, V.N. / Bhosle, R. / Toro, R. / Seidel, R. / Almo, S.C.
History
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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 / _struct_conn.pdbx_leaving_atom_flag / _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: Antibiotic biosynthesis monooxygenase
B: Antibiotic biosynthesis monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6836
Polymers26,3142
Non-polymers3684
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-36 kcal/mol
Surface area9630 Å2
MethodPISA
2
A: Antibiotic biosynthesis monooxygenase
B: Antibiotic biosynthesis monooxygenase
hetero molecules

A: Antibiotic biosynthesis monooxygenase
B: Antibiotic biosynthesis monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,36512
Polymers52,6294
Non-polymers7378
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_565x,-y+1,-z+1/21
Buried area8310 Å2
ΔGint-68 kcal/mol
Surface area17000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.511, 60.511, 135.191
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-321-

HOH

Detailsdimer

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Components

#1: Protein Antibiotic biosynthesis monooxygenase


Mass: 13157.151 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloroflexus aurantiacus (bacteria) / Strain: J-10-fl / Gene: Caur_2443 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)CODON+RIL / References: UniProt: A9WHE0
#2: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.6M Ammonium sulfate, 0.1M MES:NaOH, pH 6.5, 10% dioxane, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionRedundancy: 7.8 % / Av σ(I) over netI: 19.76 / Number: 233778 / Rmerge(I) obs: 0.127 / Χ2: 1.21 / D res high: 2.05 Å / D res low: 50 Å / Num. obs: 30159 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.565099.910.0562.2737.5
4.425.5610010.0542.1167.6
3.864.4210010.0672.57.7
3.513.8610010.0752.0797.8
3.253.5110010.081.5277.9
3.063.2510010.1061.2157.9
2.913.0610010.1321.147.9
2.782.9110010.1581.0067.8
2.682.7810010.2250.9597.9
2.582.6810010.2490.937.9
2.52.5810010.2790.9157.8
2.432.510010.3470.9057.8
2.372.4310010.3880.8737.8
2.312.3710010.4340.8747.8
2.262.3110010.4660.867.8
2.212.2610010.5380.8127.8
2.162.2110010.60.8197.8
2.122.1610010.6950.7827.7
2.092.1210010.7930.7927.6
2.052.0910010.8830.7697.2
ReflectionResolution: 2.05→50 Å / Num. obs: 30159 / % possible obs: 100 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.127 / Χ2: 1.206 / Net I/σ(I): 6.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.05-2.097.20.88315670.7691100
2.09-2.127.60.79314480.7921100
2.12-2.167.70.69515210.7821100
2.16-2.217.80.614750.8191100
2.21-2.267.80.53815530.8121100
2.26-2.317.80.46614750.861100
2.31-2.377.80.43415080.8741100
2.37-2.437.80.38815140.8731100
2.43-2.57.80.34715170.9051100
2.5-2.587.80.27914910.9151100
2.58-2.687.90.24914900.931100
2.68-2.787.90.22515250.9591100
2.78-2.917.80.15815091.0061100
2.91-3.067.90.13214731.141100
3.06-3.257.90.10615271.2151100
3.25-3.517.90.0815111.5271100
3.51-3.867.80.07514932.0791100
3.86-4.427.70.06715232.51100
4.42-5.567.60.05415102.1161100
5.56-507.50.05615292.273199.9

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
CBASSdata collection
HKL-2000data reduction
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→19.95 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.1993 / WRfactor Rwork: 0.1452 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8678 / SU B: 7.779 / SU ML: 0.095 / SU R Cruickshank DPI: 0.3342 / SU Rfree: 0.149 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.334 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2256 835 5.1 %RANDOM
Rwork0.1588 ---
obs0.162 16479 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.16 Å2 / Biso mean: 27.45 Å2 / Biso min: 14.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1434 0 22 102 1558
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0191500
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.9982048
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3355199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.524.61552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.62215213
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.068156
X-RAY DIFFRACTIONr_chiral_restr0.0850.2233
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221118
X-RAY DIFFRACTIONr_rigid_bond_restr3.34831500
X-RAY DIFFRACTIONr_sphericity_free32.107546
X-RAY DIFFRACTIONr_sphericity_bonded16.40751521
LS refinement shellResolution: 2.05→2.102 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 58 -
Rwork0.172 973 -
all-1031 -
obs--98.66 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5593-0.16590.18940.7519-0.05241.274-0.01790.04210.0688-0.0574-0.0147-0.0343-0.09640.0510.03250.0129-0.0038-0.00120.00550.01060.030247.862639.022129.2188
20.716-0.38930.18490.7963-0.2212.1796-0.0016-0.00960.09260.0192-0.0281-0.026-0.1410.06930.02960.0241-0.0047-0.00340.00450.00140.042137.035846.498714.7868
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-10 - 9999
2X-RAY DIFFRACTION2B-10 - 9999

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