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- PDB-4k2x: OxyS anhydrotetracycline hydroxylase from Streptomyces rimosus -

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Basic information

Entry
Database: PDB / ID: 4k2x
TitleOxyS anhydrotetracycline hydroxylase from Streptomyces rimosus
ComponentsPolyketide oxygenase/hydroxylase
KeywordsOXIDOREDUCTASE / FLAVOPROTEIN / para-hydroxybenzoate hydroxylase fold / hydroxylase / FAD Binding
Function / homology
Function and homology information


5a,11a-dehydrotetracycline 5-monooxygenase / anhydrotetracycline 6-monooxygenase / anhydrotetracycline monooxygenase activity / antibiotic biosynthetic process / FAD binding
Similarity search - Function
Alpha-Beta Plaits - #2450 / Glutaredoxin - #120 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Glutaredoxin / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Plaits ...Alpha-Beta Plaits - #2450 / Glutaredoxin - #120 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / Glutaredoxin / FAD/NAD(P)-binding domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 12-dehydrotetracycline 5-monooxygenase/anhydrotetracycline 6-monooxygenase
Similarity search - Component
Biological speciesStreptomyces rimosus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsWang, P. / Sawaya, M.R. / Tang, Y.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: Uncovering the Enzymes that Catalyze the Final Steps in Oxytetracycline Biosynthesis.
Authors: Wang, P. / Bashiri, G. / Gao, X. / Sawaya, M.R. / Tang, Y.
History
DepositionApr 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 15, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Sep 20, 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 / pdbx_initial_refinement_model / 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_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: Polyketide oxygenase/hydroxylase
B: Polyketide oxygenase/hydroxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,9974
Polymers113,4262
Non-polymers1,5712
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-32 kcal/mol
Surface area38430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.060, 115.130, 121.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Polyketide oxygenase/hydroxylase


Mass: 56713.074 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces rimosus (bacteria) / Strain: ATCC 10970 / Gene: oxyS, SRIM_10936 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: L8EUQ6
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 2.34 Å3/Da / Density % sol: 47.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 16% PEG-8000, 0.1M Na/K phosphate pH 6.0, 0.2M NaCl, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 3, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.55→34.05 Å / Num. all: 31457 / Num. obs: 31457 / % possible obs: 89 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 50.023 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 13.58
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
2.55-2.620.5073.37108852214185.6
2.62-2.690.4413.97108062210188.5
2.69-2.770.3834.6106622151188.4
2.77-2.850.3215.47107042140190.1
2.85-2.940.2586.64105322098190.3
2.94-3.050.2058.07102962020190.5
3.05-3.160.1679.8199471944191.1
3.16-3.290.13611.6397601918191.1
3.29-3.440.1071492091793190.7
3.44-3.610.09216.2488431720189
3.61-3.80.07818.3582241618189.1
3.8-4.030.06720.3978381557190
4.03-4.310.05723.3373071453189
4.31-4.660.05324.4866861341188.2
4.66-5.10.05225.362771256188.5
5.1-5.70.05123.4755381129188.2
5.7-6.580.04924.7152361010188.2
6.58-8.060.03927.164433861187.8
8.06-11.40.03429.763417667186

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.8 Å34.05 Å
Translation3.8 Å34.05 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.3.0phasing
BUSTER-TNTrefinement
PDB_EXTRACT3.11data extraction
ADSCQuantumdata collection
BUSTER2.10.0refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3FMW

3fmw


Resolution: 2.55→34.05 Å / Cor.coef. Fo:Fc: 0.9401 / Cor.coef. Fo:Fc free: 0.9176 / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 1.31 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2294 1573 5 %RANDOM
Rwork0.1866 ---
all0.1887 31454 --
obs0.1887 31454 89.01 %-
Displacement parametersBiso max: 146.88 Å2 / Biso mean: 48.2244 Å2 / Biso min: 14.99 Å2
Baniso -1Baniso -2Baniso -3
1-1.3445 Å20 Å20 Å2
2--7.3091 Å20 Å2
3----8.6536 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.55→34.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7434 0 106 48 7588
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2579SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes168HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1233HARMONIC5
X-RAY DIFFRACTIONt_it7722HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion970SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8670SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7722HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10537HARMONIC21.24
X-RAY DIFFRACTIONt_omega_torsion3.33
X-RAY DIFFRACTIONt_other_torsion22.01
LS refinement shellResolution: 2.55→2.63 Å / Total num. of bins used: 16
RfactorNum. reflection% reflection
Rfree0.258 138 4.99 %
Rwork0.2118 2627 -
all0.2141 2765 -
obs--89.01 %
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)
10.79140.2930.17150.5271-0.13271.1284-0.02780.1867-0.0152-0.0771-0.0096-0.0015-0.01490.08160.0374-0.10540.0008-0.0169-0.06190.0257-0.096219.383316.06729.8771
20.62470.17530.0290.5385-0.02821.1304-0.01840.03810.0491-0.0873-0.02250.01790.0175-0.04040.041-0.10070.02620.0011-0.1018-0.0041-0.0527-18.05-14.94149.2632
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 601
2X-RAY DIFFRACTION2{ B|* }B1 - 601

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