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- PDB-4eip: Native and K252c bound RebC-10x -

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Basic information

Entry
Database: PDB / ID: 4eip
TitleNative and K252c bound RebC-10x
ComponentsPutative FAD-monooxygenase
KeywordsOxidoreductase/Oxidoreductase inhibitor / flavin adenine dinucleotide / K252c / monooxygenase / indolocarbazole / Oxidoreductase-Oxidoreductase inhibitor complex
Function / homology
Function and homology information


FAD binding / methyltransferase activity / monooxygenase activity / methylation
Similarity search - Function
Aromatic-ring hydroxylase, C-terminal / Glutaredoxin - #120 / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily ...Aromatic-ring hydroxylase, C-terminal / Glutaredoxin - #120 / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Glutaredoxin / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Chem-K2C / Putative FAD-monooxygenase
Similarity search - Component
Biological speciesLechevalieria aerocolonigenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.332 Å
AuthorsGoldman, P.J. / Ryan, K.S. / Howard-Jones, A.R. / Hamill, M.J. / Elliott, S.J. / Walsh, C.T. / Drennan, C.L.
CitationJournal: Chem.Biol. / Year: 2012
Title: An Unusual Role for a Mobile Flavin in StaC-like Indolocarbazole Biosynthetic Enzymes.
Authors: Goldman, P.J. / Ryan, K.S. / Hamill, M.J. / Howard-Jones, A.R. / Walsh, C.T. / Elliott, S.J. / Drennan, C.L.
History
DepositionApr 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: Putative FAD-monooxygenase
B: Putative FAD-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,2435
Polymers119,3612
Non-polymers1,8823
Water5,477304
1
A: Putative FAD-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7773
Polymers59,6801
Non-polymers1,0972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative FAD-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4662
Polymers59,6801
Non-polymers7861
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.305, 78.593, 125.723
Angle α, β, γ (deg.)90.000, 99.870, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Putative FAD-monooxygenase / Putative monooxygenase / Putative polyketide hydroxylase / RebC


Mass: 59680.344 Da / Num. of mol.: 2
Mutation: E36D, Q37A, T38A, R46K, G48S, Q117A, F216V, A231S, R239N, T241V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lechevalieria aerocolonigenes (bacteria)
Gene: rbmD, rebC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8KI25
#2: Chemical ChemComp-K2C / 6,7,12,13-tetrahydro-5H-indolo[2,3-a]pyrrolo[3,4-c]carbazol-5-one


Mass: 311.337 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H13N3O
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


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


Mass: 18.015 Da / Num. of mol.: 304 / 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: 2.62 Å3/Da / Density % sol: 53.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM ammonium fluoride, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 14, 2009
RadiationMonochromator: Cryogenically-cooled single crystal Si(220) side bounce monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 268516 / Num. obs: 51631 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Biso Wilson estimate: 35.01 Å2
Reflection shellResolution: 2.3→2.38 Å / % possible all: 98.7

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
APEXdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHENIX1.7.3_928phasing
RefinementResolution: 2.332→41.365 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7992 / SU ML: 0.34 / σ(F): 1.35 / Phase error: 27.22 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.26 2614 5.06 %
Rwork0.2134 48996 -
obs0.2158 51610 97.68 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.002 Å2 / ksol: 0.361 e/Å3
Displacement parametersBiso max: 97.6 Å2 / Biso mean: 38.0502 Å2 / Biso min: 15.68 Å2
Baniso -1Baniso -2Baniso -3
1-2.4105 Å2-0 Å21.3048 Å2
2---1.9547 Å20 Å2
3----0.4558 Å2
Refinement stepCycle: LAST / Resolution: 2.332→41.365 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7862 0 130 304 8296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0088214
X-RAY DIFFRACTIONf_angle_d1.08911214
X-RAY DIFFRACTIONf_chiral_restr0.061234
X-RAY DIFFRACTIONf_plane_restr0.0091458
X-RAY DIFFRACTIONf_dihedral_angle_d14.7572938
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3322-2.37460.2957900.25441801189168
2.3746-2.42030.2881360.2512608274499
2.4203-2.46970.30281380.24832608274698
2.4697-2.52340.31761210.25722565268699
2.5234-2.58210.34461410.25822603274499
2.5821-2.64660.31081240.25792594271899
2.6466-2.71820.29161440.23972598274299
2.7182-2.79810.28891320.241726602792100
2.7981-2.88840.30761460.24082576272299
2.8884-2.99160.29391360.235826282764100
2.9916-3.11140.31451530.226625912744100
3.1114-3.25290.25071400.217726502790100
3.2529-3.42440.29631510.215626102761100
3.4244-3.63880.24461460.205326292775100
3.6388-3.91960.23171400.195926342774100
3.9196-4.31360.22641450.188726352780100
4.3136-4.93690.20161320.167526662798100
4.9369-6.21660.23691600.21932619277999
6.2166-41.3720.23961390.20152721286099

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