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- PDB-4eiq: Chromopyrrolic acid-soaked RebC-10x with bound 7-carboxy-K252c -

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Basic information

Entry
Database: PDB / ID: 4eiq
TitleChromopyrrolic acid-soaked RebC-10x with bound 7-carboxy-K252c
ComponentsPutative FAD-monooxygenase
KeywordsOxidoreductase/Oxidoreductase inhibitor / flavin adenine dinucleotide / 7-carboxy-K252c / monooxygenase / indolocarbazole / Oxidoreductase-Oxidoreductase inhibitor complex
Function / homology
Function and homology information


: / ubiquinone biosynthetic process / FAD binding / methyltransferase 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 / Glutaredoxin ...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 / Glutaredoxin / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-KCT / Putative FAD-monooxygenase
Similarity search - Component
Biological speciesLechevalieria aerocolonigenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.76 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)120,0714
Polymers119,3612
Non-polymers7112
Water1,11762
1
A: Putative FAD-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0362
Polymers59,6801
Non-polymers3551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative FAD-monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0362
Polymers59,6801
Non-polymers3551
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.184, 77.703, 123.145
Angle α, β, γ (deg.)90.000, 98.780, 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-KCT / (5S)-7-oxo-6,7,12,13-tetrahydro-5H-indolo[2,3-a]pyrrolo[3,4-c]carbazole-5-carboxylic acid


Mass: 355.346 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H13N3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100 mM ammonium fluoride and 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: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 21, 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: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.76→47.3 Å / Num. all: 30531 / Num. obs: 28820 / % possible obs: 94.4 % / Observed criterion σ(I): 3
Reflection shellResolution: 2.76→2.79 Å / % possible all: 97.9

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Processing

Software
NameClassification
APEXdata collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementResolution: 2.76→47.3 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2551 1458 4.8 %
Rwork0.2059 27362 -
obs-28820 94.4 %
Solvent computationBsol: 47.8933 Å2
Displacement parametersBiso max: 117.78 Å2 / Biso mean: 61.6481 Å2 / Biso min: 30.99 Å2
Baniso -1Baniso -2Baniso -3
1-7.647 Å20 Å24.773 Å2
2---2.154 Å20 Å2
3----5.493 Å2
Refinement stepCycle: LAST / Resolution: 2.76→47.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7812 0 54 62 7928
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.3471.5
X-RAY DIFFRACTIONc_scbond_it1.8412
X-RAY DIFFRACTIONc_mcangle_it2.3372
X-RAY DIFFRACTIONc_scangle_it2.8712.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_k252c_kaityfad_7carboxy_fad_no_iso1.3.parCNS_TOPPAR:dna-rna.top
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.paramCNS_TOPPAR:water.top
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.paramCNS_TOPPAR:ion.top
X-RAY DIFFRACTION4CNS_TOPPAR:ion.paramCNS_TOPPAR:carbohydrate.top
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.paramkct.top
X-RAY DIFFRACTION6kct.parprotein_k252c_kaityfad_7carboxy_fad_no_iso1.3_ile.top

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