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- PDB-2r0c: Structure of the substrate-free form of the rebeccamycin biosynth... -

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Basic information

Entry
Database: PDB / ID: 2r0c
TitleStructure of the substrate-free form of the rebeccamycin biosynthetic enzyme REBC
ComponentsRebC
KeywordsOXIDOREDUCTASE / flavin adenine dinucleotide / Monooxygenase
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / FAD binding / methyltransferase activity / methylation
Similarity search - Function
Glutaredoxin - #120 / Aromatic-ring hydroxylase, C-terminal / : / 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 - #120 / Aromatic-ring hydroxylase, C-terminal / : / 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
FLAVIN-ADENINE DINUCLEOTIDE / Putative FAD-monooxygenase
Similarity search - Component
Biological speciesLechevalieria aerocolonigenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsRyan, K.S. / Drennan, C.L.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Crystallographic trapping in the rebeccamycin biosynthetic enzyme RebC
Authors: Ryan, K.S. / Howard-Jones, A.R. / Hamill, M.J. / Elliott, S.J. / Walsh, C.T. / Drennan, C.L.
History
DepositionAug 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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

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Assembly

Deposited unit
A: RebC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,7493
Polymers59,9281
Non-polymers8212
Water7,692427
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)63.220, 77.562, 64.673
Angle α, β, γ (deg.)90.00, 108.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 59927.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lechevalieria aerocolonigenes (bacteria)
Strain: ATCC 39243 / Gene: rbmD, rebC / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8KI25
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 427 / 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: 2.52 Å3/Da / Density % sol: 51.11 %
Crystal growTemperature: 298 K / pH: 7.4
Details: 1.5 microliters of RebC (9 mg/mL in 150 mM NaCl, 10% glycerol, 25 mM HEPES pH 7.5) were incubated with 0.35 microliters of guanidine-HCl for 30 seconds, followed by addition of 1.5 ...Details: 1.5 microliters of RebC (9 mg/mL in 150 mM NaCl, 10% glycerol, 25 mM HEPES pH 7.5) were incubated with 0.35 microliters of guanidine-HCl for 30 seconds, followed by addition of 1.5 microliters of precipitant solution (19% PEG-8000, 0.1 M HEPES pH 7.4), without mixing, at room temperature and sealed over a precipitant well solution. Immediately after set up, crystal trays were placed on a gel shaker and then, after 12 hours, transferred to a storage space in vibration-isolation. Before being flash-frozen in liquid nitrogen, a crystal was soaked for five seconds in cryogenic solution (19% PEG-8000, 0.1 M HEPES pH 7.4, 20% glycerol), VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.40

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1.8455, 1.8447, 0.9798
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 9, 2006
Details: FLAT COLLIMATING MIRROR, DOUBLE CRYSTAL MONOCHROMATOR, TOROID FOCUSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.84551
21.84471
30.97981
ReflectionResolution: 1.8→50 Å / Num. obs: 52005 / % possible obs: 93.9 % / Redundancy: 7.2 % / Rsym value: 0.09 / Net I/σ(I): 25.4
Reflection shellResolution: 1.8→1.86 Å / Mean I/σ(I) obs: 2.6 / Rsym value: 0.458 / % possible all: 67.2

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→50 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2566 5 %RANDOM
Rwork0.211 ---
obs0.211 51814 94.1 %-
all-55046 --
Displacement parametersBiso mean: 41.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.011 Å20 Å25.453 Å2
2---15.012 Å20 Å2
3---11.001 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3898 0 54 427 4379
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.28
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.4471.5
X-RAY DIFFRACTIONc_mcangle_it2.1942
X-RAY DIFFRACTIONc_scbond_it1.9762
X-RAY DIFFRACTIONc_scangle_it2.8772.5
LS refinement shellResolution: 1.8→1.81 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.408 35 5.6 %
Rwork0.355 584 -
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2FAD_TAILMOVED.PAR
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4ION.PARAM

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