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- PDB-3vca: Quaternary Ammonium Oxidative Demethylation: X-ray Crystallograph... -

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Basic information

Entry
Database: PDB / ID: 3vca
TitleQuaternary Ammonium Oxidative Demethylation: X-ray Crystallographic, Resonance Raman and UV-visible Spectroscopic Analysis of a Rieske-type Demethylase
ComponentsRing-hydroxylating dioxygenase
KeywordsOXIDOREDUCTASE / Rieske-type / mononuclear non-heme iron / N-demethylase
Function / homology
Function and homology information


dioxygenase activity / 2 iron, 2 sulfur cluster binding / iron ion binding
Similarity search - Function
Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich ...Aromatic-ring-hydroxylating dioxygenase, alpha subunit / Aromatic-ring-hydroxylating dioxygenase, alpha subunit, C-terminal domain / Ring hydroxylating alpha subunit (catalytic domain) / Aromatic-ring-hydroxylating dioxygenase, 2Fe-2S-binding site / Bacterial ring hydroxylating dioxygenases alpha-subunit signature. / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 / Rieske Iron-sulfur Protein / Rieske [2Fe-2S] iron-sulphur domain / 3-layer Sandwich / Rieske [2Fe-2S] domain / Rieske [2Fe-2S] iron-sulphur domain / Rieske [2Fe-2S] iron-sulfur domain profile. / Rieske [2Fe-2S] iron-sulphur domain superfamily / Alpha-Beta Complex / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
: / FE2/S2 (INORGANIC) CLUSTER / PROLINE / Ring-hydroxylating dioxygenase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.59 Å
AuthorsDaughtry, K.D. / Xiao, Y. / Stoner-Ma, D. / Cho, E. / Orville, A.M. / Liu, P. / Allen, K.N.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Quaternary Ammonium Oxidative Demethylation: X-ray Crystallographic, Resonance Raman, and UV-Visible Spectroscopic Analysis of a Rieske-Type Demethylase.
Authors: Daughtry, K.D. / Xiao, Y. / Stoner-Ma, D. / Cho, E. / Orville, A.M. / Liu, P. / Allen, K.N.
History
DepositionJan 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 8, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 22, 2012Group: Database references
Revision 1.2Oct 30, 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Ring-hydroxylating dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,8645
Polymers46,4251
Non-polymers4394
Water10,989610
1
A: Ring-hydroxylating dioxygenase
hetero molecules

A: Ring-hydroxylating dioxygenase
hetero molecules

A: Ring-hydroxylating dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,59315
Polymers139,2763
Non-polymers1,31712
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area8750 Å2
ΔGint-129 kcal/mol
Surface area44950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.667, 97.667, 179.325
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-951-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Ring-hydroxylating dioxygenase


Mass: 46425.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Strain: 1021 / Gene: NP_435646, RA0400, SMa0751 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q92ZP9

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Non-polymers , 5 types, 614 molecules

#2: Chemical ChemComp-FES / FE2/S2 (INORGANIC) CLUSTER


Mass: 175.820 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe2S2
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PRO / PROLINE


Type: L-peptide linking / Mass: 115.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 610 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.66 Å3/Da / Density % sol: 53.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES buffer, 10 % PEG 3350, 10 % glycerol, 25 mM hexamine cobalt, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X12C11
SYNCHROTRONNSLS X12C21.738
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDMar 5, 2008
ADSC QUANTUM 2102CCDMar 5, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si(111) channel-cut crystalSINGLE WAVELENGTHMx-ray1
2Si(111) channel-cut crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
21.7381
ReflectionResolution: 1.59→28.191 Å / Num. all: 68467 / Num. obs: 68467 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 16.3 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 40.78

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXSphasing
PHENIX(phenix.refine: 1.6.2_432)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.59→28.191 Å / SU ML: 0.18 / σ(F): 0 / Phase error: 17.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1895 6532 9.95 %Random, 10%
Rwork0.1736 ---
obs0.1752 65657 95.97 %-
all-65657 --
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 36.346 Å2 / ksol: 0.355 e/Å3
Displacement parametersBiso mean: 18.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.379 Å20 Å2-0 Å2
2--0.379 Å20 Å2
3----0.758 Å2
Refinement stepCycle: LAST / Resolution: 1.59→28.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3159 0 19 610 3788
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063296
X-RAY DIFFRACTIONf_angle_d1.184496
X-RAY DIFFRACTIONf_dihedral_angle_d13.631203
X-RAY DIFFRACTIONf_chiral_restr0.075487
X-RAY DIFFRACTIONf_plane_restr0.005582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5903-1.64720.24514940.19645662X-RAY DIFFRACTION92
1.6472-1.71310.22386550.18755581X-RAY DIFFRACTION93
1.7131-1.79110.21826910.18145619X-RAY DIFFRACTION94
1.7911-1.88550.21386150.18055724X-RAY DIFFRACTION94
1.8855-2.00360.2036140.17315846X-RAY DIFFRACTION96
2.0036-2.15820.19016780.17015980X-RAY DIFFRACTION98
2.1582-2.37530.19786940.16955968X-RAY DIFFRACTION97
2.3753-2.71880.20186690.1836020X-RAY DIFFRACTION97
2.7188-3.42440.18596830.17156176X-RAY DIFFRACTION99
3.4244-28.19490.16417390.1676549X-RAY DIFFRACTION100

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