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- PDB-2cfk: AGAO in complex with wc5 (Ru-wire inhibitor, 5-carbon linker) -

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Basic information

Entry
Database: PDB / ID: 2cfk
TitleAGAO in complex with wc5 (Ru-wire inhibitor, 5-carbon linker)
ComponentsPHENYLETHYLAMINE OXIDASE
KeywordsOXIDOREDUCTASE / AMINE OXIDASE / ARTHROBACTER GLOBIFORMIS / COPPER / COPPER CONTAINING / TPQ / CUAO / QUINONE / RUTHENIUM DIIMINE WIRES / COMPETITIVE INHIBITION / METAL-BINDING
Function / homology
Function and homology information


: / : / : / primary-amine oxidase / amine metabolic process / quinone binding / copper ion binding
Similarity search - Function
Copper amine oxidase, N3 domain / Copper amine oxidase, catalytic domain / Copper amine oxidase copper-binding site signature. / Copper amine oxidase topaquinone signature. / Nuclear Transport Factor 2; Chain: A, - #40 / Copper amine oxidase / Copper amine oxidase, catalytic domain / Copper amine oxidase, N-terminal / Copper amine oxidase, catalytic domain superfamily / Copper amine oxidase, enzyme domain ...Copper amine oxidase, N3 domain / Copper amine oxidase, catalytic domain / Copper amine oxidase copper-binding site signature. / Copper amine oxidase topaquinone signature. / Nuclear Transport Factor 2; Chain: A, - #40 / Copper amine oxidase / Copper amine oxidase, catalytic domain / Copper amine oxidase, N-terminal / Copper amine oxidase, catalytic domain superfamily / Copper amine oxidase, enzyme domain / Beta-galactosidase; Chain A, domain 5 / Nuclear Transport Factor 2; Chain: A, / Distorted Sandwich / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / RUTHENIUM WIRE, 5 CARBON LINKER / RUTHENIUM WIRE WC5 / Phenylethylamine oxidase
Similarity search - Component
Biological speciesARTHROBACTER GLOBIFORMIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLangley, D.B. / Duff, A.P. / Freeman, H.C. / Guss, J.M. / Juda, G.A. / Dooley, D.M. / Contakes, S.M. / Halpern-Manners, N.W. / Dunn, A.R. / Gray, H.B.
CitationJournal: J. Am. Chem. Soc. / Year: 2008
Title: Enantiomer-specific binding of ruthenium(II) molecular wires by the amine oxidase of Arthrobacter globiformis.
Authors: Langley, D.B. / Brown, D.E. / Cheruzel, L.E. / Contakes, S.M. / Duff, A.P. / Hilmer, K.M. / Dooley, D.M. / Gray, H.B. / Guss, J.M. / Freeman, H.C.
History
DepositionFeb 21, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 19, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / citation ...atom_site / citation / database_PDB_caveat / pdbx_struct_conn_angle / struct_conn
Item: _atom_site.label_alt_id / _citation.journal_abbrev ..._atom_site.label_alt_id / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title
Revision 2.1May 8, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method
Revision 2.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHENYLETHYLAMINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,41715
Polymers71,7641
Non-polymers2,65414
Water7,656425
1
A: PHENYLETHYLAMINE OXIDASE
hetero molecules

A: PHENYLETHYLAMINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,83530
Polymers143,5282
Non-polymers5,30728
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)157.885, 62.944, 92.013
Angle α, β, γ (deg.)90.00, 112.20, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2092-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PHENYLETHYLAMINE OXIDASE / AMINE OXIDASE / COPPER AMINE OXIDASE


Mass: 71763.766 Da / Num. of mol.: 1 / Fragment: AGAO HOLOENZYME, RESIDUES 3-638
Source method: isolated from a genetically manipulated source
Details: RESIDUE A382 WAS AN ACTIVE SITE TYROSINE RESIDUE, WHICH WAS SELF-PROCESSED TO BECOME A TPQ
Source: (gene. exp.) ARTHROBACTER GLOBIFORMIS (bacteria) / Plasmid: PAGAO2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P46881, EC: 1.4.3.6

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Non-polymers , 7 types, 439 molecules

#2: Chemical ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-R5A / RUTHENIUM WIRE, 5 CARBON LINKER / BIS[1H,1'H-2,2'-BIPYRIDINATO(2-)-KAPPA~2~N~1~,N~1'~][3-{[5-(1,10-DIHYDRO-1,10-PHENANTHROLIN-4-YL-KAPPA~2~N~1~,N~10~)PENTYL]OXY}-N,N-DIMETHYLANILINATO(2-)]RUTHENIUM


Mass: 817.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H61N7ORu
#5: Chemical ChemComp-R5B / RUTHENIUM WIRE WC5 / BIS[1H,1'H-2,2'-BIPYRIDINATO(2-)-KAPPA~2~N~1~,N~1'~][3-{[5-(1,10-DIHYDRO-1,10-PHENANTHROLIN-4-YL-KAPPA~2~N~1~,N~10~)PEN TYL]OXY}-N,N-DIMETHYLANILINATO(2-)]RUTHENIUM


Mass: 817.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C45H61N7ORu
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 425 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsRESIDES 1-2, MT, ARE THOUGHT TO BE CLEAVED. THE WILD TYPE MATURE PROTEIN IS COMPOSED OF RESIDUES 3- ...RESIDES 1-2, MT, ARE THOUGHT TO BE CLEAVED. THE WILD TYPE MATURE PROTEIN IS COMPOSED OF RESIDUES 3-638. RESIDUES 639- 640, SN, IS A PRE-TAG SPACER. RESIDUES 641-648, WSHPQFEK, IS A STREP-TAG II. SEE JUDA ET AL. (2001) PROTEIN EXPRESSION AND PURIFICATION, 22, 455-461

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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: 3.06 Å3/Da / Density % sol: 59.86 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: THE CRYSTAL WAS GROWN BY HANGING DROP OVER 150 MM CITRATE PH 6.0, 800 MM NH4SO4. THE INHIBITOR WAS ADDED BY SOAKING, WITH ALL STEPS IN THE DARK, OVER THREE DAYS. 25 MG OF THE INHIBITOR (WC5) ...Details: THE CRYSTAL WAS GROWN BY HANGING DROP OVER 150 MM CITRATE PH 6.0, 800 MM NH4SO4. THE INHIBITOR WAS ADDED BY SOAKING, WITH ALL STEPS IN THE DARK, OVER THREE DAYS. 25 MG OF THE INHIBITOR (WC5) DISSOLVED IN 250 MICROLITRE ETHANOL. 1MICROLITRE OF THIS WAS ADDED TO THE 200MICROLITRE RESERVOIR. GLYCEROL WAS THEN, ADDED IN 2-3% INCREMENTS, TO THE RESERVOIR, WITH THE NEW RESERVOIR SOLUTION SUBSTITUTING THE DROP SOLUTION. THE SOAK SAT FOR 24 HOURS AT 5% GLYCEROL. THE FINAL GLYCEROL CONCENTRATION WAS 30%.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 21, 2004 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.79→15 Å / Num. obs: 322625 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 21.59 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 24.4
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 2.58 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 4.33 / % possible all: 76.8

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W6G

1w6g


Resolution: 1.8→15.02 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.967 / SU B: 1.82 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.087 / ESU R Free: 0.083 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.165 3847 5 %RANDOM
Rwork0.145 ---
obs0.146 72905 98.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.96 Å2
Baniso -1Baniso -2Baniso -3
1--1.71 Å20 Å20.14 Å2
2--3.04 Å20 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4868 0 167 425 5460
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0215189
X-RAY DIFFRACTIONr_bond_other_d0.0020.024618
X-RAY DIFFRACTIONr_angle_refined_deg1.5052.0187088
X-RAY DIFFRACTIONr_angle_other_deg0.791310682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2615619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0830.2746
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025850
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021164
X-RAY DIFFRACTIONr_nbd_refined0.1930.2841
X-RAY DIFFRACTIONr_nbd_other0.2510.25507
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0810.23159
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2324
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1710.224
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3080.2195
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.236
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.74423087
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.84334999
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.9542100
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.7662089
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.84 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.212 259
Rwork0.2 4782

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