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- PDB-2cfl: AGAO in complex with wc6b (Ru-wire inhibitor, 6-carbon linker, da... -

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Basic information

Entry
Database: PDB / ID: 2cfl
TitleAGAO in complex with wc6b (Ru-wire inhibitor, 6-carbon linker, data set b)
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 / primary methylamine oxidase activity / amine metabolic process / quinone binding / copper ion binding
Similarity search - Function
: / AGAO-like N2 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 ...: / AGAO-like N2 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, 6 CARBON LINKER / 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 22, 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 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_conn.ptnr2_label_seq_id
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)73,43012
Polymers71,7641
Non-polymers1,66611
Water6,738374
1
A: PHENYLETHYLAMINE OXIDASE
hetero molecules

A: PHENYLETHYLAMINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,86024
Polymers143,5282
Non-polymers3,33322
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)157.980, 63.097, 92.024
Angle α, β, γ (deg.)90.00, 112.22, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2072-

HOH

21A-2289-

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 , 6 types, 385 molecules

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


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-R6A / RUTHENIUM WIRE, 6 CARBON LINKER / BIS[1H,1'H-2,2'-BIPYRIDINATO(2-)-KAPPA~2~N~1~,N~1'~][3-{[6-(1,10-DIHYDRO-1,10-PHENANTHROLIN-4-YL-KAPPA~2~N~1~,N~10~)HEX YL]OXY}-N,N-DIMETHYLANILINATO(2-)]RUTHENIUM


Mass: 831.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H63N7ORu
#5: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
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: 3.07 Å3/Da / Density % sol: 59.99 %
Description: STARTING MODEL IS A STRUCTURE NOT TO BE DEPOSITED THAT WAS IN TURN DERIVED FROM 1W6G
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: THE CRYSTAL WAS GROWN BY HANGING DROP OVER 150 MM CITRATE PH 7.0, 700 MM NH4SO4. THE INHIBITOR WAS ADDED BY SOAKING, OVER SIX DAYS. 20 MG OF THE INHIBITOR (WC6) DISSOLVED IN 200 MICROLITRE ...Details: THE CRYSTAL WAS GROWN BY HANGING DROP OVER 150 MM CITRATE PH 7.0, 700 MM NH4SO4. THE INHIBITOR WAS ADDED BY SOAKING, OVER SIX DAYS. 20 MG OF THE INHIBITOR (WC6) DISSOLVED IN 200 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 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 23, 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: 474513 / % possible obs: 95 % / Observed criterion σ(I): -3 / Redundancy: 6.37 % / Biso Wilson estimate: 26.86 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 24.64
Reflection shellResolution: 1.79→1.85 Å / Redundancy: 2.93 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.44 / % possible all: 78.7

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→14.99 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.346 / SU ML: 0.069 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.178 3727 5 %RANDOM
Rwork0.156 ---
obs0.157 70735 95.8 %-
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: 29.12 Å2
Baniso -1Baniso -2Baniso -3
1--1.93 Å20 Å20.28 Å2
2--3.9 Å20 Å2
3----1.76 Å2
Refinement stepCycle: LAST / Resolution: 1.8→14.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4868 0 102 374 5344
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0215127
X-RAY DIFFRACTIONr_bond_other_d0.0020.024584
X-RAY DIFFRACTIONr_angle_refined_deg1.4871.9856989
X-RAY DIFFRACTIONr_angle_other_deg0.805310606
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4235619
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_restr0.0860.2745
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025770
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021125
X-RAY DIFFRACTIONr_nbd_refined0.1930.2823
X-RAY DIFFRACTIONr_nbd_other0.2480.25448
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0820.23109
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2303
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1360.226
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2910.2205
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.229
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.07323086
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.16834997
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.32942039
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.22461992
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
Rfree0.289 241
Rwork0.279 4470

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