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- PDB-2cfd: AGAO in complex with wc4l3 (Ru-wire inhibitor, 4-carbon linker, l... -

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Basic information

Entry
Database: PDB / ID: 2cfd
TitleAGAO in complex with wc4l3 (Ru-wire inhibitor, 4-carbon linker, lambda enantiomer, data set 3)
ComponentsPHENYLETHYLAMINE OXIDASE
KeywordsOXIDOREDUCTASE / AMINE OXIDASE / ARTHROBACTER GLOBIFORMIS / COPPER CONTAINING / TPQ / 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 / Chem-R4A / Phenylethylamine oxidase
Similarity search - Component
Biological speciesARTHROBACTER GLOBIFORMIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 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 20, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2May 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 1.3Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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_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.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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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
B: PHENYLETHYLAMINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,14817
Polymers143,5282
Non-polymers2,62015
Water11,746652
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)192.287, 62.857, 158.171
Angle α, β, γ (deg.)90.00, 117.47, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 71763.766 Da / Num. of mol.: 2 / 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 AUTOCATALYTICALLY MODIFIED TO BECOME 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, 667 molecules

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


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-R4A / BIS[1H,1'H-2,2'-BIPYRIDINATO(2-)-KAPPA~2~N~1~,N~1'~]{3-[4-(1,10-DIHYDRO-1,10-PHENANTHROLIN-4-YL-KAPPA~2~N~1~,N~10~)BUTOXY]-N,N-DIMETHYLANILINATO(2-)}RUTHENIUM


Mass: 805.071 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H61N7ORu
#5: Chemical ChemComp-SO4 / SULFATE ION


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


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


Mass: 18.015 Da / Num. of mol.: 652 / 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: 59.94 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: THE CRYSTAL WAS GROWN BY HANGING DROP OVER 150 MM CITRATE PH 7.5, 1000 MM NH4SO4. THE INHIBITOR WAS ADDED BY SOAKING, WITH ALL STEPS IN THE DARK. 3.4 MG OF THE INHIBITOR (WC4L) DISSOLVED IN ...Details: THE CRYSTAL WAS GROWN BY HANGING DROP OVER 150 MM CITRATE PH 7.5, 1000 MM NH4SO4. THE INHIBITOR WAS ADDED BY SOAKING, WITH ALL STEPS IN THE DARK. 3.4 MG OF THE INHIBITOR (WC4L) DISSOLVED IN 20 MICROLITRE ETHANOL. 1 MICROLITRE OF THIS WAS ADDED TO THE 200 MICROLITRE RESERVOIR. GLYCEROL WAS THEN ADDED IN 2-3% INCREMENTS TO THE RESERVOIR, WITH THE NEW RESERVOIR SOLUTION SUBSTITUTING FOR THE DROP SOLUTION. THE SOAK SAT FOR 24 HOURS IN 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: Aug 17, 2005 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 206776 / % possible obs: 94 % / Observed criterion σ(I): -3 / Redundancy: 5.027 % / Biso Wilson estimate: 21.49 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 9.5
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.17 / % possible all: 90.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→29.99 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.852 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 10383 5 %RANDOM
Rwork0.194 ---
obs0.195 196351 93.9 %-
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: 21.44 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å20 Å2-1.14 Å2
2--2.7 Å20 Å2
3----2.35 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9720 0 162 652 10534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02110168
X-RAY DIFFRACTIONr_bond_other_d0.0020.029073
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.98113865
X-RAY DIFFRACTIONr_angle_other_deg0.82320978
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.51951236
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_restr0.0870.21475
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211518
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022248
X-RAY DIFFRACTIONr_nbd_refined0.1930.21672
X-RAY DIFFRACTIONr_nbd_other0.2490.210968
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0820.26226
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2587
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0540.27
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2640.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1180.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6611.56158
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1529956
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.81834006
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8224.53909
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: 1.6→1.64 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.366 724
Rwork0.358 13459
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.23940.6086-2.8443-0.2873-0.88691.41330.01870.2115-0.2755-0.26420.0114-0.3246-0.23380.1626-0.03010.1150-0.00010.115100.11548.4413.0630.181
21.1169-0.66120.7701-0.6779-0.61911.33460.10660.4418-0.047-0.1957-0.09880.08480.0230.0424-0.00790.15730.0617-0.01890.1084-0.06040.119516.377-3.892-1.074
3-1.7269-1.51050.49410.8544-0.4428-0.0772-0.11190.3880.158-0.0490.03580.0159-0.22720.14220.07610.1150.0006-0.00020.1149-0.00010.115119.19221.03726.743
40.3821-0.16980.12130.34960.02490.75280.05540.1166-0.0054-0.1035-0.0706-0.0835-0.05370.12740.01510.09150.01110.04320.02290.020.114137.765-1.51725.437
50.5981-0.5287-0.55790.76220.54810.6001-0.0249-0.0707-0.0660.1281-0.00930.0884-0.0261-0.2130.03420.06010.02710.01080.0821-0.02470.078511.1064.869.689
61.74620.42430.29170.58990.07160.8924-0.0501-0.32080.05070.05230.0245-0.0804-0.02460.02240.02560.05580.0111-0.05590.0699-0.00170.076843.165-2.7871.378
7-1.55231.58810.15021.1583-0.1338-0.4095-0.2285-0.16430.15790.08860.0379-0.1922-0.3474-0.01040.19060.11500.00010.11490.00030.115441.09121.02742.664
80.3822-0.04570.16260.23880.02450.7440.0141-0.0378-0.0192-0.0194-0.0192-0.0146-0.0502-0.08880.00510.06980.008-0.00450.003-0.00220.122421.848-0.94444.721
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 99
2X-RAY DIFFRACTION2A100 - 203
3X-RAY DIFFRACTION3A204 - 229
4X-RAY DIFFRACTION4A230 - 627
5X-RAY DIFFRACTION5B9 - 99
6X-RAY DIFFRACTION6B100 - 203
7X-RAY DIFFRACTION7B204 - 229
8X-RAY DIFFRACTION8B230 - 627

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