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- PDB-1w4n: AGAO covalent complex with Tranylcypromine -

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Basic information

Entry
Database: PDB / ID: 1w4n
TitleAGAO covalent complex with Tranylcypromine
ComponentsPHENYLETHYLAMINE OXIDASE
KeywordsOXIDOREDUCTASE / AMINE OXIDASE / ARTHROBACTER GLOBIFORMIS / COPPER CONTAINING / METAL-BINDING / TCQ / QUINONE / INHIBITED / TCP / TRANYLCYPROMINE
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 / Phenylethylamine oxidase
Similarity search - Component
Biological speciesARTHROBACTER GLOBIFORMIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsDuff, A.P. / Trambaiolo, D.M. / Langley, D.B. / Juda, G.A. / Shepard, E.M. / Dooley, D.M. / Freeman, H.C. / Guss, J.M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2008
Title: Complexes of the Copper-Containing Amine Oxidase from Arthrobacter Globiformis with the Inhibitors Benzylhydrazine and Tranylcypromine.
Authors: Langley, D.B. / Trambaiolo, D.M. / Duff, A.P. / Dooley, D.M. / Freeman, H.C. / Guss, J.M.
History
DepositionJul 27, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Aug 10, 2011Group: Atomic model / Derived calculations / Non-polymer description
Revision 1.3Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.method
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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_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
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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)144,95417
Polymers143,7602
Non-polymers1,19415
Water18,6281034
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)158.113, 63.001, 184.490
Angle α, β, γ (deg.)90.00, 112.04, 90.00
Int Tables number5
Space group name H-MI121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99875, 0.049895, 0.002583), (0.049929, 0.99864, 0.015203), (-0.001821, 0.015313, -0.99988)
Vector: -34.439, 0.18581, 85.575)

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 71879.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: RESIDUES A382 AND B382 ARE ACTIVE SITE TYROSINE RESIDUES, WHICH WERE AUTOCATALYTICALLY MODIFIED TO BECOME TPQ, ARE COVALENTLY LINKED TO THE SUICIDE INHIBITOR TRANS-2-PHENYLCYCLOPROPYL-1- ...Details: RESIDUES A382 AND B382 ARE ACTIVE SITE TYROSINE RESIDUES, WHICH WERE AUTOCATALYTICALLY MODIFIED TO BECOME TPQ, ARE COVALENTLY LINKED TO THE SUICIDE INHIBITOR TRANS-2-PHENYLCYCLOPROPYL-1-AMINE. THIS MODIFIED TPQ IS NAMED TCQ
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 , 5 types, 1049 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-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1034 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCATALYTIC ACTIVITY: RCH2NH2 + H2O + O2 = RCHO + NH3 + H2O2
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 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: AGAO CRYSTALS WERE GROWN IN ABOUT 2 WEEKS BY HANGING-DROP VAPOR DIFFUSION AT 293K. THE RESERVOIR WAS 1.0-1.5M (NH4)2SO4, 2MM CUSO4, 0.15M NA CITRATE, PH 6.0-7.5. THE DROPS WERE 1.5MICROL OF ...Details: AGAO CRYSTALS WERE GROWN IN ABOUT 2 WEEKS BY HANGING-DROP VAPOR DIFFUSION AT 293K. THE RESERVOIR WAS 1.0-1.5M (NH4)2SO4, 2MM CUSO4, 0.15M NA CITRATE, PH 6.0-7.5. THE DROPS WERE 1.5MICROL OF 11.7 MG/ML PROTEIN, 0.05M HEPES, PH 7.0, PLUS 1.5MICROL OF RESERVOIR SOLUTION. A SINGLE CRYSTAL WAS SOAKED WITH TCP BY SLOWLY ADDING TCP TO THE DROP TO ACHIEVE A 100 FOLD EXCESS OF TCP OVER ENZYME ACTIVE SITES. THE CRYSTAL WAS CRYOPROTECTED BY GRADUAL INCREMENTAL SOAKING IN RESERVOIR SOLUTION MIXED WITH GLYCEROL, WITH THE CONCENTRAION OF TCP BEING MAINTAINED CONSTANT. THE CONCENTRATION OF GLYCEROL WAS INCREASED FROM 0 TO 30% IN 2-3% INCREMENTS DURING 2 HOURS.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 5, 2003 / Details: OSMIC MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→28.25 Å / Num. obs: 200663 / % possible obs: 98.2 % / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 22.32 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.73
Reflection shellResolution: 1.65→1.67 Å / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 3 / % possible all: 80

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AV4

1av4


Resolution: 1.65→28.28 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.782 / SU ML: 0.058 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.078 / ESU R Free: 0.08 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TCQ WAS INITIALLY REFINED WITH MINIMAL RESTRAINTS. IT WAS DETERMINED THAT THE TCQ WAS IN THE SUBSTRATE SCHIFF BASE FORM. IN LATE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. TCQ WAS INITIALLY REFINED WITH MINIMAL RESTRAINTS. IT WAS DETERMINED THAT THE TCQ WAS IN THE SUBSTRATE SCHIFF BASE FORM. IN LATE REFINEMENT, THE TCQ WAS RESTRAINED TO THE SUBSTRATE SCHIFF BASE FORM.
RfactorNum. reflection% reflectionSelection details
Rfree0.199 10049 5 %RANDOM
Rwork0.171 ---
obs0.172 190611 99.2 %-
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: 17.34 Å2
Baniso -1Baniso -2Baniso -3
1--1.93 Å20 Å20.04 Å2
2--2.82 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 1.65→28.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9738 0 68 1034 10840
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02110051
X-RAY DIFFRACTIONr_bond_other_d0.0020.029001
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.94413679
X-RAY DIFFRACTIONr_angle_other_deg0.88320825
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.39251236
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_restr0.0910.21481
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211366
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022182
X-RAY DIFFRACTIONr_nbd_refined0.1950.21707
X-RAY DIFFRACTIONr_nbd_other0.2520.211121
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0820.26294
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2790
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1480.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.090.224
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.89726152
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.87239938
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.1743899
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.98463735
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: 1.65→1.69 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.269 757
Rwork0.262 14044
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)
15.15051.13270.8821-0.15920.0017-0.68930.3388-0.1080.16690.0924-0.1151-0.35530.06310.228-0.22370.1361-0.0348-0.02870.13540.01360.135222.5043.56943.245
20.84940.1971-0.31880.323-0.98442.58430.00470.1007-0.0196-0.2544-0.1523-0.12590.22080.64540.14760.18380.10360.08720.34270.06190.14528.892-3.53114.25
3-0.46840.2528-0.79281.8714-1.83030.87770.13010.11310.2616-0.04360.0527-0.024-0.28430.3917-0.18280.13090.00990.03360.1263-0.00810.1312-14.94821.23929.339
40.7215-0.0654-0.29690.2896-0.20940.89120.0379-0.06890.0530.0097-0.0757-0.0772-0.00980.28260.03770.1626-0.0159-0.01840.16060.0170.1854-5.036-0.97845.428
50.6883-0.65620.30410.4509-0.32270.14020.07250.1208-0.0136-0.0129-0.00930.15710.0073-0.1309-0.06320.18020.0339-0.0140.18540.0150.1924-56.7935.43342.209
60.68370.0470.04670.36260.23721.22040.0035-0.2004-0.02830.04780.04440.0332-0.0612-0.1828-0.04790.22470.00940.02390.17010.01250.1492-43.653-2.55771.22
7-0.29530.89330.0121.99021.14631.58020.1603-0.09420.16750.24970.0365-0.0009-0.5219-0.0606-0.19690.1289-0.00250.00650.12720.00420.128-18.52421.11256.587
80.6649-0.0263-0.31330.1527-0.02150.73510.03820.08380.04910.0002-0.01140.006-0.0203-0.0688-0.02690.20910.0049-0.01170.10460.00910.1848-29.557-0.30440.08
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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