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- PDB-1w5z: AGAO covalent complex with Benzylhydrazine -

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Basic information

Entry
Database: PDB / ID: 1w5z
TitleAGAO covalent complex with Benzylhydrazine
ComponentsPHENYLETHYLAMINE OXIDASE
KeywordsOXIDOREDUCTASE / AMINE OXIDASE / ARTHROBACTER GLOBIFORMIS / COPPER CONTAINING / METAL-BINDING / TPQ / QUINONE / INHIBITED / BH / BENZYLHYDRAZINE / 3TY
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 / Phenylethylamine oxidase
Similarity search - Component
Biological speciesARTHROBACTER GLOBIFORMIS (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 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
DepositionAug 11, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 7, 2013Group: Non-polymer description / Other / Source and taxonomy
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 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _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_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.pdbx_leaving_atom_flag / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Dec 13, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
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)72,70311
Polymers71,8681
Non-polymers83510
Water9,062503
1
A: PHENYLETHYLAMINE OXIDASE
hetero molecules

A: PHENYLETHYLAMINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,40622
Polymers143,7362
Non-polymers1,67020
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
MethodPQS
Unit cell
Length a, b, c (Å)158.126, 62.665, 92.283
Angle α, β, γ (deg.)90.00, 112.07, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2117-

HOH

21A-2199-

HOH

31A-2396-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 71867.922 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: RESIDUE A382 WAS AN ACTIVE SITE TYROSINE RESIDUE, WHICH WAS AUTOCATALYTICALLY MODIFIED TO BECOME TPQ, AND WAS THEN COVALENTLY LINKED TO THE SUICIDE INHIBITOR BENZYLHYDRAZINE.
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, 513 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-SO4 / SULFATE ION / Sulfate


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


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


Mass: 18.015 Da / Num. of mol.: 503 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsCATALYTIC ACTIVITY: RCH(2)NH(2) + H(2)O + O(2) = RCHO + NH(3) + H(2)O(2).REMARK 500
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 CRYSTAL WAS CRYOPROTECTED BY GRADUAL INCREMENTAL SOAKING IN RESERVOIR SOLUTION MIXED WITH GLYCEROL. THE CONCENTRATION OF GLYCEROL WAS INCREASED FROM 0 TO 30% IN 2-3% INCREMENTS DURING 2 HOURS. FOLLOWING CRYOPROTECTION, THE CRYSTAL WAS SOAKED FOR 15 MINUTES IN CRYOPROTECTANT WITH THE ADDITION OF 2 MILLIMOLAR BENZYLHYDRAZINE DIHYDROCHLORIDE (SIGMA). THE CRYSTAL WAS THEN FROZEN IN THE CRYOSTREAM.

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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: Mar 25, 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: 1.86→29.86 Å / Num. obs: 65983 / % possible obs: 94.2 % / Observed criterion σ(I): -3 / Redundancy: 3.033 % / Biso Wilson estimate: 25.31 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.46
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 2.69 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 2.13 / % possible all: 83

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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: 1.86→29.85 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.626 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.107 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 3TY WAS INITIALLY REFINED WITH MINIMAL RESTRAINTS.IT WAS DETERMINED THAT THE 3TY WAS IN THE SUBSTRATE SCHIFF BASE FORM. IN LATE REFINEMENT, ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 3TY WAS INITIALLY REFINED WITH MINIMAL RESTRAINTS.IT WAS DETERMINED THAT THE 3TY WAS IN THE SUBSTRATE SCHIFF BASE FORM. IN LATE REFINEMENT, THE 3TY WAS RESTRAINED TO THE SUBSTRATE SCHIFF BASE FORM.
RfactorNum. reflection% reflectionSelection details
Rfree0.187 3312 5 %RANDOM
Rwork0.152 ---
obs0.154 62669 94.2 %-
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: 18.11 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å20 Å21 Å2
2--1.23 Å20 Å2
3---0.66 Å2
Refinement stepCycle: LAST / Resolution: 1.86→29.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4877 0 47 503 5427
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0215045
X-RAY DIFFRACTIONr_bond_other_d0.0020.024502
X-RAY DIFFRACTIONr_angle_refined_deg1.4651.9456861
X-RAY DIFFRACTIONr_angle_other_deg0.828310415
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4915619
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_restr0.0940.2740
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025698
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021091
X-RAY DIFFRACTIONr_nbd_refined0.20.2812
X-RAY DIFFRACTIONr_nbd_other0.2490.25361
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0830.23104
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.2389
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3150.2197
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.243
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.16423083
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.2334980
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.63141960
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.4961881
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: 1.86→1.91 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.306 206
Rwork0.269 3915
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)
11.17010.56690.55020.80390.2891-0.08070.1154-0.1551-0.0081-0.0258-0.0895-0.2328-0.01930.1697-0.02590.1732-0.0492-0.01350.26130.01140.199222.31384.576943.3472
20.7138-0.06650.12460.382-0.50681.25290.02470.1395-0.0167-0.0345-0.0162-0.03850.07230.2893-0.00860.21250.01910.0080.2484-0.00580.16238.9884-2.888614.2686
31.5202-0.20240.33312.5881-0.02182.65020.19650.22650.2591-0.2137-0.0440.0312-0.3892-0.045-0.15250.06680.03080.06660.08940.09780.1265-15.537421.266729.1349
40.5916-0.0064-0.25660.1872-0.08070.72150.0182-0.07510.04490.0192-0.0064-0.0228-0.00140.1347-0.01170.1978-0.0051-0.01790.1611-0.00590.1976-5.1053-0.528945.4886
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 - 628

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