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- PDB-1w6c: AGAO holoenzyme in a small cell, at 2.2 angstroms -

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Basic information

Entry
Database: PDB / ID: 1w6c
TitleAGAO holoenzyme in a small cell, at 2.2 angstroms
ComponentsPHENYLETHYLAMINE OXIDASE
KeywordsOXIDOREDUCTASE / AMINE OXIDASE / COPPER CONTAINING / METAL-BINDING / TPQ / QUINONE / HOLOENZYME
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDuff, A.P. / Langley, D.B. / Juda, G.A. / Shepard, E.M. / Dooley, D.M. / Freeman, H.C. / Guss, J.M.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2006
Title: The Copper Containing Amine Oxidase from Arthrobacter Globiformis: Refinement at 1.55 And 2.20 A Resolution in Two Crystal Forms.
Authors: Langley, D.B. / Duff, A.P. / Freeman, H.C. / Guss, J.M.
#1: Journal: Protein Expr.Purif. / Year: 2001
Title: Construction, Overexpression, and Purification of Arthrobacter Globiformis Amine Oxidase-Strep- Tag II Fusion Protein
Authors: Juda, G.A. / Bollinger, J.A. / Dooley, D.M.
History
DepositionAug 17, 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: Derived calculations / 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 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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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 / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,9144
Polymers71,7641
Non-polymers1503
Water2,594144
1
A: PHENYLETHYLAMINE OXIDASE
hetero molecules

A: PHENYLETHYLAMINE OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,8288
Polymers143,5282
Non-polymers3006
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area15240 Å2
ΔGint-41.5 kcal/mol
Surface area50450 Å2
MethodPQS
Unit cell
Length a, b, c (Å)158.041, 64.061, 69.693
Angle α, β, γ (deg.)90.00, 111.74, 90.00
Int Tables number5
Space group name H-MC121

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Components

#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 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
#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.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: RCH(2)NH(2) + H(2)O + O(2) = RCHO + NH(3) + H(2)O(2).
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: 2.33 Å3/Da / Density % sol: 47.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: CRYSTALS WERE GROWN IN ABOUT 2 WEEKS BY HANGING-DROP VAPOR DIFFUSION AT 293K. THE RESERVOIR WAS 0.2M MG ACETATE, 20% PEG 8K, 0.1M NA CACODYLATE PH 6.5. THE DROPS WERE 1.5MICROL OF 11.7 MG/ML ...Details: CRYSTALS WERE GROWN IN ABOUT 2 WEEKS BY HANGING-DROP VAPOR DIFFUSION AT 293K. THE RESERVOIR WAS 0.2M MG ACETATE, 20% PEG 8K, 0.1M NA CACODYLATE PH 6.5. 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. THE CRYSTAL WAS THEN FROZEN IN THE CRYOSTREAM.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 20, 2002
Details: 58 CM LONG, PT-COATED, FUSED SILICA, VERTICAL FOCUSMIRROR
RadiationMonochromator: CYCLINDRICALLY BENT TRIANGULAR SI(111) ASYMMETRIC CUT, HORIZONTAL FOCUS MONOCHROMATOR
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.2→28.25 Å / Num. obs: 31420 / % possible obs: 94.4 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Biso Wilson estimate: 29.49 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.68
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 1.96 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 3.35 / % possible all: 84.9

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Processing

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

1av4


Resolution: 2.2→32.16 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.397 / SU ML: 0.136 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.279 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. WATERS Z74, Z133 AND Z136 ARE ASSOCIATED WITH THE ACTIVE SITE COPPER ION AND ARE MODELLED DESPITE HAVING WEAK ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1544 4.9 %RANDOM
Rwork0.172 ---
obs0.175 29876 94.8 %-
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: 26.91 Å2
Baniso -1Baniso -2Baniso -3
1--1.21 Å20 Å2-1.07 Å2
2--0.57 Å20 Å2
3----0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.2→32.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4860 0 3 144 5007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0214986
X-RAY DIFFRACTIONr_bond_other_d0.0020.024458
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.9416790
X-RAY DIFFRACTIONr_angle_other_deg0.822310307
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8195619
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_restr0.0870.2733
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025678
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021082
X-RAY DIFFRACTIONr_nbd_refined0.1910.2819
X-RAY DIFFRACTIONr_nbd_other0.2390.25057
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0840.23050
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.2170
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1390.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3020.2152
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.222
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.33523081
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.56134975
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.1341903
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it6.85461815
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: 2.2→2.25 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.282 118
Rwork0.244 1951
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)
11.82830.18910.20661.151-0.50071.02530.0481-0.2042-0.0863-0.05280.03290.2127-0.0912-0.1217-0.0810.0316-0.04010.030.1127-0.00280.123126.2908-4.423433.1885
21.5582-0.21760.20121.24780.78270.9704-0.04140.2566-0.0829-0.09440.01390.2513-0.042-0.07480.02750.11730.085-0.05360.1065-0.0180.052539.76213.1243.8717
30.0777-0.45440.09890.62360.20950.31170.25230.2143-0.4659-0.1557-0.00980.10040.268-0.1372-0.24250.10020.0389-0.08990.1191-0.09990.164464.4246-20.928318.7106
40.840.0080.32540.23040.08490.56520.0639-0.099-0.0813-0.0018-0.07430.0498-0.0539-0.1250.01040.08340.00060.01490.0654-0.00890.066953.90430.817535.1832
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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