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- PDB-3wa3: Crystal structure of copper amine oxidase from arthrobacter globi... -

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Basic information

Entry
Database: PDB / ID: 3wa3
TitleCrystal structure of copper amine oxidase from arthrobacter globiformis in N2 condition
ComponentsPhenylethylamine oxidase
KeywordsOXIDOREDUCTASE / oxidase / copper binding / post-translationally derived quinone cofactor / cytoplassm
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 / NITROGEN MOLECULE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Phenylethylamine oxidase
Similarity search - Component
Biological speciesArthrobacter globiformis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsMurakawa, T. / Hayashi, H. / Sunami, T. / Kurihara, K. / Tamada, T. / Kuroki, R. / Suzuki, M. / Tanizawa, K. / Okajima, T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: High-resolution crystal structure of copper amine oxidase from Arthrobacter globiformis: assignment of bound diatomic molecules as O2
Authors: Murakawa, T. / Hayashi, H. / Sunami, T. / Kurihara, K. / Tamada, T. / Kuroki, R. / Suzuki, M. / Tanizawa, K. / Okajima, T.
History
DepositionApr 22, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 1, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_asym_id / _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_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)142,79450
Polymers138,0202
Non-polymers4,77448
Water30,7881709
1
A: Phenylethylamine oxidase
hetero molecules

A: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,67048
Polymers138,0202
Non-polymers4,65046
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area25420 Å2
ΔGint45 kcal/mol
Surface area40170 Å2
MethodPISA
2
B: Phenylethylamine oxidase
hetero molecules

B: Phenylethylamine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,91852
Polymers138,0202
Non-polymers4,89850
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,y,-z1
Buried area24590 Å2
ΔGint63 kcal/mol
Surface area40270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)191.607, 63.036, 158.006
Angle α, β, γ (deg.)90.000, 117.440, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-1615-

HOH

21B-1660-

HOH

31B-1661-

HOH

41B-1982-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Phenylethylamine oxidase / Primary amine oxidase


Mass: 69009.836 Da / Num. of mol.: 2 / Fragment: UNP residues 9-629
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arthrobacter globiformis (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P46881, primary-amine oxidase

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Non-polymers , 9 types, 1757 molecules

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


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-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C4H10O3
#9: Chemical ChemComp-HDZ / NITROGEN MOLECULE / Nitrogen


Mass: 28.013 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N2
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1709 / Source method: isolated from a natural source / Formula: H2O

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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: 59.91 %
Crystal growTemperature: 289 K / Method: microdialysis / pH: 6.8
Details: 1.05 M potassium tartrate, 25 mM HEPES, pH 6.8, MICRODIALYSIS, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 24, 2013
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 232158 / % possible obs: 95.5 % / Redundancy: 5 % / Rmerge(I) obs: 0.125 / Χ2: 4.479 / Net I/σ(I): 10.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.55-1.614.90.499230581.186195.4
1.61-1.674.80.397229881.354195.2
1.67-1.754.70.32231971.558195.6
1.75-1.844.60.257231641.981195.7
1.84-1.954.50.205232122.776195.9
1.95-2.14.50.165233433.659195.9
2.1-2.324.60.144230664.621195.3
2.32-2.654.90.132228825.639193.9
2.65-3.345.70.118231177.894194.6
3.34-506.20.1072413110.42197.2

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1iu7

1iu7


Resolution: 1.55→29.932 Å / Occupancy max: 1 / Occupancy min: 0.24 / FOM work R set: 0.8234 / SU ML: 0.16 / σ(F): 1.35 / Phase error: 24.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2099 11543 5.01 %
Rwork0.1811 --
obs0.1826 230420 94.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 118.06 Å2 / Biso mean: 22.5105 Å2 / Biso min: 8.44 Å2
Refinement stepCycle: LAST / Resolution: 1.55→29.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9752 0 308 1709 11769
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01310501
X-RAY DIFFRACTIONf_angle_d1.58114206
X-RAY DIFFRACTIONf_chiral_restr0.1091505
X-RAY DIFFRACTIONf_plane_restr0.0081878
X-RAY DIFFRACTIONf_dihedral_angle_d15.2613953
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.55-1.5660.28873720.26477182755494
1.566-1.58440.29783740.25447278765295
1.5844-1.60370.27873960.24317314771095
1.6037-1.6240.28823780.24437228760695
1.624-1.64540.26473540.23897304765895
1.6454-1.66790.2563980.22717217761595
1.6679-1.69170.25513740.237294766895
1.6917-1.7170.2613830.22827307769095
1.717-1.74380.27053580.22877337769595
1.7438-1.77240.27893990.21927277767695
1.7724-1.8030.23623580.2147316767495
1.803-1.83570.27383870.20827234762195
1.8357-1.87110.24633800.21187249762995
1.8711-1.90920.22663900.2077282767295
1.9092-1.95070.22553910.19557223761495
1.9507-1.99610.23243790.19737302768195
1.9961-2.0460.21963850.19037355774095
2.046-2.10130.21453630.18357387775095
2.1013-2.16310.20064080.17927264767295
2.1631-2.23290.2254030.18127223762694
2.2329-2.31270.20533950.17377218761394
2.3127-2.40530.20063860.17417200758693
2.4053-2.51470.19274040.17447167757193
2.5147-2.64720.22913660.17277128749492
2.6472-2.81290.19763540.17327151750593
2.8129-3.02990.21513810.17897282766394
3.0299-3.33450.20084150.17167353776895
3.3345-3.81620.17823970.15117492788997
3.8162-4.80480.14083930.1367532792596
4.8048-29.93790.20324220.17467781820398
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)
10.1503-0.2605-0.15040.46710.23750.13210.25930.21330.1846-0.5051-0.4364-0.2874-0.28010.1626-0.51240.34750.04370.1260.45260.23550.1658172.295210.793234.1443
20.4994-0.4214-0.55671.6127-0.21282.30330.09710.31130.0866-0.3379-0.3165-0.4914-0.41630.4483-0.17370.25310.08480.11220.43240.15250.2372175.23452.212935.7311
30.983-0.01450.33920.129-0.16060.80270.00030.28750.0813-0.0762-0.04030.0172-0.13420.02820.00250.14990.0388-0.01380.19610.0190.1549146.86894.092842.1274
40.5175-0.12840.40630.16560.10411.0257-0.01010.0930.1375-0.0356-0.0755-0.0233-0.25910.08680.06610.1758-0.02560.00330.14660.02610.1724162.24388.94957.6523
50.6851-0.06840.34430.2671-0.06450.7460.01770.1011-0.0119-0.0057-0.0282-0.01310.01810.11610.00620.09830.00720.00770.1145-0.00120.1231162.6035-5.142961.5166
61.0985-0.3065-0.1110.96510.28860.09450.0114-0.11450.01110.1293-0.05010.0062-0.1795-0.30190.00960.17690.07370.03970.2134-0.04910.1305173.6388-20.666435.4744
71.34680.3064-0.86612.0220.74520.9871-0.0707-0.1193-0.14760.1717-0.02450.3996-0.0341-0.4004-0.0130.12620.02530.06580.2337-0.03160.1626170.8059-29.337834.0957
82.79040.44560.45440.12070.21480.3736-0.0574-0.44570.0670.09210.04840.02470.0262-0.03510.00470.13880.0204-0.01730.20970.01540.1297202.3439-32.80438.4965
90.86290.02460.19420.29020.01240.7548-0.0334-0.17950.06840.07830.0089-0.0288-0.16560.03-0.01440.12280.0145-0.00410.092-0.03360.1014198.051-24.355723.273
100.41110.13820.18250.020.02260.9226-0.017-0.05080.05410.0081-0.0091-0.0006-0.1734-0.06260.02870.13950.0330.00750.0969-0.00570.1436184.2437-22.288212.3795
110.39020.07250.21740.1490.03260.8485-0.0047-0.0444-0.05240.00750.01960.00460.0594-0.1131-0.01670.11630.00480.00570.09930.00750.1412183.772-36.28458.2989
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A and (resid 9 through 44 )A0
2X-RAY DIFFRACTION2chain A and (resid 45 through 95 )A0
3X-RAY DIFFRACTION3chain A and (resid 96 through 250 )A0
4X-RAY DIFFRACTION4chain A and (resid 251 through 368 )A0
5X-RAY DIFFRACTION5chain A and (resid 369 through 629 )A0
6X-RAY DIFFRACTION6chain B and (resid 9 through 44 )B0
7X-RAY DIFFRACTION7chain B and (resid 45 through 95 )B0
8X-RAY DIFFRACTION8chain B and (resid 96 through 144 )B0
9X-RAY DIFFRACTION9chain B and (resid 145 through 250 )B0
10X-RAY DIFFRACTION10chain B and (resid 251 through 368 )B0
11X-RAY DIFFRACTION11chain B and (resid 369 through 629 )B0

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