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- PDB-4z11: Latent aurone synthase (polyphenol oxidase) from natural source -

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Basic information

Entry
Database: PDB / ID: 4z11
TitleLatent aurone synthase (polyphenol oxidase) from natural source
ComponentsAurone synthase
KeywordsOXIDOREDUCTASE / Polyphenol oxidase / Type III copper protein / Latent / Aurone synthase
Function / homology
Function and homology information


catechol oxidase activity / pigment biosynthetic process / metal ion binding
Similarity search - Function
Polyphenol oxidase / Polyphenol oxidase, C-terminal / Protein of unknown function (DUF_B2219) / Polyphenol oxidase, central domain / Polyphenol oxidase middle domain / di-copper center containing domain from catechol oxidase / Di-copper center containing domain from catechol oxidase / Tyrosinase CuA-binding region signature. / Common central domain of tyrosinase / Tyrosinase and hemocyanins CuB-binding region signature. ...Polyphenol oxidase / Polyphenol oxidase, C-terminal / Protein of unknown function (DUF_B2219) / Polyphenol oxidase, central domain / Polyphenol oxidase middle domain / di-copper center containing domain from catechol oxidase / Di-copper center containing domain from catechol oxidase / Tyrosinase CuA-binding region signature. / Common central domain of tyrosinase / Tyrosinase and hemocyanins CuB-binding region signature. / Tyrosinase copper-binding domain / Di-copper centre-containing domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / Aurone synthase
Similarity search - Component
Biological speciesCoreopsis grandiflora (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMolitor, C. / Mauracher, S.G. / Rompel, A.
Funding support Austria, 1items
OrganizationGrant numberCountry
Austrian Science FundP25217-N28 Austria
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: Aurone synthase is a catechol oxidase with hydroxylase activity and provides insights into the mechanism of plant polyphenol oxidases.
Authors: Molitor, C. / Mauracher, S.G. / Rompel, A.
History
DepositionMar 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 23, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 2016Group: Database references
Revision 1.2Apr 13, 2016Group: Database references
Revision 1.3Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_close_contact ...pdbx_data_processing_status / pdbx_validate_close_contact / struct_conn / struct_conn_type
Revision 1.4Jan 10, 2024Group: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aurone synthase
B: Aurone synthase
C: Aurone synthase
D: Aurone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,56512
Polymers236,0574
Non-polymers5088
Water9,368520
1
A: Aurone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1413
Polymers59,0141
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Aurone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1413
Polymers59,0141
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Aurone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1413
Polymers59,0141
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Aurone synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1413
Polymers59,0141
Non-polymers1272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.570, 174.100, 102.540
Angle α, β, γ (deg.)90.00, 105.27, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Aurone synthase


Mass: 59014.273 Da / Num. of mol.: 4 / Fragment: residues 86-602 / Source method: isolated from a natural source / Details: latent proenzyme / Source: (natural) Coreopsis grandiflora (plant) / Tissue: petals / References: UniProt: A0A075DN54
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 520 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 15 % PEG-4000, 100 mM magnesium chloride, 60 mM sodium citrate, pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972499 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972499 Å / Relative weight: 1
ReflectionResolution: 2.5→48.77 Å / Num. obs: 71373 / % possible obs: 97.84 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.145 / Net I/σ(I): 7.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.43 % / Rmerge(I) obs: 0.862 / Mean I/σ(I) obs: 2 / % possible all: 97.68

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.4_1496)refinement
XDSdata reduction
PHASERphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4z0y
Resolution: 2.5→46.381 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2344 3568 5 %
Rwork0.1831 --
obs0.1857 71341 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→46.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15732 0 8 520 16260
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00416217
X-RAY DIFFRACTIONf_angle_d0.65922034
X-RAY DIFFRACTIONf_dihedral_angle_d10.55792
X-RAY DIFFRACTIONf_chiral_restr0.0272351
X-RAY DIFFRACTIONf_plane_restr0.0022915
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.53430.37071390.2932648X-RAY DIFFRACTION98
2.5343-2.57050.31191440.2882728X-RAY DIFFRACTION98
2.5705-2.60880.33931430.27112716X-RAY DIFFRACTION97
2.6088-2.64960.30711390.26172639X-RAY DIFFRACTION97
2.6496-2.6930.35331410.2742672X-RAY DIFFRACTION96
2.693-2.73940.30671400.2592666X-RAY DIFFRACTION97
2.7394-2.78930.30271430.2592718X-RAY DIFFRACTION98
2.7893-2.84290.3161450.2592761X-RAY DIFFRACTION98
2.8429-2.90090.32321410.24682661X-RAY DIFFRACTION98
2.9009-2.9640.27931420.23872702X-RAY DIFFRACTION98
2.964-3.03290.27671420.23242703X-RAY DIFFRACTION97
3.0329-3.10870.3031430.21282725X-RAY DIFFRACTION98
3.1087-3.19280.25711440.20282728X-RAY DIFFRACTION99
3.1928-3.28670.23041450.1882747X-RAY DIFFRACTION99
3.2867-3.39280.27781410.18352697X-RAY DIFFRACTION99
3.3928-3.5140.21881430.18572715X-RAY DIFFRACTION97
3.514-3.65460.21721440.16912723X-RAY DIFFRACTION98
3.6546-3.82090.2331420.16162708X-RAY DIFFRACTION99
3.8209-4.02220.21131450.14912744X-RAY DIFFRACTION99
4.0222-4.27410.18471430.14772733X-RAY DIFFRACTION99
4.2741-4.60380.15921440.12822724X-RAY DIFFRACTION97
4.6038-5.06660.18561430.14542721X-RAY DIFFRACTION98
5.0666-5.79850.20651430.16512715X-RAY DIFFRACTION97
5.7985-7.30090.23141440.17142744X-RAY DIFFRACTION98
7.3009-46.38890.20661450.16342735X-RAY DIFFRACTION97
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.47230.1863-0.15970.0503-0.05040.06770.01560.4185-0.0487-0.12840.0741-0.1718-0.19830.077-00.4487-0.06980.04330.6166-0.07910.512624.189521.0721-13.2706
20.3169-0.1452-0.21170.1670.01380.12330.19140.15070.203-0.1373-0.16330.50241.01790.06770.00020.8361-0.0072-0.020.8452-0.24480.777421.0252-4.2544-10.9866
30.01850.0140.03350.02810.00990.06020.5747-0.2937-0.4822-0.0136-0.527-0.24220.35870.22940.00010.4513-0.0773-0.00970.5564-0.08430.605725.2169-1.05917.6029
40.9682-0.1608-0.15570.2520.04440.9498-0.04010.1175-0.14660.00230.1267-0.22490.12710.05300.3962-0.0519-0.01130.4801-0.1280.469826.384710.0087-0.0667
50.39370.2775-0.47340.1473-0.33610.5749-0.16270.1159-0.067-0.01980.13580.0012-0.2236-0.357600.4823-0.028-0.01960.5474-0.070.446710.794416.090911.84
60.0511-0.0711-0.09540.13950.13430.13870.1713-0.19860.54330.05680.22580.6234-0.54380.1610.00130.4024-0.1051-0.02921.029-0.13570.71084.31223.2268-5.2211
70.0728-0.0783-0.0330.29730.28520.2601-0.048-0.02220.12840.08960.0889-0.14640.07440.0374-00.4374-0.0567-0.03150.5198-0.06640.431821.551516.52234.5431
80.9001-0.1881-0.38240.66120.28870.1094-0.14260.2848-0.24630.09640.0783-0.00820.2346-0.293400.4626-0.0164-0.04620.4856-0.10070.418610.17264.45383.8251
90.3114-0.10280.2560.0662-0.16240.34750.23670.18240.16580.2888-0.12010.4129-0.1132-0.2462-0.00010.4442-0.0630.02820.6008-0.0710.591-6.522532.41312.1816
100.7944-0.75210.01940.62830.10730.2809-0.07610.17270.04070.0060.0676-0.0137-0.0201-0.13440.00040.4913-0.09930.00240.57-0.05450.46081.291421.82612.2624
110.3933-0.2015-0.03270.6290.53360.42850.02880.1036-0.03160.0233-0.02150.26090.0857-0.121600.4876-0.0471-0.03970.56370.0390.4094-1.726625.28179.1001
121.8339-0.0552-0.44340.34160.67031.0258-0.0662-0.2371-0.11740.0408-0.0109-0.01490.11960.073300.48180.0191-0.03190.39050.00590.459132.772513.084862.8501
130.0027-0.0027-0.0130.06080.01540.04390.151-0.42560.39060.1356-0.5189-0.14140.3234-0.4531-0.00060.5689-0.15050.04930.5150.03830.597840.992420.326442.8737
141.7021-0.18860.08430.57290.33791.0354-0.098-0.1388-0.1704-0.02710.0864-0.1142-0.02810.075500.371-0.0122-0.01630.37160.02360.381231.278910.798558.2632
150.35340.1836-0.09420.47550.30170.2484-0.2930.3286-0.8652-0.41580.1416-0.41860.20180.1023-0.00240.53460.01120.05680.4911-0.09760.499334.30582.431940.8031
161.74180.34960.06990.1552-0.23550.6508-0.15450.0529-0.3333-0.04250.07260.05380.0262-0.058200.4293-0.01070.0240.357-0.03250.475819.17567.180148.5689
170.57970.4856-0.04290.68090.08930.0276-0.0637-0.31860.5184-0.0073-0.0476-0.0854-0.14240.0574-0.00390.47240.0354-0.03420.4363-0.09330.366424.351420.155862.1134
18-0.00040.0074-0.00090.0559-0.00080.0091-0.1322-0.80880.4784-0.33790.1228-0.3887-0.2382-0.3614-0.00060.98230.01590.10470.4986-0.01630.417116.49420.059338.8602
190.6934-0.3059-0.04140.36980.27990.282-0.11740.2778-0.6012-0.007-0.02380.01150.0251-0.03230.00010.4428-0.01750.00640.51360.01410.55-3.88644.508138.9878
201.92231.37360.44130.97410.36690.6707-0.68380.2051-1.42570.35220.43860.5167-0.04360.035-0.18880.5070.1230.11270.42030.03370.7969-1.9036-8.697450.9167
211.10870.1268-0.22040.23550.27620.4383-0.0912-0.52590.3221-0.0192-0.2447-0.53920.02390.2432-0.0850.3510.01480.00250.43470.11330.4962-1.72088.48152.4994
221.93140.543-0.97891.11340.17410.5448-0.1609-0.1189-0.1060.00950.224-0.09980.2109-0.15770.00180.40460.0157-0.01180.3813-0.04320.43392.31322.803846.186
230.7201-0.0358-0.49540.0218-0.01180.2123-0.03920.1733-0.3125-0.1059-0.10940.3939-0.222-0.1775-00.57710.012-0.0540.6813-0.00230.64846.889857.8736-8.2891
240.1993-0.01660.12850.06580.1050.13360.26510.2762-0.5522-0.11890.21930.1778-0.24350.23820.00010.82850.03430.0790.6-0.01620.66659.693381.70160.479
250.2278-0.19220.10820.1699-0.09040.05130.78420.1366-0.6041-0.482-0.18260.3869-0.046-0.3860.01610.6670.08040.05830.6901-0.0610.58135.632573.726717.8623
260.76110.1408-0.28610.5515-0.00870.7644-0.0691-0.00940.03320.04420.0090.2786-0.0899-0.223800.47190.06070.01070.54040.02850.54344.470564.93227.5757
270.4082-0.34280.07120.86410.2280.0843-0.1825-0.0157-0.0763-0.0377-0.0842-0.0512-0.04490.039400.48880.00120.01490.43630.00360.425220.060256.053517.2481
283.2092-2.5195-0.08022.05140.21220.3307-0.2685-0.18090.59610.13490.2228-0.2936-0.05780.3049-0.53370.4855-0.13920.18360.4980.08940.486126.816653.656-1.234
290.2071-0.38570.07380.6098-0.14340.11640.05430.1002-0.0316-0.0296-0.01910.0842-0.0953-0.098700.47570.01250.01720.49840.03060.5439.257257.525410.311
300.8445-0.4309-0.25180.6623-0.04260.02580.00410.09520.27990.0840.01-0.0289-0.1736-0.0714-00.5448-0.0253-0.00450.39280.02610.479420.90868.984812.3485
310.6915-0.5764-0.38080.44180.29050.28290.11930.32620.1380.063-0.1653-0.0186-0.01130.0758-00.5076-0.020.00340.5488-0.01190.515237.37540.111313.5816
320.3556-0.2484-0.48540.3870.41050.5368-0.05860.04990.01060.11580.050.0153-0.0050.0033-00.476-0.0288-0.02220.3955-0.01290.474729.471150.246516.8168
330.6068-0.3151-0.61030.90390.26730.5944-0.1087-0.13910.0287-0.1355-0.0569-0.17840.05620.02010.00010.4502-0.05240.01270.43970.01360.446132.679147.621912.7496
340.19710.0880.06570.21780.18080.22460.1335-0.30610.74180.4863-0.1782-0.4254-0.3697-0.0166-0.00240.6641-0.00090.08220.67240.02680.6672-1.105358.17875.5204
350.1564-0.0682-0.06250.17710.18770.1289-0.43-0.2242-0.12140.0433-0.135-0.04760.53660.0777-0.00790.6179-0.08620.11230.45120.10390.7956-3.047934.340267.8967
360.0047-0.00660.01050.04990.01240.01630.15460.1415-0.143-0.3004-0.4154-0.01490.50150.49360.00010.63330.07620.05660.4543-0.15550.7772-1.580542.395849.6783
371.4867-0.1453-0.05910.6588-0.33450.363-0.00650.1342-0.1482-0.0303-0.02690.08430.0816-0.0984-00.41570.0060.04040.42090.0050.457-2.137151.456659.7169
380.80760.05770.34270.0222-0.07680.2104-0.07950.0642-0.10050.11230.0092-0.0126-0.16410.140800.4440.05670.04760.44130.07950.48716.620355.491253.3234
390.0068-0.00720.03780.0104-0.04240.20830.0463-0.3684-0.2421-0.3694-0.66120.0275-0.0662-0.237-0.00070.5161-0.1554-0.03230.77750.10140.44120.139954.479566.8131
400.36920.2246-0.08940.48470.20490.1171-0.0143-0.30950.13120.00170.1342-0.0831-0.04860.0902-00.42410.06460.02920.36650.01830.47284.867657.393857.9071
410.99510.52060.16361.0124-0.26030.0435-0.18910.0142-0.3117-0.10510.0351-0.00330.21320.1167-00.54410.06640.01740.42440.02990.560313.073543.179857.9131
420.447-0.03020.48490.17680.19480.4926-0.0351-0.48370.0105-0.1303-0.0956-0.2324-0.20390.32070.00010.3765-0.01920.07130.5662-0.09240.630436.565866.269260.2502
430.8713-0.31960.40610.51720.05630.288-0.1048-0.2023-0.149-0.02790.13230.0541-0.005-0.05010.00060.3720.02850.04590.50660.0080.523227.219758.305854.8592
440.41410.226-0.25270.4470.28950.7810.1607-0.5217-0.03990.15710.2255-0.0002-0.31020.11970.01560.5007-0.00490.01260.54460.03380.715829.795560.542560.3438
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 3:37)
2X-RAY DIFFRACTION2(chain A and resid 38:52)
3X-RAY DIFFRACTION3(chain A and resid 53:56)
4X-RAY DIFFRACTION4(chain A and resid 57:185)
5X-RAY DIFFRACTION5(chain A and resid 186:236)
6X-RAY DIFFRACTION6(chain A and resid 237:244)
7X-RAY DIFFRACTION7(chain A and resid 245:295)
8X-RAY DIFFRACTION8(chain A and resid 296:372)
9X-RAY DIFFRACTION9(chain A and resid 373:399)
10X-RAY DIFFRACTION10(chain A and resid 400:486)
11X-RAY DIFFRACTION11(chain A and resid 487:519)
12X-RAY DIFFRACTION12(chain B and resid 3:61)
13X-RAY DIFFRACTION13(chain B and resid 62:65)
14X-RAY DIFFRACTION14(chain B and resid 66:158)
15X-RAY DIFFRACTION15(chain B and resid 159:188)
16X-RAY DIFFRACTION16(chain B and resid 189:302)
17X-RAY DIFFRACTION17(chain B and resid 303:349)
18X-RAY DIFFRACTION18(chain B and resid 350:354)
19X-RAY DIFFRACTION19(chain B and resid 355:380)
20X-RAY DIFFRACTION20(chain B and resid 381:394)
21X-RAY DIFFRACTION21(chain B and resid 395:424)
22X-RAY DIFFRACTION22(chain B and resid 425:519)
23X-RAY DIFFRACTION23(chain C and resid 3:37)
24X-RAY DIFFRACTION24(chain C and resid 38:52)
25X-RAY DIFFRACTION25(chain C and resid 53:56)
26X-RAY DIFFRACTION26(chain C and resid 57:185)
27X-RAY DIFFRACTION27(chain C and resid 186:236)
28X-RAY DIFFRACTION28(chain C and resid 237:244)
29X-RAY DIFFRACTION29(chain C and resid 245:295)
30X-RAY DIFFRACTION30(chain C and resid 296:372)
31X-RAY DIFFRACTION31(chain C and resid 373:399)
32X-RAY DIFFRACTION32(chain C and resid 400:486)
33X-RAY DIFFRACTION33(chain C and resid 487:519)
34X-RAY DIFFRACTION34(chain D and resid 3:37)
35X-RAY DIFFRACTION35(chain D and resid 38:52)
36X-RAY DIFFRACTION36(chain D and resid 53:56)
37X-RAY DIFFRACTION37(chain D and resid 57:185)
38X-RAY DIFFRACTION38(chain D and resid 186:236)
39X-RAY DIFFRACTION39(chain D and resid 237:244)
40X-RAY DIFFRACTION40(chain D and resid 245:295)
41X-RAY DIFFRACTION41(chain D and resid 296:372)
42X-RAY DIFFRACTION42(chain D and resid 373:399)
43X-RAY DIFFRACTION43(chain D and resid 400:486)
44X-RAY DIFFRACTION44(chain D and resid 487:519)

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