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- PDB-5m6b: structure of recombinant mushroom tyrosinase (abPPO4) -

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Basic information

Entry
Database: PDB / ID: 5m6b
Titlestructure of recombinant mushroom tyrosinase (abPPO4)
ComponentsPolyphenol oxidase 4
KeywordsOXIDOREDUCTASE / heterologous expression / polyphenol oxidase / tyrosinase activity / agaricus bisporus
Function / homology
Function and homology information


tyrosinase / tyrosinase activity / melanin biosynthetic process / metal ion binding
Similarity search - Function
Monophenol monooxygenase, fungi / Tyosinase, C-terminal / Tyrosinase C-terminal 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 ...Monophenol monooxygenase, fungi / Tyosinase, C-terminal / Tyrosinase C-terminal 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 / OXYGEN ATOM / Polyphenol oxidase 4
Similarity search - Component
Biological speciesAgaricus bisporus (button mushroom)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsPretzler, M. / Bijelic, A. / Rompel, A.
CitationJournal: Sci Rep / Year: 2017
Title: Heterologous expression and characterization of functional mushroom tyrosinase (AbPPO4).
Authors: Pretzler, M. / Bijelic, A. / Rompel, A.
History
DepositionOct 24, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Jun 20, 2018Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Refinement description
Category: pdbx_validate_close_contact / refine_hist ...pdbx_validate_close_contact / refine_hist / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _refine_hist.d_res_low
Revision 1.3Jan 17, 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
B: Polyphenol oxidase 4
A: Polyphenol oxidase 4
C: Polyphenol oxidase 4
D: Polyphenol oxidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)261,26113
Polymers260,7364
Non-polymers5249
Water00
1
B: Polyphenol oxidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3113
Polymers65,1841
Non-polymers1272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Polyphenol oxidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3274
Polymers65,1841
Non-polymers1433
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Polyphenol oxidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3113
Polymers65,1841
Non-polymers1272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Polyphenol oxidase 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3113
Polymers65,1841
Non-polymers1272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)287.300, 52.090, 152.660
Angle α, β, γ (deg.)90.00, 98.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Polyphenol oxidase 4 / Phenolase 4 / Cresolase / Tyrosinase 4


Mass: 65184.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agaricus bisporus (button mushroom) / Gene: PPO4 / Production host: Escherichia coli (E. coli) / References: UniProt: C7FF05, tyrosinase
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O

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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: 2.17 Å3/Da / Density % sol: 43.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.8
Details: 50 mM sodium cacodylate pH 5.8 and 13 % (w/w) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.873 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 3.25→48.9 Å / Num. obs: 35520 / % possible obs: 98.4 % / Redundancy: 4.2 % / CC1/2: 0.994 / Rmerge(I) obs: 0.251 / Net I/σ(I): 5.68
Reflection shellResolution: 3.25→3.37 Å / Redundancy: 4.4 % / Rmerge(I) obs: 1.108 / Mean I/σ(I) obs: 1.91 / Num. unique all: 3462 / CC1/2: 0.826

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASER(1.10.1-2155)phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OUA

4oua


Resolution: 3.25→48.9 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 29.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2754 3229 4.99 %
Rwork0.251 --
obs0.2522 35512 93.82 %
all-64684 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.25→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16259 0 9 0 16268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916767
X-RAY DIFFRACTIONf_angle_d0.69523006
X-RAY DIFFRACTIONf_dihedral_angle_d9.939588
X-RAY DIFFRACTIONf_chiral_restr0.0442599
X-RAY DIFFRACTIONf_plane_restr0.0073018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2501-3.29860.41521360.39562649X-RAY DIFFRACTION94
3.2986-3.35010.34351390.36112620X-RAY DIFFRACTION93
3.3501-3.4050.37321420.35892671X-RAY DIFFRACTION93
3.405-3.46370.35941410.34322600X-RAY DIFFRACTION90
3.4637-3.52670.37041250.35832440X-RAY DIFFRACTION88
3.5267-3.59450.32871270.33982533X-RAY DIFFRACTION89
3.5945-3.66780.36481460.32942691X-RAY DIFFRACTION94
3.6678-3.74760.30761380.30492746X-RAY DIFFRACTION95
3.7476-3.83470.3481410.29342680X-RAY DIFFRACTION96
3.8347-3.93060.32171430.30122779X-RAY DIFFRACTION97
3.9306-4.03680.31261520.26722810X-RAY DIFFRACTION97
4.0368-4.15550.2881410.27232639X-RAY DIFFRACTION96
4.1555-4.28960.27021450.25492803X-RAY DIFFRACTION96
4.2896-4.44280.27331410.24542691X-RAY DIFFRACTION95
4.4428-4.62050.27791420.22622692X-RAY DIFFRACTION94
4.6205-4.83060.26451450.21232687X-RAY DIFFRACTION94
4.8306-5.08510.26561320.21472602X-RAY DIFFRACTION91
5.0851-5.40330.23781360.21372592X-RAY DIFFRACTION91
5.4033-5.81990.24111480.2312736X-RAY DIFFRACTION95
5.8199-6.40440.26071440.25072713X-RAY DIFFRACTION96
6.4044-7.32850.26771480.23032743X-RAY DIFFRACTION96
7.3285-9.2230.24841360.20782639X-RAY DIFFRACTION93
9.223-48.90740.19961410.19722699X-RAY DIFFRACTION94
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)
14.50760.13181.19823.5428-0.33784.5037-0.76251.51980.7018-1.06620.45020.7511-1.20270.1127-0.17991.9711-0.3811-0.37931.64950.27921.0294-40.8515-20.515.5579
23.98560.46311.76423.3283-0.39736.5271-0.55980.1360.3671-0.03160.25070.5755-1.0338-0.13520.06881.4038-0.1014-0.10890.88980.11530.6366-36.2162-22.37621.0211
34.5968-0.22120.73973.2791.38843.6909-0.1820.60110.3585-0.24270.3019-0.0444-0.75870.8304-0.00031.4036-0.45930.10491.6299-0.09410.6977-15.2719-29.427720.489
47.6433-0.93311.41341.94670.25912.8653-0.1614-1.9517-0.51310.58570.25820.37250.8387-3.3630.56760.90260.00530.18561.9080.12650.5264-41.0698-34.961866.4395
55.9304-0.98652.23131.12450.20569.17860.04120.0969-0.1832-0.3722-0.20430.19130.7935-1.47530.10710.8003-0.04630.13670.79280.01470.4593-36.4395-33.27351.0031
66.7335-0.59470.34531.4983.53818.8656-0.2545-0.04530.9893-0.2937-0.1012-0.0005-1.62641.8790.33151.4313-0.2443-0.04621.51110.10350.8618-18.6454-21.479851.8934
77.7719-2.7371-1.3096.01261.35619.7512-0.1201-0.4511-0.70940.64270.11320.07231.54411.7662-0.28971.67520.5081-0.09521.49180.23781.1605-16.8906-37.761757.5158
82.70170.21782.27515.70472.628110.019-0.68130.43150.36270.12840.6404-0.6044-0.97952.85080.0921.2943-0.15640.09172.17180.22121.039-9.0475-28.5750.0413
913.0761-4.93221.8955.11160.27646.70591.14724.6513-3.2525-0.81710.00711.22040.4572-0.50612.72060.5656-0.028-0.24721.6435-1.0750.838813.1422-55.666224.7531
1012.1402-0.90112.19787.50520.23896.34780.21712.4644-1.6926-0.2377-0.32360.06010.05381.04310.24170.5870.10780.01071.004-0.39690.768226.1138-53.981432.3656
119.5936-4.16361.40878.1045-0.40225.6994-0.8015-2.01161.37830.78960.9553-0.1758-1.166-0.44130.04520.80940.1593-0.12371.2981-0.23110.837719.1522-41.505747.8354
127.93543.77094.15052.5381-0.70615.908-0.9625-2.5166-3.82110.95141.05622.16660.7081-0.68520.23040.8647-0.15510.25260.82090.45471.321512.3759-55.24449.1368
135.3341-6.6159-0.12917.3376-1.59313.2299-1.0328-2.9519-0.14561.47850.79280.1774-0.7324-0.8343-0.03861.60760.45610.07692.1928-0.04471.029317.6054-47.310557.708
149.18640.99072.94272.80680.80894.9401-0.86072.47951.5104-0.55390.5005-0.2955-0.68682.21560.14821.1642-0.2876-0.23312.17560.46951.3071-73.6347-16.352343.1918
1511.5334-0.36134.50683.89831.50637.3327-1.132.211.7822-0.5095-0.26280.3385-1.12430.994-0.16091.0441-0.2417-0.29931.17720.40511.1534-89.7829-17.087942.4673
169.5835-2.11720.92337.32811.45876.4168-0.1494-1.6118-1.32131.14570.27610.05741.2503-0.6158-0.12010.9784-0.086-0.22991.1930.10660.9648-94.972-29.340659.4528
177.9496-3.930.9985.9552-4.283.0275-1.2146-0.84941.4261.22140.4218-0.9536-1.9042-0.27160.72471.8229-0.0301-0.67571.5864-0.39591.8863-90.2831-12.014462.5159
189.25140.54756.60679.79133.56695.2312-0.3941-3.35760.78430.8239-0.25460.9560.325-1.36010.43221.6990.05310.23242.1163-0.01241.5301-99.6889-21.988867.5927
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 3 through 225 )
2X-RAY DIFFRACTION2chain 'B' and (resid 226 through 364 )
3X-RAY DIFFRACTION3chain 'B' and (resid 365 through 557 )
4X-RAY DIFFRACTION4chain 'A' and (resid 3 through 225 )
5X-RAY DIFFRACTION5chain 'A' and (resid 226 through 364 )
6X-RAY DIFFRACTION6chain 'A' and (resid 365 through 434 )
7X-RAY DIFFRACTION7chain 'A' and (resid 435 through 478 )
8X-RAY DIFFRACTION8chain 'A' and (resid 479 through 557 )
9X-RAY DIFFRACTION9chain 'C' and (resid 3 through 225 )
10X-RAY DIFFRACTION10chain 'C' and (resid 226 through 364 )
11X-RAY DIFFRACTION11chain 'C' and (resid 365 through 434 )
12X-RAY DIFFRACTION12chain 'C' and (resid 435 through 478 )
13X-RAY DIFFRACTION13chain 'C' and (resid 479 through 558 )
14X-RAY DIFFRACTION14chain 'D' and (resid 3 through 225 )
15X-RAY DIFFRACTION15chain 'D' and (resid 226 through 364 )
16X-RAY DIFFRACTION16chain 'D' and (resid 365 through 434 )
17X-RAY DIFFRACTION17chain 'D' and (resid 435 through 478 )
18X-RAY DIFFRACTION18chain 'D' and (resid 479 through 558 )

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