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- PDB-3w6w: Crystal structure of melB holo-protyrosinase from Asperugillus oryzae -

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Basic information

Entry
Database: PDB / ID: 3w6w
TitleCrystal structure of melB holo-protyrosinase from Asperugillus oryzae
ComponentsTyrosinase
KeywordsOXIDOREDUCTASE / Four helix bundle / METAL BINDING PROTEIN
Function / homology
Function and homology information


tyrosinase / tyrosinase activity / melanin biosynthetic process / nucleus / metal ion binding
Similarity search - Function
Hemocyanin; Chain: A, domain 2 - #20 / Domain of Unknown Function (DUF1907) / Hemocyanin; Chain: A, domain 2 / Domain of unknown function DUF1907 / DUF1907 / 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. ...Hemocyanin; Chain: A, domain 2 - #20 / Domain of Unknown Function (DUF1907) / Hemocyanin; Chain: A, domain 2 / Domain of unknown function DUF1907 / DUF1907 / 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 copper-binding domain / Di-copper centre-containing domain superfamily / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / tyrosinase
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.394 Å
AuthorsFujieda, N. / Yabuta, S. / Ikeda, T. / Oyama, T. / Muraki, N. / Kurisu, G. / Itoh, S.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Crystal structures of copper-depleted and copper-bound fungal pro-tyrosinase: insights into endogenous cysteine-dependent copper incorporation.
Authors: Fujieda, N. / Yabuta, S. / Ikeda, T. / Oyama, T. / Muraki, N. / Kurisu, G. / Itoh, S.
History
DepositionFeb 22, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _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: Tyrosinase
B: Tyrosinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,9836
Polymers142,7292
Non-polymers2544
Water19,7261095
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-69 kcal/mol
Surface area41180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.313, 118.086, 84.207
Angle α, β, γ (deg.)90.00, 97.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosinase


Mass: 71364.578 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q2UP46*PLUS
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1095 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 1.81 Å3/Da / Density % sol: 31.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 18% PEG 3350, 50mM Ammonium Fluoride, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Dec 7, 2011
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.38→50 Å / Num. obs: 198757 / Observed criterion σ(F): 0 / Biso Wilson estimate: 13.99 Å2
Reflection shellResolution: 1.4→1.42 Å / % possible all: 96.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(AutoSol)model building
PHENIX(phenix.refine: 1.8_1069)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIX(AutoSol)phasing
RefinementMethod to determine structure: SAD / Resolution: 1.394→34.074 Å / Occupancy max: 1 / Occupancy min: 0.15 / FOM work R set: 0.8651 / SU ML: 0.14 / σ(F): 1.34 / Phase error: 20.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1992 9914 5.05 %
Rwork0.1774 --
obs0.1785 196359 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.51 Å2 / Biso mean: 19.107 Å2 / Biso min: 6.89 Å2
Refinement stepCycle: LAST / Resolution: 1.394→34.074 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9291 0 4 1095 10390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910319
X-RAY DIFFRACTIONf_angle_d1.10214184
X-RAY DIFFRACTIONf_dihedral_angle_d13.1333958
X-RAY DIFFRACTIONf_chiral_restr0.0781462
X-RAY DIFFRACTIONf_plane_restr0.0051859
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 (%)
1.3942-1.410.31162870.27964979526678
1.41-1.42660.29723400.27066071641197
1.4266-1.4440.27583560.2676127648397
1.444-1.46230.28153200.24936196651697
1.4623-1.48150.2513260.24626121644797
1.4815-1.50180.2573370.24326250658797
1.5018-1.52330.24133230.2266133645697
1.5233-1.5460.24873380.22036204654297
1.546-1.57020.25863470.22026129647697
1.5702-1.59590.24483190.21096240655998
1.5959-1.62340.23213400.20456201654198
1.6234-1.6530.22773560.19946179653598
1.653-1.68480.20623320.19386251658398
1.6848-1.71910.22663560.19036188654498
1.7191-1.75650.2063240.18686275659998
1.7565-1.79740.20033260.18856272659898
1.7974-1.84230.21043380.18386204654298
1.8423-1.89210.20793480.18456246659499
1.8921-1.94780.19963370.18116312664999
1.9478-2.01070.20563010.17986350665199
2.0107-2.08250.20783100.17596287659799
2.0825-2.16590.19313250.16936331665699
2.1659-2.26440.23350.17476327666299
2.2644-2.38380.18283330.17566327666099
2.3838-2.53310.20533480.17976316666499
2.5331-2.72860.20493120.179864066718100
2.7286-3.00310.2013340.174563316665100
3.0031-3.43720.17673300.156863906720100
3.4372-4.32920.15033140.141164436757100
4.3292-34.0840.1743220.15266359668198
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)
10.7450.2806-0.33240.8068-0.41581.3991-0.0813-0.0357-0.1427-0.04540.0076-0.0170.19060.00580.05320.10770.0119-0.00410.0540.01820.1032-9.8399-23.5976-8.1918
20.9506-0.093-0.05990.7409-0.10060.96780.01580.0103-0.0429-0.0435-0.01180.03360.0722-0.00020.00050.1017-0.0017-0.00730.06680.01820.0777-15.5995-11.5716-15.3246
31.0776-0.16520.14120.6632-0.14570.7637-0.0229-0.14210.04730.09820.02320.0283-0.1033-0.01690.00930.0978-0.0060.00510.06090.00470.0672-15.3038-5.23870.0983
40.88580.09940.11011.44980.0060.882-0.0221-0.3061-0.15690.2523-0.0708-0.1140.12920.15580.05180.1590.0186-0.01710.15950.06450.1239-5.866-23.79228.7493
51.5654-0.5572-0.04110.778-0.00621.11130.0028-0.18210.09860.0810.0407-0.001-0.06010.0714-0.040.17-0.01510.01030.1063-0.02040.1233-15.85411.90153.2021
61.2328-0.15220.69480.98760.49521.4463-0.0328-0.21840.24630.01390.03150.0711-0.146-0.00270.01120.1452-0.00790.04210.1287-0.03330.1584-22.08411.24854.9436
75.12490.75423.51441.75730.7355.2953-0.0783-0.33430.39630.2581-0.0003-0.0927-0.18670.10140.08060.2702-0.00590.0580.1333-0.05230.2003-20.600310.55169.6238
81.06290.1252-0.22961.4064-0.15291.0666-0.01530.1787-0.0347-0.11910.03030.06950.0948-0.1268-0.00390.0818-0.0086-0.03110.12990.00290.065-31.2101-7.9692-44.7745
91.5572-0.1468-0.08461.3710.04271.46490.01890.1547-0.1541-0.0605-0.0063-0.07810.21160.052-0.02350.13240.0083-0.02580.0863-0.00020.0814-21.416-11.0869-34.5961
100.65830.08380.04680.7392-0.02390.74120.01590.05390.10910.018-0.00850.0459-0.1028-0.02640.00090.08170.00070.010.07520.02870.0876-24.42759.6509-34.0642
110.58060.11940.14061.54450.44440.91440.01590.22060.1313-0.1982-0.03260.2812-0.1111-0.22730.01580.13370.0293-0.04120.25770.08790.1722-36.110.508-49.4169
121.8776-0.3147-0.15332.108-0.13921.5110.00310.06690.16740.0869-0.032-0.0039-0.1595-0.00910.03050.1397-0.01290.00910.0810.03130.1403-20.983925.1593-31.3771
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 0:125 )
2X-RAY DIFFRACTION2chain 'A' and (resseq 126:277 )
3X-RAY DIFFRACTION3chain 'A' and (resseq 278:385 )
4X-RAY DIFFRACTION4chain 'A' and (resseq 386:440 )
5X-RAY DIFFRACTION5chain 'A' and (resseq 441:533 )
6X-RAY DIFFRACTION6chain 'A' and (resseq 534:575 )
7X-RAY DIFFRACTION7chain 'A' and (resseq 576:616 )
8X-RAY DIFFRACTION8chain 'B' and (resseq 1:163 )
9X-RAY DIFFRACTION9chain 'B' and (resseq 164:229 )
10X-RAY DIFFRACTION10chain 'B' and (resseq 230:385 )
11X-RAY DIFFRACTION11chain 'B' and (resseq 386:474 )
12X-RAY DIFFRACTION12chain 'B' and (resseq 475:616 )

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