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- PDB-7xio: Crystal structure of TYR from Ralstonia -

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Basic information

Entry
Database: PDB / ID: 7xio
TitleCrystal structure of TYR from Ralstonia
ComponentsPolyphenol oxidase
KeywordsOXIDOREDUCTASE / Tyrosinase / Tyrosine / L-Dopa / Ralstonia / METAL BINDING PROTEIN
Function / homology
Function and homology information


tyrosinase / catechol oxidase activity / tyrosinase activity / metal ion binding
Similarity search - Function
Polyphenol oxidase, C-terminal / Chloroplastic Polyphenol Oxidase C-terminal domain / 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 / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence
Similarity search - Domain/homology
PHOSPHATE ION / Polyphenol oxidase with tyrosine hydroxylase activity oxidoreductase protein
Similarity search - Component
Biological speciesRalstonia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsSun, D.Y. / Cui, P.P. / Liao, L.J. / Liu, X.K. / Liu, B. / Guo, Y. / Feng, Z. / Zhang, J. / Li, X. / Zeng, Z.X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of TYR from Ralstonia
Authors: Sun, D.Y. / Cui, P.P. / Liao, L.J. / Liu, X.K. / Liu, B. / Guo, Y. / Feng, Z. / Zhang, J. / Li, X. / Zeng, Z.X.
History
DepositionApr 13, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyphenol oxidase
B: Polyphenol oxidase
C: Polyphenol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,0366
Polymers163,7513
Non-polymers2853
Water3,297183
1
A: Polyphenol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6792
Polymers54,5841
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Polyphenol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6792
Polymers54,5841
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Polyphenol oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6792
Polymers54,5841
Non-polymers951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)190.897, 190.897, 402.109
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 35 through 40 or resid 42...
d_2ens_1(chain "B" and (resid 35 through 40 or resid 42...
d_3ens_1(chain "C" and (resid 35 through 40 or resid 42...

NCS oper:
IDCodeMatrixVector
1given(-0.472459746561, 0.406226470957, -0.782152058217), (0.450772189068, -0.651214843919, -0.610510983212), (-0.757354752704, -0.641014259867, 0.124557204544)-146.239592194, 146.99037599, -18.9015372036
2given(-0.178558243141, -0.323468959887, -0.929238820646), (-0.700216893228, -0.621706113981, 0.350966964651), (-0.691240375154, 0.713336764669, -0.115487678685)-46.4694029642, 81.5456745619, -105.40907707

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Components

#1: Protein Polyphenol oxidase / Polyphenol oxidase with tyrosine hydroxylase activity oxidoreductase protein / Tyrosinase


Mass: 54583.801 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia (bacteria)
Gene: CJO87_16720, MAFF211479_31910, RD1301_v1_4420004, RUN1744_v1_120005, RUN215_v1_900048, TD1301_v1_1720005, TF3108_v1_180005, TO10_v1_260005
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: A0A0K1ZP03, tyrosinase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 183 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.31 Å3/Da / Density % sol: 71.46 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.015M Magnesium acetate tetrahydrate,0.05M Sodium cacodylate trihydrate,pH 6.0,1.7M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.64→152.9 Å / Num. obs: 1386447 / % possible obs: 99.9842 % / Redundancy: 19.4 % / Biso Wilson estimate: 68.05 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.045 / Rrim(I) all: 0.142 / Net I/σ(I): 82467
Reflection shellResolution: 2.75→2.9 Å / Rmerge(I) obs: 1.343 / Num. unique obs: 206653 / CC1/2: 0.83 / Rpim(I) all: 0.313

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Processing

Software
NameVersionClassification
HKL-3000data collection
PHENIX1.19.1_4122refinement
DIALSdata reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X3P

4x3p


Resolution: 2.64→48.09 Å / SU ML: 0.3833 / Cross valid method: FREE R-VALUE / σ(F): 0.31 / Phase error: 19.5194
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2017 4105 4.98 %
Rwork0.1814 78332 -
obs0.1824 82437 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.59 Å2
Refinement stepCycle: LAST / Resolution: 2.64→48.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9935 0 15 183 10133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002710211
X-RAY DIFFRACTIONf_angle_d0.621513976
X-RAY DIFFRACTIONf_chiral_restr0.04481568
X-RAY DIFFRACTIONf_plane_restr0.00631825
X-RAY DIFFRACTIONf_dihedral_angle_d5.39571392
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AX-RAY DIFFRACTIONTorsion NCS0.420597311596
ens_1d_3AX-RAY DIFFRACTIONTorsion NCS0.441983118392
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.670.40021410.36832693X-RAY DIFFRACTION100
2.67-2.710.3151370.34472673X-RAY DIFFRACTION100
2.71-2.740.34541410.32082677X-RAY DIFFRACTION100
2.74-2.780.33741430.28382659X-RAY DIFFRACTION100
2.78-2.820.26761510.26572670X-RAY DIFFRACTION100
2.82-2.860.26141320.25222701X-RAY DIFFRACTION100
2.86-2.90.27531230.2352703X-RAY DIFFRACTION99.96
2.9-2.940.27351690.22172638X-RAY DIFFRACTION100
2.94-2.990.23111530.21492669X-RAY DIFFRACTION100
2.99-3.040.23621480.21092664X-RAY DIFFRACTION100
3.04-3.10.24211460.21252698X-RAY DIFFRACTION100
3.1-3.160.25361210.22382694X-RAY DIFFRACTION99.96
3.16-3.220.25011490.22552684X-RAY DIFFRACTION100
3.22-3.290.2341400.23552673X-RAY DIFFRACTION100
3.29-3.370.27451230.24612686X-RAY DIFFRACTION100
3.37-3.450.27351350.25742722X-RAY DIFFRACTION100
3.45-3.550.24121310.20462692X-RAY DIFFRACTION99.96
3.55-3.650.20171470.1852686X-RAY DIFFRACTION100
3.65-3.770.20611510.17382705X-RAY DIFFRACTION99.93
3.77-3.90.20751450.16942672X-RAY DIFFRACTION100
3.9-4.060.16421490.15412703X-RAY DIFFRACTION100
4.06-4.240.17051570.15032700X-RAY DIFFRACTION99.9
4.24-4.470.17551370.14122709X-RAY DIFFRACTION100
4.47-4.750.14221340.12362712X-RAY DIFFRACTION100
4.75-5.110.14171460.12992724X-RAY DIFFRACTION100
5.12-5.630.17111310.1532739X-RAY DIFFRACTION100
5.63-6.440.19771470.16662740X-RAY DIFFRACTION100
6.44-8.110.18011400.15992766X-RAY DIFFRACTION99.9
8.11-48.090.17121380.16832880X-RAY DIFFRACTION99.67
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)
12.736136496180.1989471256640.9765423069551.83081243502-0.004368020315732.42216292666-0.01015875117420.2343696696550.1520172390740.007457947774060.0687833052496-0.297908977113-0.192379736390.300864448205-0.06097819403860.450924770346-0.0302195417120.06345777821080.391161277605-0.126816083980.397823751068-58.69128024682.3207851317-63.9039933017
21.072144643320.2095260046910.3785932368671.705769617450.3220773245062.077145169380.0630394390216-0.04548183802990.01780543468810.1427171660070.136435586552-0.2628681192080.1009107072120.118863053233-0.1995443830310.476564561019-0.002090567956790.01227463354540.424849593691-0.1426147530730.458098635973-58.880981048675.4112394068-54.9078525773
30.183116753372-0.3840008557620.1563073538482.827616946530.6361676004972.1126194951-0.174483932875-0.35717179687-0.02714317194320.935028673170.322788471611-0.4145839110820.178284613870.252659887941-0.1447993084850.6566020346690.0746460689762-0.07920173221340.656778890451-0.1201937064930.548463819335-58.404496177771.4808931307-40.8770487752
43.00008628487-0.132782864286-0.128662783693.270196525710.5782162466742.82556416963-0.255980207016-0.396833789104-0.09762495257310.8976877322620.361905599088-0.3070612409180.4348658180460.0557137050187-0.1176686099720.8687461267550.143677472212-0.1382696619860.544269912961-0.09489382324390.477682078217-57.130058219154.917328711-43.4276629769
51.970817041810.3316861596-0.07854149769581.852114094660.8878965117941.824925388460.06246194393560.111631059206-0.101529618317-0.1400818259710.135434884671-0.431462778006-0.07169314173950.165916161942-0.1939856832890.5073726883790.021169291746-0.01970890144220.399485486116-0.1595330070790.545957736569-41.7831521408104.634297419-31.4352188321
60.8157310491670.0817874045464-0.5142786469432.517546733431.514531695581.37362209168-0.1801607203340.249627021622-0.4928048956840.464187962534-0.06351590910040.4228104892680.20823575895-0.3975633696840.2237287862860.668027848365-0.037229913983-0.05695556054710.586491625988-0.0138753875340.755262472809-61.20201915292.4817925273-25.445090775
74.159595793150.418623243361-0.6464531416231.893123923290.1730193437213.063492738050.229166709609-0.3192649654710.208129584012-0.0244986262824-0.2071770162250.211464919826-0.0951728123313-0.2482519536770.005176420590540.560699413707-0.05625833015730.002082380888910.665652729714-0.1363072883060.553877365002-71.2812948691110.31207683-15.2484721539
82.400989286130.354053632899-0.6372701080132.09271608322-0.5657433003972.227838500220.163519053791-0.193698967984-0.01159809960350.216115895268-0.112726651190.054489664861-0.172671301556-0.0798522118079-0.04784209469180.4363803730620.0409804989416-0.0512636237970.393742002393-0.100827622730.406433845244-61.9174072075112.467128104-16.1002920011
93.228553480580.192367450703-0.06298806417811.38520714971-0.1312015434181.33524994166-0.0291452790203-0.222146803751-0.01963557708080.04325586451530.07629620641820.1348133066960.121451900884-0.0207039721552-0.04694686864860.423191375739-0.09517295374490.1086229374980.5792217630050.06487748778690.514841169331-7.4810256742154.1803182894-2.81545449391
101.48512730379-0.421004909146-0.08033854331011.40039781621-0.2629494772870.7697242636530.0215500343271-0.4357024971770.0367083105326-0.06524789156580.1996130175550.798065525923-0.26229937147-0.834071014458-0.2217108001160.530910853401-0.06894002332060.06436998311630.854170232263-0.003984910648750.863185231594-24.817456928861.8567120199-3.0863060291
112.30533591945-0.6127053635950.3296819371942.337621406080.3953020362642.303787066290.1272159817270.4627521780620.537783279957-0.235074596981-0.0200062779980.117085970772-0.251865282049-0.375760741406-0.09981996942470.49584370918-0.03549055942680.0585867086040.7597040394170.210816793940.732655760102-12.933775244771.8417531668-22.5911290241
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 35 through 117 )AA35 - 1171 - 83
22chain 'A' and (resid 118 through 299 )AA118 - 29984 - 265
33chain 'A' and (resid 300 through 363 )AA300 - 363266 - 318
44chain 'A' and (resid 364 through 497 )AA364 - 497319 - 431
55chain 'B' and (resid 35 through 310 )BB35 - 3101 - 276
66chain 'B' and (resid 311 through 349 )BB311 - 349277 - 306
77chain 'B' and (resid 350 through 390 )BB350 - 390307 - 338
88chain 'B' and (resid 391 through 497 )BB391 - 497339 - 438
99chain 'C' and (resid 35 through 299 )CC35 - 2991 - 265
1010chain 'C' and (resid 300 through 349 )CC300 - 349266 - 306
1111chain 'C' and (resid 350 through 496 )CC350 - 496307 - 428

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