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- PDB-7b4y: Structure of the M298L mutant of the Streptomyces coelicolor smal... -

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Basic information

Entry
Database: PDB / ID: 7b4y
TitleStructure of the M298L mutant of the Streptomyces coelicolor small laccase T1 copper axial ligand
ComponentsPutative copper oxidase
KeywordsOXIDOREDUCTASE / small laccase / T1 copper / point mutation / M298L
Function / homology
Function and homology information


oxidoreductase activity / copper ion binding
Similarity search - Function
Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / Copper oxidase
Similarity search - Component
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.19 Å
AuthorsZovo, K. / Majumdar, S. / Lukk, T.
Funding support Estonia, 1items
OrganizationGrant numberCountry
Estonian Research CouncilMOBTT60 Estonia
CitationJournal: Acs Omega / Year: 2022
Title: Substitution of the Methionine Axial Ligand of the T1 Copper for the Fungal-like Phenylalanine Ligand (M298F) Causes Local Structural Perturbations that Lead to Thermal Instability and Reduced ...Title: Substitution of the Methionine Axial Ligand of the T1 Copper for the Fungal-like Phenylalanine Ligand (M298F) Causes Local Structural Perturbations that Lead to Thermal Instability and Reduced Catalytic Efficiency of the Small Laccase from Streptomyces coelicolor A3(2).
Authors: Zovo, K. / Pupart, H. / Van Wieren, A. / Gillilan, R.E. / Huang, Q. / Majumdar, S. / Lukk, T.
History
DepositionDec 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 9, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Mar 9, 2022Group: 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 1.3Jan 31, 2024Group: 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

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Assembly

Deposited unit
A: Putative copper oxidase
B: Putative copper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,07410
Polymers73,5662
Non-polymers5088
Water7,800433
1
A: Putative copper oxidase
hetero molecules

A: Putative copper oxidase
hetero molecules

A: Putative copper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,11115
Polymers110,3483
Non-polymers76312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
Buried area12170 Å2
ΔGint-150 kcal/mol
Surface area27700 Å2
MethodPISA
2
B: Putative copper oxidase
hetero molecules

B: Putative copper oxidase
hetero molecules

B: Putative copper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,11115
Polymers110,3483
Non-polymers76312
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area12170 Å2
ΔGint-145 kcal/mol
Surface area27650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.200, 177.200, 177.200
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-716-

HOH

21A-719-

HOH

31B-702-

HOH

41B-708-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 38 through 95 or resid 97...
21(chain B and (resid 38 through 95 or resid 97...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 38 through 95 or resid 97...A38 - 95
121(chain A and (resid 38 through 95 or resid 97...A97 - 132
131(chain A and (resid 38 through 95 or resid 97...A134 - 138
141(chain A and (resid 38 through 95 or resid 97...A140
151(chain A and (resid 38 through 95 or resid 97...A142 - 210
161(chain A and (resid 38 through 95 or resid 97...A212 - 319
211(chain B and (resid 38 through 95 or resid 97...B38 - 95
221(chain B and (resid 38 through 95 or resid 97...B97 - 132
231(chain B and (resid 38 through 95 or resid 97...B134 - 138
241(chain B and (resid 38 through 95 or resid 97...B38 - 314
251(chain B and (resid 38 through 95 or resid 97...B142 - 210
261(chain B and (resid 38 through 95 or resid 97...B212 - 319

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Components

#1: Protein Putative copper oxidase


Mass: 36782.773 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (strain ATCC BAA-471 / A3(2) / M145) (bacteria)
Strain: ATCC BAA-471 / A3(2) / M145 / Gene: SCO6712 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q9XAL8
#2: Chemical
ChemComp-CU / COPPER (II) ION


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


Mass: 18.015 Da / Num. of mol.: 433 / 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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein concentration was 20 mg/ml in 20 mM Tris-HCl buffer (pH 7.5). Mother liquor was made up of 40% MPD, 200 mM NH4-OAc and 100 mM HEPES (pH 7.5). The protein was mixed in 2:1 ratio with ...Details: Protein concentration was 20 mg/ml in 20 mM Tris-HCl buffer (pH 7.5). Mother liquor was made up of 40% MPD, 200 mM NH4-OAc and 100 mM HEPES (pH 7.5). The protein was mixed in 2:1 ratio with protein to mother liquor.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97917 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 22, 2018
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 2.19→72.34 Å / Num. obs: 94266 / % possible obs: 99.2 % / Redundancy: 5.8 % / CC1/2: 0.987 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.069 / Rrim(I) all: 0.173 / Net I/σ(I): 7.1 / Num. measured all: 543286 / Scaling rejects: 590
Reflection shell

Diffraction-ID: 1 / Redundancy: 6 %

Resolution (Å)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.19-2.230.7092787046780.750.3140.7782.699.5
11.99-72.340.07337556290.9820.0310.08112.497.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CG8

3cg8


Resolution: 2.19→62.65 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1583 4738 5.03 %
Rwork0.1498 89421 -
obs0.1502 94159 98.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.61 Å2 / Biso mean: 30.715 Å2 / Biso min: 17 Å2
Refinement stepCycle: final / Resolution: 2.19→62.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4284 0 8 433 4725
Biso mean--37.71 40.5 -
Num. residues----554
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2608X-RAY DIFFRACTION3.683TORSIONAL
12B2608X-RAY DIFFRACTION3.683TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.19-2.210.20981150.21652990310599
2.21-2.240.28881370.21132994313199
2.24-2.270.23311440.20122961310599
2.27-2.30.20141570.20222957311499
2.3-2.330.2261460.19472949309599
2.33-2.360.19741870.18582944313199
2.36-2.390.20941560.18452934309099
2.39-2.430.21211570.18372962311998
2.43-2.460.20911780.18762905308398
2.46-2.50.19491460.18072949309598
2.5-2.550.2371710.16612932310399
2.55-2.590.20491750.16762965314099
2.59-2.640.15931720.16372961313399
2.64-2.70.16591520.15752988314099
2.7-2.760.1671830.15962960314399
2.76-2.820.19111480.15722962311099
2.82-2.890.16651630.15012999316299
2.89-2.970.13691960.14132953314999
2.97-3.060.16151310.14942983311498
3.06-3.160.16871460.13852971311799
3.16-3.270.15771450.1423019316499
3.27-3.40.15091350.12982997313298
3.4-3.550.10961530.12182966311999
3.55-3.740.12431870.128230243211100
3.74-3.980.13911560.12552952310898
3.98-4.280.10521710.11883008317999
4.29-4.710.13561530.115930503203100
4.71-5.390.12381400.133830733213100
5.4-6.80.17631680.16143023319198
6.81-62.650.15981700.18333090326097
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)
10.66220.0892-0.0270.899-0.51130.92930.02040.1104-0.0324-0.1007-0.02760.052-0.0526-0.1350.00190.22110.0561-0.02180.2683-0.03470.2283-4.3799-70.4689-30.3907
20.6581-0.20060.19050.29780.20390.6992-0.00720.02180.04660.0456-0.01310.0081-0.0684-0.08370.01840.24430.0343-0.01610.2292-0.01590.21284.2314-63.26-12.6237
33.5348-1.1437-0.54021.42220.28550.7759-0.06460.23770.20320.04490.0094-0.124-0.2746-0.06940.06410.28240.0123-0.03480.2393-0.00450.223511.9542-53.4576-13.0286
47.1835-1.97441.10935.90841.03096.0708-0.47310.50661.2442-0.4165-0.1061-0.09-1.2030.32090.56680.61290.0013-0.12320.36390.01420.56280.7296-42.7191-3.6704
51.04410.40690.90040.80050.13041.46640.0211-0.0069-0.17770.00730.0009-0.05430.22870.1277-0.03290.30180.09110.02670.2587-0.00190.2977-19.7358-53.3199-17.2934
60.53370.22420.090.340.15320.8045-0.0398-0.0846-0.09240.11380.05490.03420.15050.1608-0.05240.2880.06930.02780.23380.02330.2529-23.1095-50.3339-12.1464
71.43820.00141.31250.74020.23591.8552-0.102-0.21980.1020.1593-0.0330.1770.1688-0.09530.11230.29820.03610.05890.25840.02890.2853-35.0485-49.1801-12.4598
80.8212-0.19460.15140.4329-0.12210.5735-0.0586-0.0280.01050.06440.00510.03020.03640.04150.06090.24270.02750.01870.21370.02130.202-26.2233-44.4096-19.7444
91.5670.0895-0.40712.11490.45531.3870.03440.07210.03110.1307-0.0636-0.1170.03870.36930.03110.26590.04670.00340.29850.03730.2292-10.591-37.9418-23.5801
100.3768-0.185-0.00240.32750.09180.5229-0.02550.00180.03960.09480.0243-0.04210.06620.09480.01370.25520.03390.01310.25440.02570.2072-18.38-39.1239-32.1428
110.3826-0.4276-0.25870.5340.1110.6531-0.00560.0914-0.0092-0.03280.00650.0130.118-0.0307-0.01110.2540.0280.0130.25450.01080.2405-21.6556-38.1993-36.7951
121.3943-1.1055-0.23593.83190.70990.80820.00940.0850.09960.2666-0.0773-0.18360.07830.25790.0570.24180.01570.00740.29430.03510.2096-9.1527-32.364-31.2662
135.1012-1.6197-1.48876.709-1.41234.8803-0.0212-0.42220.04150.5464-0.3448-1.1898-0.31741.05270.35610.34780.00490.01920.58610.08830.56711.6112-43.5762-40.6297
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 38 through 173 )A38 - 173
2X-RAY DIFFRACTION2chain 'A' and (resid 174 through 288 )A174 - 288
3X-RAY DIFFRACTION3chain 'A' and (resid 289 through 305 )A289 - 305
4X-RAY DIFFRACTION4chain 'A' and (resid 306 through 319 )A306 - 319
5X-RAY DIFFRACTION5chain 'B' and (resid 38 through 66 )B38 - 66
6X-RAY DIFFRACTION6chain 'B' and (resid 67 through 112 )B67 - 112
7X-RAY DIFFRACTION7chain 'B' and (resid 113 through 143 )B113 - 143
8X-RAY DIFFRACTION8chain 'B' and (resid 144 through 188 )B144 - 188
9X-RAY DIFFRACTION9chain 'B' and (resid 189 through 210 )B189 - 210
10X-RAY DIFFRACTION10chain 'B' and (resid 211 through 245 )B211 - 245
11X-RAY DIFFRACTION11chain 'B' and (resid 246 through 288 )B246 - 288
12X-RAY DIFFRACTION12chain 'B' and (resid 289 through 305 )B289 - 305
13X-RAY DIFFRACTION13chain 'B' and (resid 306 through 319 )B306 - 319

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