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- PDB-7bdn: Structure of the Streptomyces coelicolor small laccase - cubic cr... -

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Basic information

Entry
Database: PDB / ID: 7bdn
TitleStructure of the Streptomyces coelicolor small laccase - cubic crystal form
ComponentsPutative copper oxidase
KeywordsOXIDOREDUCTASE / small laccase / cubic crystal form
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 / Multicopper oxidase, C-terminal / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 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 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Category: citation / citation_author / Item: _citation.title / _citation_author.identifier_ORCID
Revision 1.2Feb 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 1.3Mar 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 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,2458
Polymers73,8642
Non-polymers3816
Water6,395355
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)111,36812
Polymers110,7963
Non-polymers5729
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 area11830 Å2
ΔGint-118 kcal/mol
Surface area27710 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)111,36812
Polymers110,7963
Non-polymers5729
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
Buried area11790 Å2
ΔGint-126 kcal/mol
Surface area27740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)176.981, 176.981, 176.981
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-661-

HOH

21A-670-

HOH

31A-675-

HOH

41B-668-

HOH

51B-673-

HOH

61B-677-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: TYR / End label comp-ID: TYR / Auth seq-ID: 38 - 314 / Label seq-ID: 38 - 314

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Putative copper oxidase


Mass: 36932.008 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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9XAL8
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / 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, 20 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, 20 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: 123 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.5419 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Apr 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.7→29.5 Å / Num. obs: 50726 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.995 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.065 / Rrim(I) all: 0.179 / Net I/σ(I): 10.1 / Num. measured all: 376482 / Scaling rejects: 29
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.7-2.797.40.7423420746380.8990.2920.798399.6
10.81-29.56.60.04854398240.9990.020.05222.195

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.55 Å29.5 Å
Translation5.55 Å29.5 Å

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Processing

Software
NameVersionClassificationNB
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3CG8

3cg8


Resolution: 2.7→29.5 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2217 2567 5.07 %
Rwork0.1995 48046 -
obs0.2007 50613 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.69 Å2 / Biso mean: 35.5813 Å2 / Biso min: 23.17 Å2
Refinement stepCycle: final / Resolution: 2.7→29.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4284 0 6 355 4645
Biso mean--52.41 39.95 -
Num. residues----554
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2605X-RAY DIFFRACTION6.27TORSIONAL
12B2605X-RAY DIFFRACTION6.27TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.750.26231230.2372696281999
2.75-2.810.25511420.23226192761100
2.81-2.870.22091280.218126622790100
2.87-2.940.23911320.213626512783100
2.94-3.010.29341500.204226232773100
3.01-3.090.23991320.2226942826100
3.09-3.180.23451270.208626242751100
3.18-3.290.26491620.206826442806100
3.29-3.40.19541350.205326752810100
3.4-3.540.21331510.205626522803100
3.54-3.70.21391670.187226202787100
3.7-3.890.22111530.192326632816100
3.9-4.140.21911190.185226852804100
4.14-4.460.17911430.170526782821100
4.46-4.90.20121350.177626912826100
4.9-5.610.2231480.186926922840100
5.61-7.040.21871550.225726992854100
7.05-29.50.22751650.21262778294399
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)
10.35620.16820.24550.542-0.20590.6952-0.00280.10190.0122-0.0718-0.02580.1144-0.0768-0.10270.02740.26690.0809-0.00980.3431-0.02790.2955-4.4105-70.1883-30.405
20.66650.03190.32110.4472-0.02280.6436-0.0199-0.04710.06020.11770.01050.0382-0.1003-0.03640.00790.28970.0458-0.00340.255-0.01240.23654.6339-61.2344-11.8419
30.62650.14690.17760.3604-0.16480.6354-0.0732-0.0934-0.11740.11210.02140.01010.08810.04120.03630.33560.07150.02930.27070.00960.2997-25.9369-48.6517-13.8355
40.47830.04110.12990.6266-0.2630.57430.00140.121-0.0343-0.0792-0.0121-0.0610.03160.09370.02210.25220.03940.01740.29070.00830.2265-16.9885-39.6119-32.4004
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 314 )A174 - 314
3X-RAY DIFFRACTION3chain 'B' and (resid 38 through 173 )B38 - 173
4X-RAY DIFFRACTION4chain 'B' and (resid 174 through 314 )B174 - 314

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