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- PDB-8p4g: Crystal structure of a multicopper oxidase 3F3 variant from Pyrob... -

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Basic information

Entry
Database: PDB / ID: 8p4g
TitleCrystal structure of a multicopper oxidase 3F3 variant from Pyrobaculum aerophilum
ComponentsMulticopper oxidase
KeywordsOXIDOREDUCTASE / hyperthermophiles / metallo-oxidases / laccases / enzyme engineering / biocatalysis
Function / homology
Function and homology information


oxidoreductase activity / copper ion binding / membrane
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 / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / Multicopper oxidase
Similarity search - Component
Biological speciesPyrobaculum aerophilum str. IM2 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsBorges, P.T. / Brissos, V. / Frazao, C. / Martins, L.O.
Funding support Portugal, 1items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a Tecnologia Portugal
CitationJournal: J.Biol.Inorg.Chem. / Year: 2024
Title: Flexible active-site loops fine-tune substrate specificity of hyperthermophilic metallo-oxidases.
Authors: Brissos, V. / Borges, P.T. / Sancho, F. / Lucas, M.F. / Frazao, C. / Conzuelo, F. / Martins, L.O.
History
DepositionMay 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 21, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multicopper oxidase
B: Multicopper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,14011
Polymers97,5962
Non-polymers5449
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2880 Å2
ΔGint-89 kcal/mol
Surface area30450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.395, 128.395, 124.965
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Multicopper oxidase /


Mass: 48797.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum str. IM2 (archaea)
Gene: PAE1888 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8ZWA8
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.55 Å3/Da / Density % sol: 51.71 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 2.0 M Ammonium sulfate, 0.1 M Sodium HEPES pH 7.5, and 2 % (v/v) PEG 400.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 11, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.59→73.45 Å / Num. obs: 32726 / % possible obs: 99.1 % / Redundancy: 5.5 % / CC1/2: 0.986 / Net I/σ(I): 7.48
Reflection shellResolution: 2.59→2.69 Å / Num. unique obs: 5178 / CC1/2: 0.322

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
XDSdata reduction
XDSdata scaling
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→73.45 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 25.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2597 500 1.53 %
Rwork0.2131 --
obs0.2138 32700 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→73.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6785 0 1 142 6928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026985
X-RAY DIFFRACTIONf_angle_d0.5779513
X-RAY DIFFRACTIONf_dihedral_angle_d16.6632571
X-RAY DIFFRACTIONf_chiral_restr0.0451048
X-RAY DIFFRACTIONf_plane_restr0.0041239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.850.35291240.3367914X-RAY DIFFRACTION99
2.85-3.270.35231280.28087981X-RAY DIFFRACTION100
3.27-4.110.20231260.20368070X-RAY DIFFRACTION100
4.11-73.450.25141220.16818235X-RAY DIFFRACTION98
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)
12.0904-0.52881.22892.16430.18792.07940.11840.159-0.2822-0.13910.01690.02650.31540.0488-0.10380.5219-0.01490.0140.47250.02140.4343-42.7267-1.1917-22.2536
20.8913-0.14960.92082.0755-1.75193.673-0.0099-0.0451-0.00620.03480.01350.009-0.1218-0.1644-0.02850.4014-0.0152-0.00740.5645-0.02280.422-46.622911.4081-11.3783
31.74180.111-0.26731.87750.52061.6885-0.003-0.15160.1570.08440.1037-0.0671-0.05630.2617-0.07810.37360.0133-0.02190.5342-0.01490.3862-39.031511.7761-0.7481
41.39420.2911-1.12861.9445-0.68872.580.0649-0.0314-0.0702-0.0015-0.1121-0.40830.02670.50290.07940.3801-0.0283-0.08570.5697-0.04910.5669-26.51918.2114-12.2828
51.87650.09050.42082.048-0.01993.04170.01050.04630.1119-0.14190.025-0.4838-0.08310.4834-0.04660.3683-0.0190.07120.49280.02220.5184-25.452512.5427-20.1031
61.8863-0.06950.59851.368-0.56042.47610.0143-0.2818-0.01790.00490.00160.277-0.0532-0.3177-0.00060.4637-0.008-0.04810.4794-0.02120.4751-69.958420.7118-35.0106
71.5878-0.3494-0.19050.8928-0.30632.46590.130.03010.0803-0.1211-0.079-0.0509-0.0459-0.0175-0.02080.4889-00.0090.351-0.00080.4133-59.82324.5544-52.1058
83.93962.27132.90674.9824.32876.4948-0.16270.36590.1577-0.20860.24-0.3508-0.14860.7785-0.02670.48570.01670.06260.49010.08020.4307-49.692224.757-55.7099
90.71320.20020.29882.09730.88622.8979-0.04870.03270.2086-0.25-0.04930.1263-0.6182-0.01120.05330.57260.01740.07770.5804-0.00310.6478-64.341238.6047-45.0074
102.3565-0.49070.060.7915-0.17933.28480.0882-0.27730.4732-0.1093-0.03180.0608-0.4787-0.1239-0.03960.5463-0.0462-0.01140.3996-0.05710.5491-60.326140.6146-37.2223
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 38:154)
2X-RAY DIFFRACTION2(chain A and resid 155:208)
3X-RAY DIFFRACTION3(chain A and resid 209:318)
4X-RAY DIFFRACTION4(chain A and resid 319:357)
5X-RAY DIFFRACTION5(chain A and resid 358:477)
6X-RAY DIFFRACTION6(chain B and resid 38:154)
7X-RAY DIFFRACTION7(chain B and resid 155:278)
8X-RAY DIFFRACTION8(chain B and resid 279:318)
9X-RAY DIFFRACTION9(chain B and resid 319:357)
10X-RAY DIFFRACTION10(chain B and resid 358:477)

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