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- PDB-6ttd: Crystal structure of McoA multicopper oxidase 2F4 variant from th... -

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Basic information

Entry
Database: PDB / ID: 6ttd
TitleCrystal structure of McoA multicopper oxidase 2F4 variant from the hyperthermophile Aquifex aeolicus
ComponentsMulticopper oxidase
KeywordsOXIDOREDUCTASE / multicopper oxidase / hyperthermophiles / Met-rich loops / laccases / directed evolution
Function / homologyCOPPER (II) ION / OXYGEN MOLECULE
Function and homology information
Biological speciesAquifex aeolicus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.801 Å
AuthorsBorges, P.T. / Brissos, V. / Cordeiro, T.N. / Martins, L.O. / Frazao, C.
Funding support Portugal, 3items
OrganizationGrant numberCountry
Fundacao para a Ciencia e a TecnologiaPTDC/BBBEBB/0122/2014 Portugal
Fundacao para a Ciencia e a TecnologiaPTDC/BII-BBF/29564/2017 Portugal
Other governmentLISBOA-01-0145-FEDER-007660 Portugal
CitationJournal: Acs Catalysis / Year: 2022
Title: Distal Mutations Shape Substrate-Binding Sites during Evolution of a Metallo-Oxidase into a Laccase
Authors: Brissos, V. / Borges, P.T. / Nunez-Franco, R. / Lucas, M.F. / Frazao, C. / Monza, E. / Masgrau, L. / Cordeiro, T.N. / Martins, L.O.
History
DepositionDec 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Experimental preparation / Category: database_2 / exptl_crystal_grow
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _exptl_crystal_grow.pdbx_details
Revision 1.2Apr 27, 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 1.3Jan 24, 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

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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)119,91319
Polymers118,6802
Non-polymers1,23317
Water14,268792
1
A: Multicopper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,09811
Polymers59,3401
Non-polymers75910
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Multicopper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8148
Polymers59,3401
Non-polymers4747
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.200, 89.580, 86.850
Angle α, β, γ (deg.)90.000, 106.070, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: CU / End label comp-ID: CU / Auth seq-ID: 45 - 704 / Label seq-ID: 45

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

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Multicopper oxidase


Mass: 59339.926 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: sufI, aq_1130 / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 809 molecules

#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: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 792 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.99 Å3/Da / Density % sol: 38.29 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: One week, 20C, 2 M ammonium sulfate, 15mg/mL protein

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.801→48.22 Å / Num. obs: 169152 / % possible obs: 99 % / Redundancy: 4.1 % / Biso Wilson estimate: 18.05 Å2 / Rrim(I) all: 0.125 / Net I/σ(I): 10.39
Reflection shellResolution: 1.801→1.9 Å / Num. unique obs: 56362 / Rrim(I) all: 0.95

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AW5

3aw5


Resolution: 1.801→48.22 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.68
Details: McoA 2F4 refinement converged to Rwork and Rfree of 0.160 and 0.198, respectively using a Rfree test set size of 1.15% (1922 reflections). The final model was refined versus the full data, ...Details: McoA 2F4 refinement converged to Rwork and Rfree of 0.160 and 0.198, respectively using a Rfree test set size of 1.15% (1922 reflections). The final model was refined versus the full data, resulting in R value of 0.1604.
RfactorNum. reflection% reflection
Rfree0.1604 167176 100 %
Rwork0.1604 --
obs0.1604 167176 98.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.36 Å2 / Biso mean: 25.6795 Å2 / Biso min: 6.65 Å2
Refinement stepCycle: final / Resolution: 1.801→48.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7378 0 74 792 8244
Biso mean--43.14 36.36 -
Num. residues----914
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4501X-RAY DIFFRACTION7.001TORSIONAL
12B4501X-RAY DIFFRACTION7.001TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8011-1.82160.305849030.3058490388
1.8216-1.8430.288656740.28865674100
1.843-1.86550.276756900.27675690100
1.8655-1.88910.270155970.27015597100
1.8891-1.9140.268856300.26885630100
1.914-1.94020.255555970.25555597100
1.9402-1.96790.249356180.24935618100
1.9679-1.99730.240856520.24085652100
1.9973-2.02850.226656190.22665619100
2.0285-2.06180.228256450.22825645100
2.0618-2.09730.210556340.21055634100
2.0973-2.13550.207355620.20735562100
2.1355-2.17650.201356780.20135678100
2.1765-2.2210.188355910.18835591100
2.221-2.26930.184656290.18465629100
2.2693-2.32210.181756560.18175656100
2.3221-2.38010.176656110.17665611100
2.3801-2.44450.17356030.1735603100
2.4445-2.51640.179356250.17935625100
2.5164-2.59760.164756210.16475621100
2.5976-2.69050.160556250.1605562599
2.6905-2.79820.155555770.1555557798
2.7982-2.92550.141853910.1418539197
2.9255-3.07970.134153850.1341538596
3.0797-3.27260.122452490.1224524992
3.2726-3.52520.111855790.1118557999
3.5252-3.87990.10356690.1035669100
3.8799-4.44090.089656120.08965612100
4.4409-5.59380.098756380.09875638100
5.5938-48.220.146956160.14695616100
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)
10.14540.04430.02020.2918-0.00030.0026-0.00380.0315-0.0949-0.0825-0.0075-0.00040.0280.0437-0.00330.09640.00390.00290.1175-0.01130.117168.0097-18.872378.6065
20.0067-0.0098-0.02550.01450.03750.0969-0.03380.0631-0.0523-0.02650.01470.16980.08170.0656-0.00480.0640.0104-0.02980.1315-0.02630.194849.3335-13.911777.9388
30.163-0.137-0.04540.27850.02340.04910.00740.01-0.0399-0.0373-0.01090.02540.02650.0441-0.00090.0648-0.00560.00050.1125-0.00010.09267.4717-12.181279.9586
40.00270.017-0.00640.1012-0.03360.0109-0.0193-0.0412-0.0210.1225-0.0363-0.0301-0.1329-0.0197-0.01210.10190.02080.00130.1333-0.01210.074170.3073-10.742597.2443
50.0782-0.0447-0.02790.0822-0.00040.0136-0.0064-0.03340.02770.0494-0.0106-0.07770.03640.0374-0.01960.0629-0.00560.00020.1294-0.0040.127180.8937-1.729585.9957
60.0532-0.0970.00140.23290.01740.0051-0.015-0.00670.0730.0215-0.0309-0.08580.0126-0.0002-0.02170.04250.0039-0.00530.11730.00610.106379.68662.316485.6434
70.01150.00410.00070.0031-0.00240.0036-0.0270.03910.0353-0.0993-0.0699-0.0319-0.0371-0.065700.11370.00180.00740.15560.0360.110674.83869.875868.0936
80.0610.00670.03340.030.03160.04470.0781-0.0240.22980.01580.05820.2164-0.03920.01460.00140.12790.06750.01790.19010.02140.255950.02428.675582.9385
90.090.1059-0.02310.2054-0.12850.1313-0.0669-0.0646-0.080.10920.03620.20210.0129-0.00550.00350.08170.01010.02130.1560.01840.235244.4391-7.296193.5429
100.18670.0773-0.1140.217-0.10330.16060.00330.00060.03450.03520.01510.1815-0.0618-0.02240.01540.04620.012-0.01140.1116-0.0220.14553.00231.182683.2031
110.1214-0.00740.04980.30160.07610.0528-0.02050.10560.07690.03290.0197-0.0596-0.1504-0.0222-0.00250.2397-0.00020.02390.11640.00740.097588.0247-6.825639.364
120.0002-0.00010.00030.00380.00050.00020.07740.03620.01630.08720.1587-0.0736-0.0280.0540.00030.295-0.012-0.07410.2105-0.01190.2552103.86-12.334748.9918
130.2186-0.26830.13850.4838-0.04840.1622-0.02250.02710.03270.04260.0089-0.0624-0.0962-0.0040.00390.202-0.00360.02170.103-0.00690.0787.5878-13.517240.6467
140.17640.08960.06610.05340.02470.0355-0.1453-0.025-0.06830.143-0.00070.08990.0389-0.0914-0.09650.34050.0460.10770.1643-0.00160.16775.64-15.064853.4192
150.0523-0.07420.01920.11-0.01740.0215-0.01990.028-0.08240.1416-0.00530.2465-0.0584-0.05280.00040.2211-0.00410.03660.1537-0.01650.195372.8363-23.582538.0207
160.1616-0.14140.04170.35070.03440.05560.0404-0.0038-0.10420.1297-0.07220.25980.0786-0.04970.01430.213-0.02720.04780.158-0.02080.176973.7966-27.751638.194
170.00760.0086-0.00280.0096-0.00280.00830.00490.0162-0.0878-0.0102-0.04920.01810.0070.0477-0.00130.25610.04510.02880.1301-0.04210.162487.4532-35.350726.2818
180.36070.09480.1130.1179-0.09040.18650.10250.0167-0.02620.20580.0032-0.17920.11710.05370.00840.4150.1106-0.08690.1869-0.00930.1548100.0792-34.684952.3917
190.0476-0.06910.03330.1717-0.01650.0383-0.038-0.19640.07050.20020.1214-0.11460.0180.0180.00990.50260.0099-0.13110.225-0.02470.208299.0895-19.161764.539
200.30230.28040.01130.82280.0560.2794-0.0269-0.033-0.0550.36510.092-0.21160.09260.02480.32430.3020.0208-0.05240.09910.01130.09197.5225-27.283651.091
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 45:125)A45 - 125
2X-RAY DIFFRACTION2(chain A and resid 126:134)A126 - 134
3X-RAY DIFFRACTION3(chain A and resid 135:218)A135 - 218
4X-RAY DIFFRACTION4(chain A and resid 219:238)A219 - 238
5X-RAY DIFFRACTION5(chain A and resid 239:270)A239 - 270
6X-RAY DIFFRACTION6(chain A and resid 271:377)A271 - 377
7X-RAY DIFFRACTION7(chain A and resid 378:384)A378 - 384
8X-RAY DIFFRACTION8(chain A and resid 385:403)A385 - 403
9X-RAY DIFFRACTION9(chain A and resid 404:422)A404 - 422
10X-RAY DIFFRACTION10(chain A and resid 423:525)A423 - 525
11X-RAY DIFFRACTION11(chain B and resid 45:125)B45 - 125
12X-RAY DIFFRACTION12(chain B and resid 126:134)B126 - 134
13X-RAY DIFFRACTION13(chain B and resid 135:218)B135 - 218
14X-RAY DIFFRACTION14(chain B and resid 219:238)B219 - 238
15X-RAY DIFFRACTION15(chain B and resid 239:270)B239 - 270
16X-RAY DIFFRACTION16(chain B and resid 271:377)B271 - 377
17X-RAY DIFFRACTION17(chain B and resid 378:384)B378 - 384
18X-RAY DIFFRACTION18(chain B and resid 385:403)B385 - 403
19X-RAY DIFFRACTION19(chain B and resid 404:422)B404 - 422
20X-RAY DIFFRACTION20(chain B and resid 423:525)B423 - 525

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