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- PDB-9bwf: Crystal structure of cellulose oxidative enzyme without ligand -

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Basic information

Entry
Database: PDB / ID: 9bwf
TitleCrystal structure of cellulose oxidative enzyme without ligand
ComponentsCellulose oxidative enzyme
KeywordsOXIDOREDUCTASE / Carbohydrate oxidase / copper complex
Function / homologyCOPPER (II) ION
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMorais, M.A.B. / Santos, C.A. / Araujo, E.A. / Santos, C.R. / Morao, L.G. / Motta, M.L. / Murakami, M.T.
Funding support Brazil, 1items
OrganizationGrant numberCountry
Sao Paulo Research Foundation (FAPESP)21/04891-3 Brazil
CitationJournal: Nature / Year: 2025
Title: A metagenomic 'dark matter' enzyme catalyses oxidative cellulose conversion.
Authors: Santos, C.A. / Morais, M.A.B. / Mandelli, F. / Lima, E.A. / Miyamoto, R.Y. / Higasi, P.M.R. / Araujo, E.A. / Paixao, D.A.A. / Junior, J.M. / Motta, M.L. / Streit, R.S.A. / Morao, L.G. / ...Authors: Santos, C.A. / Morais, M.A.B. / Mandelli, F. / Lima, E.A. / Miyamoto, R.Y. / Higasi, P.M.R. / Araujo, E.A. / Paixao, D.A.A. / Junior, J.M. / Motta, M.L. / Streit, R.S.A. / Morao, L.G. / Silva, C.B.C. / Wolf, L.D. / Terrasan, C.R.F. / Bulka, N.R. / Diogo, J.A. / Fuzita, F.J. / Colombari, F.M. / Santos, C.R. / Rodrigues, P.T. / Silva, D.B. / Grisel, S. / Bernardes, J.S. / Terrapon, N. / Lombard, V. / Filho, A.J.C. / Henrissat, B. / Bissaro, B. / Berrin, J.G. / Persinoti, G.F. / Murakami, M.T.
History
DepositionMay 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 26, 2025Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Apr 2, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cellulose oxidative enzyme
B: Cellulose oxidative enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,6734
Polymers31,5462
Non-polymers1272
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-45 kcal/mol
Surface area9920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.218, 72.218, 94.943
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Cellulose oxidative enzyme


Mass: 15772.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.27 Å3/Da / Density % sol: 45.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 6.5 / Details: PEGl 8000, 2-methyl-2,4-pentanediol, imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: LNLS SIRIUS / Beamline: MANACA / Wavelength: 1.3699 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3699 Å / Relative weight: 1
ReflectionResolution: 2.2→37.81 Å / Num. obs: 28104 / % possible obs: 100 % / Redundancy: 19.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.149 / Rrim(I) all: 0.157 / Net I/σ(I): 10.05
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.2-2.263.18320860.4543.351
2.26-2.322.66920170.4572.8021
2.32-2.392.64619800.5042.7791
2.39-2.462.33118880.542.4491
2.46-2.542.02418760.6072.1271
2.54-2.631.59117710.6611.6731
2.63-2.731.28517210.8221.3521
2.73-2.840.84916820.9110.8941
2.84-2.970.59916100.940.6321
2.97-3.110.33915090.9770.3591
3.11-3.280.2414860.9880.2531
3.28-3.480.14713540.9960.1551
3.48-3.720.12512890.9960.1321
3.72-4.020.112200.9980.1041
4.02-4.40.0710950.9990.0741
4.4-4.920.0589950.9990.0611
4.92-5.680.0688900.9990.0711
5.68-6.960.0717360.9990.0751
6.96-9.840.055850.9990.0531

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata scaling
XDSJan 10, 2022data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→37.81 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 37.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2724 751 5.01 %
Rwork0.2253 --
obs0.2276 14989 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→37.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1882 0 2 14 1898
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021928
X-RAY DIFFRACTIONf_angle_d0.5542616
X-RAY DIFFRACTIONf_dihedral_angle_d15.254714
X-RAY DIFFRACTIONf_chiral_restr0.046295
X-RAY DIFFRACTIONf_plane_restr0.004327
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.370.43021470.39262781X-RAY DIFFRACTION100
2.37-2.610.41181480.35132801X-RAY DIFFRACTION100
2.61-2.990.36891490.30342835X-RAY DIFFRACTION100
2.99-3.760.26591500.22562845X-RAY DIFFRACTION100
3.76-37.810.22291570.17622976X-RAY DIFFRACTION100
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)
16.4909-3.54252.2518.6782-1.18194.977-0.57640.1526-0.24830.17661.06610.13840.5431-0.4323-0.66040.8836-0.2557-0.03660.59730.10770.7653-32.83056.61384.7968
25.6270.65940.57083.8304-0.99822.8105-0.21520.3611-0.8317-0.04470.3762-0.28280.07320.3283-0.24250.7011-0.1810.0050.3356-0.03020.3785-21.77412.16176.0763
36.55570.4529-0.19516.13832.90928.5102-0.5269-0.2301-0.08670.9120.1044-1.1974-0.46250.93580.44840.7681-0.1525-0.15420.42950.07960.734-14.401219.53988.6293
46.3892-2.89671.90834.4491-0.21053.5729-1.0884-0.2828-0.69370.72290.432-1.1004-0.38160.4770.35410.7976-0.1657-0.00730.35390.00790.5551-19.936412.470210.7252
58.76413.0834-0.18363.6305-2.50933.5392-0.96290.0598-1.1332-1.23160.7388-0.6792-0.20150.45740.12361.0453-0.33880.04880.6166-0.12570.9138-29.44627.0163-3.0608
64.71841.71070.62065.9656-2.60583.3323-0.18450.10050.74020.64490.13520.0299-0.54730.23330.11250.8338-0.17180.03020.34530.13610.5961-26.437529.78537.2075
76.05490.5922-1.4770.40130.14980.602-0.50021.35051.05530.83390.5960.51460.1861-0.464-0.22571.0634-0.0259-0.06060.68350.27650.7632-40.06430.5707-0.3359
86.8723-0.4956-0.61122.9935-1.28062.8691-0.41140.8565-0.76630.1670.60480.65320.2868-0.5665-0.23730.6896-0.2689-0.0140.65340.26260.7189-40.239620.25610.4772
94.05410.0008-1.18761.4547-0.61173.1207-0.33170.71630.7594-0.11640.55330.8413-0.2911-0.5854-0.08460.8709-0.1346-0.03010.43960.1680.6553-30.697629.77744.1072
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 16 )
2X-RAY DIFFRACTION2chain 'A' and (resid 17 through 63 )
3X-RAY DIFFRACTION3chain 'A' and (resid 64 through 83 )
4X-RAY DIFFRACTION4chain 'A' and (resid 84 through 99 )
5X-RAY DIFFRACTION5chain 'A' and (resid 100 through 115 )
6X-RAY DIFFRACTION6chain 'B' and (resid -2 through 35 )
7X-RAY DIFFRACTION7chain 'B' and (resid 36 through 48 )
8X-RAY DIFFRACTION8chain 'B' and (resid 49 through 83 )
9X-RAY DIFFRACTION9chain 'B' and (resid 84 through 115 )

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