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- PDB-6xiz: Crystal structure of multi-copper oxidase from Pediococcus acidil... -

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Basic information

Entry
Database: PDB / ID: 6xiz
TitleCrystal structure of multi-copper oxidase from Pediococcus acidilactici
ComponentsCopper oxidase
KeywordsOXIDOREDUCTASE / LACCASE / COPPER OXIDASE / ACOUSTIC DROPLET EJECTION / LIGNIN / COMBINATORIAL CRYSTALLIZATION
Function / homology
Function and homology information


bilirubin oxidase activity / bilirubin oxidase / copper ion binding
Similarity search - Function
Multicopper oxidases, conserved site / Multicopper oxidases signature 1. / Multicopper oxidase, copper-binding site / Multicopper oxidases signature 2. / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, type 1 / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxin
Similarity search - Domain/homology
BENZAMIDINE / CU-O-CU LINKAGE / COPPER (II) ION / Bilirubin oxidase
Similarity search - Component
Biological speciesPediococcus acidilactici (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsPardo, I. / Soares, A.S. / Collins, R. / Partowmah, S.H. / Coler, E.A.
Funding support United States, 6items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P41GM111244 United States
Department of Energy (DOE, United States)KP1605010 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1R21GM129570-01 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1P30GM133893 United States
Department of Energy (DOE, United States)BER- BO 070 United States
Department of Energy (DOE, United States)BES-FWP-PS001 United States
CitationJournal: Microb Biotechnol / Year: 2021
Title: Structural analysis and biochemical properties of laccase enzymes from two Pediococcus species.
Authors: Olmeda, I. / Casino, P. / Collins, R.E. / Sendra, R. / Callejon, S. / Huesa, J. / Soares, A.S. / Ferrer, S. / Pardo, I.
History
DepositionJun 22, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2021Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: 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
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)109,50211
Polymers108,7702
Non-polymers7319
Water10,971609
1
A: Copper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6915
Polymers54,3851
Non-polymers3064
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Copper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,8116
Polymers54,3851
Non-polymers4265
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.060, 147.300, 65.460
Angle α, β, γ (deg.)90.00, 98.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Copper oxidase


Mass: 54385.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pediococcus acidilactici (bacteria) / Gene: BTW26_06860, FEZ49_06610 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1A5VCP7

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Non-polymers , 5 types, 618 molecules

#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-C2O / CU-O-CU LINKAGE / Copper(I) oxide


Mass: 143.091 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 609 / 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: 2.47 Å3/Da / Density % sol: 50.22 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop
Details: 52.5 nL drop composed of 95 mM Sodium Citrate buffer, pH 3.0, 3% polyethylene glycol 8000, 7.8% polyethylene glycol 400, 1.2% dimethyl sulfoxide, 114 mM benzamidine hydrochloride, and 5.0-10. ...Details: 52.5 nL drop composed of 95 mM Sodium Citrate buffer, pH 3.0, 3% polyethylene glycol 8000, 7.8% polyethylene glycol 400, 1.2% dimethyl sulfoxide, 114 mM benzamidine hydrochloride, and 5.0-10.0 mg/mL protein in 5 mM Tris-HCL pH 7.2 Mylar was initially used as the surface, resulting in thin polycrystalline needles. Changing the surface to COC (cyclic olefin copolymer) resulted in large high-quality single crystals.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9202 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9202 Å / Relative weight: 1
ReflectionResolution: 1.78→73.65 Å / Num. obs: 98773 / % possible obs: 98.3 % / Redundancy: 25.53 % / CC1/2: 0.999 / Rmerge(I) obs: 0.185 / Net I/σ(I): 10.37
Reflection shellResolution: 1.78→1.82 Å / Rmerge(I) obs: 0.4263 / Mean I/σ(I) obs: 0.71 / Num. unique obs: 5726 / CC1/2: 0.476 / % possible all: 77.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.8→73.65 Å / Cor.coef. Fo:Fc: 0.988 / Cor.coef. Fo:Fc free: 0.98 / SU B: 6.337 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.144 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.161 4742 4.9 %RANDOM
Rwork0.1139 ---
obs0.11624 92098 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.028 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å2-0 Å21 Å2
2---0.23 Å2-0 Å2
3----0.48 Å2
Refinement stepCycle: 1 / Resolution: 1.8→73.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7622 0 21 609 8252
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.030.0197913
X-RAY DIFFRACTIONr_bond_other_d0.0030.027316
X-RAY DIFFRACTIONr_angle_refined_deg2.5791.94110777
X-RAY DIFFRACTIONr_angle_other_deg1.275316870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5735959
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.00724.629404
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.097151276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0551539
X-RAY DIFFRACTIONr_chiral_restr0.20.21143
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0219063
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021865
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.9784.2213824
X-RAY DIFFRACTIONr_mcbond_other5.9584.2193823
X-RAY DIFFRACTIONr_mcangle_it6.6136.3194787
X-RAY DIFFRACTIONr_mcangle_other6.6146.3214788
X-RAY DIFFRACTIONr_scbond_it9.2294.9014089
X-RAY DIFFRACTIONr_scbond_other9.2294.9014090
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.5097.0775991
X-RAY DIFFRACTIONr_long_range_B_refined8.30135.5289098
X-RAY DIFFRACTIONr_long_range_B_other8.22635.1488879
X-RAY DIFFRACTIONr_rigid_bond_restr6.057315229
X-RAY DIFFRACTIONr_sphericity_free29.4635229
X-RAY DIFFRACTIONr_sphericity_bonded18.229515396
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.418 305 -
Rwork0.374 6827 -
obs--99.99 %

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