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- PDB-7rac: Crystal structure of a dodecameric multicopper oxidase from M. hy... -

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Basic information

Entry
Database: PDB / ID: 7rac
TitleCrystal structure of a dodecameric multicopper oxidase from M. hydrothermalis in an orthorhombic lattice
Componentsmulticopper oxidase
KeywordsOXIDOREDUCTASE / multicopper oxidase thermophile dodecamer laccase
Function / homology
Function and homology information


nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / copper ion binding
Similarity search - Function
Nitrite reductase, copper-type / Multicopper oxidase, C-terminal / Multicopper oxidase / 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-containing nitrite reductase
Similarity search - Component
Biological speciesMarinithermus hydrothermalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.36 Å
AuthorsGeorgiadis, M.M. / Ogata, C.M.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Crystal structures of a dodecameric multicopper oxidase from Marinithermus hydrothermalis.
Authors: Paavola, J.L. / Battistin, U. / Ogata, C.M. / Georgiadis, M.M.
History
DepositionJun 30, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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
C: multicopper oxidase
D: multicopper oxidase
E: multicopper oxidase
F: multicopper oxidase
G: multicopper oxidase
H: multicopper oxidase
I: multicopper oxidase
J: multicopper oxidase
K: multicopper oxidase
L: multicopper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)477,90475
Polymers473,09712
Non-polymers4,80663
Water28,2111566
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, Protein elutes from gel filtration column at a size of ~ 200 kDa, larger than expected for a trimer and smaller than a hexamer. Dodecamer is seen in two distinct crystal ...Evidence: gel filtration, Protein elutes from gel filtration column at a size of ~ 200 kDa, larger than expected for a trimer and smaller than a hexamer. Dodecamer is seen in two distinct crystal lattices obtained from completely different precipitant solutions.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)169.304, 176.193, 176.952
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
multicopper oxidase


Mass: 39424.773 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinithermus hydrothermalis (bacteria)
Gene: Marky_0543 / Production host: Escherichia coli (E. coli) / References: UniProt: F2NNS0, laccase
#2: Chemical...
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical...
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1566 / 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: 2.79 Å3/Da / Density % sol: 55.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.2 M CaCl2, 0.1 M Bis-Tris 6.5, 45% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03321 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 2.36→176.95 Å / Num. obs: 216725 / % possible obs: 100 % / Redundancy: 13.5 % / Biso Wilson estimate: 23.05 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.056 / Rrim(I) all: 0.207 / Net I/σ(I): 11.8 / Num. measured all: 2933251 / Scaling rejects: 16
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
2.36-2.412.60.751134625106550.9020.220.7833.9100
12.93-176.9511.80.0831779315030.9970.0250.08721.799.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: M. hydrothermalis MCO

Resolution: 2.36→61.039 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1771 10721 4.95 %
Rwork0.1386 205834 -
obs0.1405 216555 99.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.82 Å2 / Biso mean: 22.4281 Å2 / Biso min: 6.99 Å2
Refinement stepCycle: final / Resolution: 2.36→61.039 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28992 0 217 1570 30779
Biso mean--40.43 26.97 -
Num. residues----3588
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00730425
X-RAY DIFFRACTIONf_angle_d0.89541547
X-RAY DIFFRACTIONf_dihedral_angle_d3.77923964
X-RAY DIFFRACTIONf_chiral_restr0.0574187
X-RAY DIFFRACTIONf_plane_restr0.0065498
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.36-2.38680.25323440.17986812
2.3868-2.41490.25213190.17996842
2.4149-2.44440.23753530.16856805
2.4444-2.47530.22633900.16456749
2.4753-2.50790.23293080.16956784
2.5079-2.54220.23233520.17016826
2.5422-2.57850.23133370.16736872
2.5785-2.6170.23252770.15856868
2.617-2.65790.21223260.1566852
2.6579-2.70150.22863530.15836785
2.7015-2.74810.20463920.166820
2.7481-2.79810.20113380.15696826
2.7981-2.85190.20883920.15646773
2.8519-2.91010.19813730.15826825
2.9101-2.97340.2184180.16096757
2.9734-3.04250.18383160.1496881
3.0425-3.11860.17543040.14666862
3.1186-3.20290.18473370.14236895
3.2029-3.29720.1683490.13676845
3.2972-3.40360.18083560.13346870
3.4036-3.52520.16743400.13166848
3.5252-3.66630.15743550.12466880
3.6663-3.83320.14723830.11276853
3.8332-4.03520.13474440.10356792
4.0352-4.2880.12924050.10316867
4.288-4.6190.1293750.09676894
4.619-5.08360.13024360.10726850
5.0836-5.81870.17563620.14236988
5.8187-7.3290.19863190.15247066
7.329-61.0390.17873680.16517247

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