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

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Basic information

Entry
Database: PDB / ID: 7rab
TitleCrystal structure of a dodecameric multicopper oxidase from M. hydrothermalis in a cubic 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: 1.92 Å
AuthorsGeorgiadis, M.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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)316,60932
Polymers315,3988
Non-polymers1,21124
Water11,151619
1
A: multicopper oxidase
C: multicopper oxidase
E: multicopper oxidase
H: multicopper oxidase
hetero molecules

A: multicopper oxidase
C: multicopper oxidase
E: multicopper oxidase
H: multicopper oxidase
hetero molecules

A: multicopper oxidase
C: multicopper oxidase
E: multicopper oxidase
H: multicopper oxidase
hetero molecules


  • defined by author&software
  • Evidence: gel filtration, The protein elutes with a molecular weight that is larger than a trimer but smaller than a hexamer. Within the asymmetric unit, there are 8 molecules; two trimers and two ...Evidence: gel filtration, The protein elutes with a molecular weight that is larger than a trimer but smaller than a hexamer. Within the asymmetric unit, there are 8 molecules; two trimers and two single subunits. These chains along with symmetry mates generate two dodecamers in the A.U. Each single subunit (chains F and A) with its symmetry mates comprises a second trimer. Symmetry mates of each trimer (CEH or BGD) make up the remaining two trimers that form a dodecamer.
  • 475 kDa, 12 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)474,91448
Polymers473,09712
Non-polymers1,81736
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
MethodPISA
2
B: multicopper oxidase
D: multicopper oxidase
F: multicopper oxidase
G: multicopper oxidase
hetero molecules

B: multicopper oxidase
D: multicopper oxidase
F: multicopper oxidase
G: multicopper oxidase
hetero molecules

B: multicopper oxidase
D: multicopper oxidase
F: multicopper oxidase
G: multicopper oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)474,91448
Polymers473,09712
Non-polymers1,81736
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555z,x,y1
crystal symmetry operation9_555y,z,x1
MethodPISA
Unit cell
Length a, b, c (Å)224.241, 224.241, 224.241
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11H-563-

HOH

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Components

#1: Protein
multicopper oxidase


Mass: 39424.773 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Marinithermus hydrothermalis (bacteria)
Gene: Marky_0543 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta / References: UniProt: F2NNS0, laccase
#2: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 619 / 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: 2.98 Å3/Da / Density % sol: 58.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 0.1 M HEPES 7.5, 25% PEG 335
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 1.37623 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.37623 Å / Relative weight: 1
ReflectionResolution: 1.915→129.47 Å / Num. obs: 284806 / % possible obs: 99.7 % / Redundancy: 39 % / Biso Wilson estimate: 27.16 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.17 / Rpim(I) all: 0.028 / Rrim(I) all: 0.173 / Net I/σ(I): 10.6
Reflection shell

Diffraction-ID: 1 / % possible all: 99.8

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs
1.92-2.0240.21.6041665919414390.9620.2561.6252.5
6.06-129.4738.60.066362861941010.0110.06727.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.13_2998refinement
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GDC_A

Resolution: 1.92→56.06 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 43.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2983 13962 4.99 %
Rwork0.2701 265961 -
obs0.2715 279923 98.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.94 Å2 / Biso mean: 30.3317 Å2 / Biso min: 15.65 Å2
Refinement stepCycle: final / Resolution: 1.92→56.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19324 0 24 619 19967
Biso mean--47.81 32.46 -
Num. residues----2392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00720176
X-RAY DIFFRACTIONf_angle_d0.89427544
X-RAY DIFFRACTIONf_dihedral_angle_d3.57215944
X-RAY DIFFRACTIONf_chiral_restr0.062776
X-RAY DIFFRACTIONf_plane_restr0.0073664
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.92-1.93690.39624420.3633898599
1.9369-1.95970.37444760.3461895499
1.9597-1.98360.3754200.3377900399
1.9836-2.00870.36844910.3366888299
2.0087-2.03510.37614880.3317895799
2.0351-2.0630.38054840.3317891099
2.063-2.09250.35554060.32639027100
2.0925-2.12370.34344730.3182889799
2.1237-2.15690.33464600.3119896999
2.1569-2.19230.32714540.3086884299
2.1923-2.23010.33294430.3029893099
2.2301-2.27060.34784540.2967891899
2.2706-2.31430.30965800.2935881699
2.3143-2.36150.32894960.2842885899
2.3615-2.41290.32344830.2865889999
2.4129-2.4690.33334840.2915884098
2.469-2.53070.35274610.2881883098
2.5307-2.59920.30284580.2902888398
2.5992-2.67560.32074290.2779881097
2.6756-2.7620.32594330.2823882397
2.762-2.86070.32015130.2746881498
2.8607-2.97530.31254780.2825877798
2.9753-3.11070.30684450.2847882397
3.1107-3.27460.31694350.2823874697
3.2746-3.47980.29674210.2715883897
3.4798-3.74840.28974420.262876996
3.7484-4.12550.24974790.233877897
4.1255-4.72220.23244440.2104879796
4.7222-5.94840.25475250.2206884197
5.9484-56.060.23154650.2244874593

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