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- PDB-9cck: Multi-copper oxidase with a C-terminal cupredoxin domain from Nit... -

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Basic information

Entry
Database: PDB / ID: 9cck
TitleMulti-copper oxidase with a C-terminal cupredoxin domain from Nitrosopumilus maritimus
Components(Copper-containing nitrite reductase) x 2
KeywordsOXIDOREDUCTASE / Copper / trinuclear / hydroxylamine / cupredoxin
Function / homology
Function and homology information


nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / electron transfer activity / oxidoreductase activity / copper ion binding / membrane
Similarity search - Function
: / Nitrite reductase, copper-type / Blue (type 1) copper domain / Copper binding proteins, plastocyanin/azurin family / Multicopper oxidase, C-terminal / Multicopper oxidase / Multicopper oxidase, N-terminal / Multicopper oxidase / Cupredoxin
Similarity search - Domain/homology
COPPER (II) ION / Copper-containing nitrite reductase
Similarity search - Component
Biological speciesNitrosopumilus maritimus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsVoland, R.W. / Lancaster, K.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM124908 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Nitrous oxide production via enzymatic nitroxyl from the nitrifying archaeon Nitrosopumilus maritimus.
Authors: Voland, R.W. / Wang, H. / Abruna, H.D. / Lancaster, K.M.
History
DepositionJun 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Copper-containing nitrite reductase
B: Copper-containing nitrite reductase
C: Copper-containing nitrite reductase
D: Copper-containing nitrite reductase
E: Copper-containing nitrite reductase
F: Copper-containing nitrite reductase
G: Copper-containing nitrite reductase
H: Copper-containing nitrite reductase
I: Copper-containing nitrite reductase
J: Copper-containing nitrite reductase
K: Copper-containing nitrite reductase
L: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)510,88068
Polymers507,32212
Non-polymers3,55956
Water69,6643867
1
A: Copper-containing nitrite reductase
B: Copper-containing nitrite reductase
C: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,72017
Polymers126,8303
Non-polymers89014
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Copper-containing nitrite reductase
E: Copper-containing nitrite reductase
F: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,72017
Polymers126,8303
Non-polymers89014
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Copper-containing nitrite reductase
H: Copper-containing nitrite reductase
I: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,72017
Polymers126,8303
Non-polymers89014
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: Copper-containing nitrite reductase
K: Copper-containing nitrite reductase
L: Copper-containing nitrite reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,72017
Polymers126,8303
Non-polymers89014
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)173.292, 92.976, 204.483
Angle α, β, γ (deg.)90.000, 95.791, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Copper-containing nitrite reductase


Mass: 45943.699 Da / Num. of mol.: 8 / Fragment: residues 36-444
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosopumilus maritimus (archaea) / Gene: Nmar_1354 / Production host: Escherichia coli (E. coli) / References: UniProt: A9A2L1, nitrite reductase (NO-forming)
#2: Protein
Copper-containing nitrite reductase


Mass: 34942.988 Da / Num. of mol.: 4 / Fragment: residues 36-344
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosopumilus maritimus (archaea) / Gene: Nmar_1354 / Production host: Escherichia coli (E. coli) / References: UniProt: A9A2L1, nitrite reductase (NO-forming)
#3: Chemical...
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 56 / Source method: obtained synthetically / Formula: Cu / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3867 / 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: 3.23 Å3/Da / Density % sol: 61.93 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: potassium phosphate dibasic, BIS-TRIS propane, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.84→138.61 Å / Num. obs: 556905 / % possible obs: 99.1 % / Redundancy: 3.5 % / Biso Wilson estimate: 24.36 Å2 / CC1/2: 0.983 / Rpim(I) all: 0.135 / Rrim(I) all: 0.355 / Net I/av σ(I): 6.4 / Net I/σ(I): 1.31
Reflection shellResolution: 1.84→1.87 Å / Mean I/σ(I) obs: 0.9 / Num. unique obs: 27367 / CC1/2: 0.42 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.84→84.56 Å / SU ML: 0.2409 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.0063
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2258 27653 4.99 %
Rwork0.1988 526801 -
obs0.2002 554454 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.03 Å2
Refinement stepCycle: LAST / Resolution: 1.84→84.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms35764 0 56 3867 39687
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008336868
X-RAY DIFFRACTIONf_angle_d1.003950344
X-RAY DIFFRACTIONf_chiral_restr0.06475364
X-RAY DIFFRACTIONf_plane_restr0.00826620
X-RAY DIFFRACTIONf_dihedral_angle_d7.15634844
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.860.37718880.359216870X-RAY DIFFRACTION95.69
1.86-1.880.36599130.3517135X-RAY DIFFRACTION97.55
1.88-1.910.36188990.337117375X-RAY DIFFRACTION98.33
1.91-1.930.36059210.331817430X-RAY DIFFRACTION98.77
1.93-1.950.34369250.322817441X-RAY DIFFRACTION99.03
1.95-1.980.33429310.310917534X-RAY DIFFRACTION99.19
1.98-2.010.32349200.291417462X-RAY DIFFRACTION99.07
2.01-2.040.31459170.277617508X-RAY DIFFRACTION99.17
2.04-2.070.28389440.258917520X-RAY DIFFRACTION99.25
2.07-2.110.27368820.243317519X-RAY DIFFRACTION99.22
2.11-2.140.27769250.244117511X-RAY DIFFRACTION99.29
2.14-2.180.26569630.230917497X-RAY DIFFRACTION99.09
2.18-2.220.27078860.232317628X-RAY DIFFRACTION99.28
2.22-2.270.27388860.228717621X-RAY DIFFRACTION99.41
2.27-2.320.25659150.227717574X-RAY DIFFRACTION99.33
2.32-2.370.2548980.226217512X-RAY DIFFRACTION99.06
2.37-2.430.26949240.231517344X-RAY DIFFRACTION98.39
2.43-2.50.23559170.209317696X-RAY DIFFRACTION99.73
2.5-2.570.24569020.206417651X-RAY DIFFRACTION99.8
2.57-2.650.22249370.191817733X-RAY DIFFRACTION99.73
2.65-2.750.23559290.195317544X-RAY DIFFRACTION99.64
2.75-2.860.22679040.191617745X-RAY DIFFRACTION99.72
2.86-2.990.21789770.188717688X-RAY DIFFRACTION99.71
2.99-3.150.22249200.183617678X-RAY DIFFRACTION99.76
3.15-3.340.20259180.172617759X-RAY DIFFRACTION99.72
3.34-3.60.18029400.160417665X-RAY DIFFRACTION99.49
3.6-3.960.17699590.155817642X-RAY DIFFRACTION99.26
3.96-4.540.1589050.137717613X-RAY DIFFRACTION98.53
4.54-5.720.16069840.143917733X-RAY DIFFRACTION99.23
5.72-84.560.19389240.173918173X-RAY DIFFRACTION99.18

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