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- PDB-1qni: Crystal Structure of Nitrous Oxide Reductase from Pseudomonas nau... -

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Basic information

Entry
Database: PDB / ID: 1qni
TitleCrystal Structure of Nitrous Oxide Reductase from Pseudomonas nautica, at 2.4A Resolution
ComponentsNITROUS-OXIDE REDUCTASE
KeywordsOXIDOREDUCTASE / DENITRIFICATION / MAD / ELECTRON TRANSFER
Function / homology
Function and homology information


nitrous-oxide reductase activity / cytochrome-c oxidase activity / periplasmic space / copper ion binding / calcium ion binding / membrane
Similarity search - Function
Nitrous-oxide reductase / Nitrous-oxide reductase, C-terminal / Nitrous oxide reductase, propeller repeat 1 / Nitrous oxide reductase, propeller repeat 2 / Nitrous oxide reductase propeller repeat / Nitrous oxide reductase propeller repeat 2 / Nitrous oxide reductase, N-terminal / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome c oxidase subunit II-like C-terminal ...Nitrous-oxide reductase / Nitrous-oxide reductase, C-terminal / Nitrous oxide reductase, propeller repeat 1 / Nitrous oxide reductase, propeller repeat 2 / Nitrous oxide reductase propeller repeat / Nitrous oxide reductase propeller repeat 2 / Nitrous oxide reductase, N-terminal / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Cupredoxins - blue copper proteins / Cupredoxin / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DINUCLEAR COPPER ION / (MU-4-SULFIDO)-TETRA-NUCLEAR COPPER ION / Oxidoreductase
Similarity search - Component
Biological speciesPSEUDOMONAS NAUTICA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.4 Å
AuthorsBrown, K. / Tegoni, M. / Cambillau, C.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: A novel type of catalytic copper cluster in nitrous oxide reductase.
Authors: Brown, K. / Tegoni, M. / Prudencio, M. / Pereira, A.S. / Besson, S. / Moura, J.J. / Moura, I. / Cambillau, C.
History
DepositionOct 15, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jun 26, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Experimental preparation / Other
Category: atom_site / citation ...atom_site / citation / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.pdbx_auth_atom_name / _citation.page_last / _citation.title / _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.ptnr1_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NITROUS-OXIDE REDUCTASE
B: NITROUS-OXIDE REDUCTASE
C: NITROUS-OXIDE REDUCTASE
D: NITROUS-OXIDE REDUCTASE
E: NITROUS-OXIDE REDUCTASE
F: NITROUS-OXIDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)394,55536
Polymers391,3816
Non-polymers3,17430
Water23,6001310
1
A: NITROUS-OXIDE REDUCTASE
B: NITROUS-OXIDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,51812
Polymers130,4602
Non-polymers1,05810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13750 Å2
ΔGint-101.4 kcal/mol
Surface area42760 Å2
MethodPQS
2
C: NITROUS-OXIDE REDUCTASE
D: NITROUS-OXIDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,51812
Polymers130,4602
Non-polymers1,05810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13540 Å2
ΔGint-99.9 kcal/mol
Surface area42800 Å2
MethodPQS
3
E: NITROUS-OXIDE REDUCTASE
F: NITROUS-OXIDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,51812
Polymers130,4602
Non-polymers1,05810
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13470 Å2
ΔGint-96 kcal/mol
Surface area43160 Å2
MethodPQS
Unit cell
Length a, b, c (Å)211.290, 211.290, 166.457
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.9266, -0.24422, -0.28597), (-0.24636, -0.18031, 0.95226), (-0.28412, 0.95281, 0.10691)181.73224, 122.57094, -58.75915
2given(0.83031, -0.17162, -0.53022), (-0.47625, -0.7126, -0.51515), (-0.28942, 0.68025, -0.67342)-22.18087, 137.6907, -61.4898
3given(-0.57425, -0.67752, -0.45956), (0.76445, -0.24285, -0.5972), (0.29301, -0.69425, 0.65739)138.6917, -6.33528, 8.7709
4given(0.03797, 0.2788, 0.9596), (0.91125, -0.40375, 0.08125), (0.41009, 0.87135, -0.26939)82.62242, -16.00419, -134.53084
5given(-0.37888, 0.85383, 0.35696), (-0.76352, -0.07043, -0.64193), (-0.52296, -0.51577, 0.6786)67.70197, 94.71862, 63.40869
DetailsTHERE ARE 3 COPIES OF THE BIOMOLECULE WHICH CONSISTS OFA HOMO-DIMERIC-COMPLEX OF BIOPOLYMERS

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
NITROUS-OXIDE REDUCTASE /


Mass: 65230.176 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) PSEUDOMONAS NAUTICA (bacteria) / Cellular location: PERIPLASM / References: UniProt: Q7SIA3*PLUS

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Non-polymers , 5 types, 1340 molecules

#2: Chemical
ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu2
#3: Chemical
ChemComp-CUZ / (MU-4-SULFIDO)-TETRA-NUCLEAR COPPER ION


Mass: 286.249 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu4S
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1310 / Source method: isolated from a natural source / Formula: H2O

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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: 2.74 Å3/Da / Density % sol: 48 %
Crystal growMethod: vapor diffusion / pH: 9.5 / Details: pH 9.50
Crystal grow
*PLUS
pH: 7.6 / Method: vapor diffusion
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15 mg/mlprotein1drop
2100 mMTris-HCl1drop
318 %PEG40001reservoir
40.1 MBicine1reservoir
50.6 M1reservoirNaCl
615 %isopropano;1reservoir
710 mMspermine-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.8850, 1.3751, 1.3793
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.8851
21.37511
31.37931
ReflectionResolution: 2.9→30 Å / Num. obs: 92030 / % possible obs: 100 % / Redundancy: 3.7 % / Biso Wilson estimate: 44.8 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 7.3
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 1.6 / Rsym value: 0.236 / % possible all: 100
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALAdata scaling
CNS0.9phasing
RefinementMethod to determine structure: MAD / Resolution: 2.4→20 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 4539041.77 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.261 2683 1.8 %RANDOM
Rwork0.2277 ---
obs0.2277 148914 90.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.8973 Å2 / ksol: 0.301225 e/Å3
Displacement parametersBiso mean: 59.9 Å2
Baniso -1Baniso -2Baniso -3
1-11.863 Å2-0.441 Å20 Å2
2--11.863 Å20 Å2
3----23.726 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27078 0 60 1310 28448
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.8461.5
X-RAY DIFFRACTIONc_mcangle_it1.4052
X-RAY DIFFRACTIONc_scbond_it1.4432
X-RAY DIFFRACTIONc_scangle_it2.1682.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.369 431 1.8 %
Rwork0.323 23576 -
obs--88.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.82

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