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- PDB-3sbr: Pseudomonas stutzeri nitrous oxide reductase, P1 crystal form wit... -

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Basic information

Entry
Database: PDB / ID: 3sbr
TitlePseudomonas stutzeri nitrous oxide reductase, P1 crystal form with substrate
ComponentsNitrous-oxide reductase
KeywordsOXIDOREDUCTASE / beta-propeller / cupredoxin domain / reductase / copper-containing / periplasmic
Function / homology
Function and homology information


nitrous-oxide reductase / nitrous-oxide reductase activity / copper ion import / denitrification pathway / 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. ...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. / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / YVTN repeat-like/Quinoprotein amine dehydrogenase / Cupredoxin / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
DINUCLEAR COPPER ION / [4Cu:2S] cluster / IMIDAZOLE / : / NITROUS OXIDE / Nitrous-oxide reductase
Similarity search - Component
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsPomowski, A. / Zumft, W.G. / Kroneck, P.M.H. / Einsle, O.
CitationJournal: Nature / Year: 2011
Title: N2O binding at a [4Cu:2S] copper-sulphur cluster in nitrous oxide reductase.
Authors: Pomowski, A. / Zumft, W.G. / Kroneck, P.M. / Einsle, O.
History
DepositionJun 6, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Database references
Revision 1.2Sep 21, 2011Group: Database references
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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
G: Nitrous-oxide reductase
H: Nitrous-oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)572,31456
Polymers567,3318
Non-polymers4,98348
Water47,3432628
1
A: Nitrous-oxide reductase
B: Nitrous-oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,95312
Polymers141,8332
Non-polymers1,12010
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12410 Å2
ΔGint-109 kcal/mol
Surface area35450 Å2
MethodPISA
2
C: Nitrous-oxide reductase
D: Nitrous-oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,06614
Polymers141,8332
Non-polymers1,23312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12880 Å2
ΔGint-104 kcal/mol
Surface area36040 Å2
MethodPISA
3
E: Nitrous-oxide reductase
F: Nitrous-oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,16015
Polymers141,8332
Non-polymers1,32713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12770 Å2
ΔGint-98 kcal/mol
Surface area35220 Å2
MethodPISA
4
G: Nitrous-oxide reductase
H: Nitrous-oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,13515
Polymers141,8332
Non-polymers1,30213
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13080 Å2
ΔGint-96 kcal/mol
Surface area35630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.577, 106.453, 130.876
Angle α, β, γ (deg.)111.45, 107.22, 90.72
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 8 molecules ABCDEFGH

#1: Protein
Nitrous-oxide reductase / N(2)OR / N2O reductase


Mass: 70916.406 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Pseudomonas stutzeri (bacteria) / References: UniProt: P19573, EC: 1.7.99.6

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Non-polymers , 8 types, 2676 molecules

#2: Chemical
ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu2
#3: Chemical
ChemComp-CUK / [4Cu:2S] cluster


Mass: 318.314 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu4S2
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#7: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H5N2
#8: Chemical ChemComp-N2O / NITROUS OXIDE / NITROGEN OXIDE


Mass: 44.013 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N2O
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2628 / 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: 2.09 Å3/Da / Density % sol: 41.12 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 16 % PEG 6000, 0.2 M imidazole/malate buffer, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 10, 2010 / Details: mirrors
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.24→95.05 Å / Num. all: 205995 / Num. obs: 194872 / % possible obs: 94.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.8

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FWX

1fwx


Resolution: 2.24→95 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.893 / SU B: 13.963 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R Free: 0.238 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22655 10299 5 %RANDOM
Rwork0.17317 ---
obs0.17584 194872 93.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.219 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å2-0.09 Å2-0.03 Å2
2---0.13 Å2-0.03 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.24→95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36623 0 124 2628 39375
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02237767
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3171.94251151
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.04554685
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.77124.5421790
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.055156368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.96915184
X-RAY DIFFRACTIONr_chiral_restr0.0950.25485
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02129020
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.4741.523253
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.909237611
X-RAY DIFFRACTIONr_scbond_it1.556314514
X-RAY DIFFRACTIONr_scangle_it2.5394.513516
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.24→2.301 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 616 -
Rwork0.377 10888 -
obs--70.31 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0435-0.0362-0.10590.90860.16920.3012-0.03910.02010.0733-0.18970.25910.0250.0146-0.0388-0.220.0663-0.0709-0.04060.11590.07740.158824.1206-9.5015-62.2193
20.06270.0568-0.10190.82170.00410.2261-0.069-0.01190.0471-0.10220.2303-0.0620.04790.0524-0.16130.0593-0.0248-0.00120.1229-0.05050.104438.1401-38.3301-57.599
30.07070.10290.07230.19270.13760.28580.036-0.01610.02380.0147-0.02860.00850.0084-0.0472-0.00750.06360.00150.00780.0781-0.00570.0608-22.513445.9978-53.6173
40.04330.02260.04990.2105-0.09680.25870.0548-0.00060.0006-0.0210.0032-0.0170.11940.0096-0.05790.1368-0.0031-0.04310.04340.00230.0618-13.284414.9641-55.9276
50.05990.0670.04340.2853-0.00480.06630.00110.00970.03060.01720.00320.03360.01320.0078-0.00430.04420.00750.00870.08540.0020.07334.163321.3889-0.443
60.1004-0.00430.04790.2058-0.10770.08120.03470.0187-0.0121-0.0009-0.0292-0.00440.02290.0408-0.00550.06540.0258-0.00740.0814-0.00840.057915.2296-9.19420.4321
70.0838-0.094-0.08150.45030.25990.21950.08690.00570.0169-0.09330.0049-0.108-0.1052-0.0579-0.09180.11170.01830.0620.06130.01590.0973-44.861470.8045-3.3921
80.10220.0579-0.11650.21110.0360.23610.0294-0.0122-0.00020.03740.0523-0.0454-0.00180.0334-0.08170.03080.0124-0.01640.0751-0.00870.106-34.963840.44942.0959
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A58 - 638
2X-RAY DIFFRACTION2B58 - 638
3X-RAY DIFFRACTION3C58 - 638
4X-RAY DIFFRACTION4D51 - 638
5X-RAY DIFFRACTION5E58 - 638
6X-RAY DIFFRACTION6F58 - 638
7X-RAY DIFFRACTION7G54 - 638
8X-RAY DIFFRACTION8H58 - 638

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