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- PDB-3sbp: Pseudomonas stutzeri nitrous oxide reductase, P1 crystal form -

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Basic information

Entry
Database: PDB / ID: 3sbp
TitlePseudomonas stutzeri nitrous oxide reductase, P1 crystal form
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. / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal ...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. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Cupredoxins - blue copper proteins / Twin arginine translocation (Tat) signal profile. / Twin-arginine translocation pathway, signal sequence / Cupredoxin / 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 reductase
Similarity search - Component
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 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 1.3Sep 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)572,22654
Polymers567,3318
Non-polymers4,89546
Water53,5052970
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 area12530 Å2
ΔGint-123 kcal/mol
Surface area35620 Å2
MethodPISA
2
C: Nitrous-oxide reductase
D: Nitrous-oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,02213
Polymers141,8332
Non-polymers1,18911
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12680 Å2
ΔGint-101 kcal/mol
Surface area36150 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 area12780 Å2
ΔGint-96 kcal/mol
Surface area35420 Å2
MethodPISA
4
G: Nitrous-oxide reductase
H: Nitrous-oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,09114
Polymers141,8332
Non-polymers1,25812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12900 Å2
ΔGint-100 kcal/mol
Surface area35800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.890, 106.700, 131.139
Angle α, β, γ (deg.)111.34, 107.33, 90.74
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 , 7 types, 3016 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2970 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.56 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 15, 2009 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→46.1 Å / Num. obs: 242775 / % possible obs: 94.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 16.7

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0109refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1FWX

1fwx


Resolution: 2.1→46.02 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.916 / SU B: 12.99 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R Free: 0.208 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23554 12842 5 %RANDOM
Rwork0.17715 ---
obs0.18007 242755 94.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.708 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å2-0.05 Å20.02 Å2
2---0.1 Å2-0.01 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.1→46.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms36623 0 118 2970 39711
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02237763
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.331.94251149
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.98254685
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02124.5421790
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.301156368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.98315184
X-RAY DIFFRACTIONr_chiral_restr0.0940.25485
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02129020
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_it0.471.523253
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.888237611
X-RAY DIFFRACTIONr_scbond_it1.539314510
X-RAY DIFFRACTIONr_scangle_it2.4564.513514
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 942 -
Rwork0.269 17307 -
obs--91.46 %
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)
10.137-0.0944-0.18940.79810.41430.4524-0.0043-0.0060.0527-0.20710.1358-0.0355-0.09660.0107-0.13150.0705-0.03420.01240.06080.03060.057124.1199-9.577-62.4325
20.05460.0573-0.10520.73710.0560.3264-0.0358-0.02440.0261-0.06710.178-0.07970.02660.1115-0.14220.0202-0.00810.00510.1161-0.05770.069438.3051-38.4555-57.8551
30.0740.09090.0730.21120.11680.26990.0209-0.01750.02710.0133-0.01910.01190.0121-0.0582-0.00180.01940.0090.00060.0553-0.00490.0269-22.479845.8813-53.6668
40.0420.01990.00840.2354-0.11670.24460.0336-0.00720.0024-0.02880.0028-0.02510.11790.0047-0.03650.0981-0.0012-0.03350.03070.00140.0296-13.187814.7273-55.9943
50.11340.11090.03060.33380.00850.0859-0.00370.00280.03420.01380.00670.0324-0.0036-0.002-0.0030.00830.017-0.00320.04330.00230.03654.199621.4736-0.4578
60.1210.01610.04370.2875-0.08870.10540.0150.0106-0.0249-0.0064-0.0117-0.03540.02550.0262-0.00330.01980.0256-0.01130.0432-0.00290.027215.3598-9.21520.4778
70.0844-0.0252-0.01730.38890.18380.17690.0527-0.00140.0131-0.06590.0112-0.0367-0.078-0.0316-0.06390.06610.01710.04280.02830.00920.0469-45.177470.9688-3.5345
80.12880.0708-0.12210.29990.04950.23420.0257-0.0192-0.0170.0320.0391-0.047-0.00490.037-0.06480.01610.0153-0.0190.0464-0.00580.0702-35.152240.5052.0474
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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