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- PDB-6rl0: Recombinant Pseudomonas stutzeri nitrous oxide reductase, form I -

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Basic information

Entry
Database: PDB / ID: 6rl0
TitleRecombinant Pseudomonas stutzeri nitrous oxide reductase, form I
ComponentsNitrous-oxide reductase
KeywordsMETAL BINDING PROTEIN / denitrification / cofactor biogenesis
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 / : / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Copper centre Cu(A) ...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 / : / Twin-arginine translocation pathway, signal sequence, bacterial/archaeal / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / 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 / FORMIC ACID / : / Nitrous-oxide reductase
Similarity search - Component
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
AuthorsZhang, L. / Wuest, A. / Prasser, B. / Mueller, C. / Einsle, O.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Research Council310656 Germany
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Functional assembly of nitrous oxide reductase provides insights into copper site maturation.
Authors: Zhang, L. / Wust, A. / Prasser, B. / Muller, C. / Einsle, O.
History
DepositionApr 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 24, 2024Group: 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_ncs_dom_lim
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_alt_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,35737
Polymers283,6664
Non-polymers3,69233
Water26,2121455
1
A: Nitrous-oxide reductase
D: Nitrous-oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,65618
Polymers141,8332
Non-polymers1,82316
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nitrous-oxide reductase
C: Nitrous-oxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,70219
Polymers141,8332
Non-polymers1,86917
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.916, 73.372, 136.342
Angle α, β, γ (deg.)90.00, 95.07, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUALAALAAA55 - 63855 - 638
21GLUGLUALAALABB55 - 63855 - 638
12LYSLYSPROPROAA57 - 63757 - 637
22LYSLYSPROPROCC57 - 63757 - 637
13GLNGLNPROPROAA58 - 63758 - 637
23GLNGLNPROPRODD58 - 63758 - 637
14LYSLYSPROPROBB57 - 63757 - 637
24LYSLYSPROPROCC57 - 63757 - 637
15GLNGLNPROPROBB58 - 63758 - 637
25GLNGLNPROPRODD58 - 63758 - 637
16GLNGLNPROPROCC58 - 63758 - 637
26GLNGLNPROPRODD58 - 63758 - 637

NCS ensembles :
IDDetails
5B, D
1A, B
2A, C
3A, D
4B, C
6C, D

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Components

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Protein , 1 types, 4 molecules ABCD

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


Mass: 70916.406 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas stutzeri (bacteria) / Gene: nosZ / Production host: Escherichia coli (E. coli) / References: UniProt: P19573, nitrous-oxide reductase

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Non-polymers , 9 types, 1488 molecules

#2: Chemical
ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-CUK / [4Cu:2S] cluster


Mass: 318.314 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu4S2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical
ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu2
#7: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CH2O2
#8: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#9: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1455 / 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 % sol: 35.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M bis-tris propane buffer at pH 8.5, 0.1 M sodium formate, 0.1 M sodium chloride, and 25% (w/v) of a medium molecular weight (MMW) polyethylene glycol mixture (PEG 2K, 3350, 4K and 5K MME)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.36999 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.36999 Å / Relative weight: 1
ReflectionResolution: 1.78→48.91 Å / Num. obs: 205189 / % possible obs: 100 % / Redundancy: 13 % / Net I/σ(I): 15.7
Reflection shellResolution: 1.78→1.81 Å / Num. unique obs: 205189

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SBQ

3sbq


Resolution: 1.78→48.91 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.961 / SU B: 4.71 / SU ML: 0.076 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19225 10243 5 %RANDOM
Rwork0.157 ---
obs0.15876 194905 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 28.816 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å2-0 Å20.33 Å2
2--0.04 Å20 Å2
3---0.48 Å2
Refinement stepCycle: 1 / Resolution: 1.78→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18329 0 139 1455 19923
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.01918980
X-RAY DIFFRACTIONr_bond_other_d0.0010.0217198
X-RAY DIFFRACTIONr_angle_refined_deg1.9461.94325691
X-RAY DIFFRACTIONr_angle_other_deg0.95340046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.22652351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32524.545902
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89153195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3461592
X-RAY DIFFRACTIONr_chiral_restr0.1450.22755
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02121176
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023816
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_it2.0042.2739344
X-RAY DIFFRACTIONr_mcbond_other2.0042.2739345
X-RAY DIFFRACTIONr_mcangle_it2.8023.39911679
X-RAY DIFFRACTIONr_mcangle_other2.8033.39911680
X-RAY DIFFRACTIONr_scbond_it2.8492.5989636
X-RAY DIFFRACTIONr_scbond_other2.8382.5989623
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3723.75113989
X-RAY DIFFRACTIONr_long_range_B_refined5.76927.80521097
X-RAY DIFFRACTIONr_long_range_B_other5.7427.49420791
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A197720.08
12B197720.08
21A195900.08
22C195900.08
31A196510.08
32D196510.08
41B195130.09
42C195130.09
51B195440.08
52D195440.08
61C196220.07
62D196220.07
LS refinement shellResolution: 1.78→1.826 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 786 -
Rwork0.269 14322 -
obs--100 %
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)
10.06160.01540.01770.29760.06340.16780.0053-0.00730.0020.0135-0.01430.0307-0.01-0.01280.0090.0246-0.0099-0.00320.0391-0.0010.004111.8019-1.460759.1375
20.0531-0.014-0.03570.23650.05210.12470.0015-0.0002-0.0080.0446-0.00370.0247-0.0128-0.00320.00220.0513-0.0146-0.0040.03140.00310.006417.5548-1.0831-7.2091
30.0517-0.0837-0.03050.22070.00050.12870.0044-0.00210.008-0.0084-0.0068-0.0476-0.00670.06070.00240.0154-0.0138-0.00470.05390.00350.021340.1825-19.7514-21.0977
40.044-0.0462-0.00750.5402-0.04020.1660.0075-0.011-0.0024-0.0687-0.0111-0.1376-0.00280.06550.00360.0092-0.00130.01740.050.00430.040835.6716-20.087647.5382
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A55 - 638
2X-RAY DIFFRACTION2B55 - 638
3X-RAY DIFFRACTION3C57 - 638
4X-RAY DIFFRACTION4D58 - 638

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