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- PDB-6rkz: Recombinant Pseudomonas stutzeri nitrous oxide reductase, form II -

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Basic information

Entry
Database: PDB / ID: 6rkz
TitleRecombinant Pseudomonas stutzeri nitrous oxide reductase, form II
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. / 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 / (MU-4-SULFIDO)-TETRA-NUCLEAR COPPER ION / FORMIC ACID / : / Nitrous-oxide reductase
Similarity search - Component
Biological speciesPseudomonas stutzeri (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.601 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 / software / struct_conn
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_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_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 / _software.name / _struct_conn.pdbx_dist_value / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,03326
Polymers143,9172
Non-polymers2,11624
Water16,592921
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15040 Å2
ΔGint-122 kcal/mol
Surface area35880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.887, 76.789, 108.823
Angle α, β, γ (deg.)90.00, 93.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 71958.555 Da / Num. of mol.: 2
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, 945 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.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#6: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: CH2O2
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-CUZ / (MU-4-SULFIDO)-TETRA-NUCLEAR COPPER ION


Mass: 286.249 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu4S / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 921 / 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 Å3/Da / Density % sol: 38.39 %
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: Mar 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.36999 Å / Relative weight: 1
ReflectionResolution: 1.6→76.79 Å / Num. obs: 190846 / % possible obs: 92.2 % / Redundancy: 7 % / Net I/σ(I): 14
Reflection shellResolution: 1.6→1.79 Å / Num. unique obs: 97861

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3SBQ

3sbq


Resolution: 1.601→59.696 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.94 / Phase error: 25.56
RfactorNum. reflection% reflection
Rfree0.1911 9558 5.01 %
Rwork0.1518 --
obs0.1539 190846 65.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.601→59.696 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9221 0 88 921 10230
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019544
X-RAY DIFFRACTIONf_angle_d1.09712916
X-RAY DIFFRACTIONf_dihedral_angle_d13.2675692
X-RAY DIFFRACTIONf_chiral_restr0.0681380
X-RAY DIFFRACTIONf_plane_restr0.0061686
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.601-1.61920.375440.3511103X-RAY DIFFRACTION1
1.6192-1.63830.46350.3136306X-RAY DIFFRACTION3
1.6383-1.65830.381210.3572605X-RAY DIFFRACTION6
1.6583-1.67930.3412430.3241777X-RAY DIFFRACTION8
1.6793-1.70130.2953590.32651022X-RAY DIFFRACTION11
1.7013-1.72470.3188660.31131292X-RAY DIFFRACTION14
1.7247-1.74930.3683730.30671662X-RAY DIFFRACTION18
1.7493-1.77540.36391260.30642026X-RAY DIFFRACTION22
1.7754-1.80320.30141410.28222728X-RAY DIFFRACTION30
1.8032-1.83270.32921660.26523454X-RAY DIFFRACTION37
1.8327-1.86430.31851940.2634148X-RAY DIFFRACTION44
1.8643-1.89820.28032890.25075353X-RAY DIFFRACTION58
1.8982-1.93470.28063700.24616917X-RAY DIFFRACTION74
1.9347-1.97420.284550.23848089X-RAY DIFFRACTION87
1.9742-2.01720.26995270.22818828X-RAY DIFFRACTION95
2.0172-2.06410.25264370.21558881X-RAY DIFFRACTION96
2.0641-2.11570.21874380.20858882X-RAY DIFFRACTION96
2.1157-2.17290.22024520.19548896X-RAY DIFFRACTION96
2.1729-2.23690.20514660.17588970X-RAY DIFFRACTION96
2.2369-2.30910.21654180.17458994X-RAY DIFFRACTION96
2.3091-2.39160.21874770.16928972X-RAY DIFFRACTION96
2.3916-2.48730.2314260.16518325X-RAY DIFFRACTION90
2.4873-2.60060.19865150.15988992X-RAY DIFFRACTION97
2.6006-2.73770.21924950.16279123X-RAY DIFFRACTION98
2.7377-2.90920.20684540.15329110X-RAY DIFFRACTION98
2.9092-3.13380.18715010.14089128X-RAY DIFFRACTION98
3.1338-3.44910.18354620.13249038X-RAY DIFFRACTION97
3.4491-3.94810.14845190.11068914X-RAY DIFFRACTION97
3.9481-4.97390.12734510.09058532X-RAY DIFFRACTION92
4.9739-59.73720.15245080.1259221X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 14.1471 Å / Origin y: 9.9333 Å / Origin z: 26.7473 Å
111213212223313233
T0.1268 Å2-0.0183 Å2-0.0192 Å2-0.1589 Å20.0083 Å2--0.102 Å2
L0.5672 °20.0718 °2-0.173 °2-0.8373 °20.099 °2--0.6242 °2
S-0.0254 Å °0.0554 Å °-0.018 Å °-0.1332 Å °0.0892 Å °0.0077 Å °-0.1061 Å °-0.0828 Å °-0.0491 Å °
Refinement TLS groupSelection details: all

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