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- PDB-1fwx: CRYSTAL STRUCTURE OF NITROUS OXIDE REDUCTASE FROM P. DENITRIFICANS -

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Basic information

Entry
Database: PDB / ID: 1fwx
TitleCRYSTAL STRUCTURE OF NITROUS OXIDE REDUCTASE FROM P. DENITRIFICANS
ComponentsNITROUS OXIDE REDUCTASE
KeywordsOXIDOREDUCTASE / Beta-propeller domain / cupredoxin domain / CuZ site / CuA site
Function / homology
Function and homology information


nitrous-oxide reductase / nitrous-oxide reductase activity / denitrification pathway / cytochrome-c oxidase activity / periplasmic space / copper ion binding / calcium ion binding / membrane
Similarity search - Function
Cupredoxin-like domain / 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 / : / Cytochrome c oxidase subunit II-like C-terminal ...Cupredoxin-like domain / 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 / : / 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 / (MU-4-SULFIDO)-TETRA-NUCLEAR COPPER ION / Nitrous-oxide reductase
Similarity search - Component
Biological speciesParacoccus denitrificans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsBrown, K. / Djinovic-Carugo, K. / Haltia, T. / Cabrito, I. / Saraste, M. / Moura, J.J. / Moura, I. / Tegoni, M. / Cambillau, C.
Citation
Journal: J.Biol.Chem. / Year: 2000
Title: Revisiting the Catalytic CuZ Cluster of Nitrous Oxide (N2O) Reductase. Evidence of a Bridging Inorganic Sulfur
Authors: Brown, K. / Djinovic-Carugo, K. / Haltia, T. / Cabrito, I. / Saraste, M. / Moura, J.J. / Moura, I. / Tegoni, M. / Cambillau, C.
#1: Journal: BIOCHEM.J. / Year: 2003
Title: Crystal structure of nitrous oxide reductase from Paracoccus denitrificans at 1.6 A resolution
Authors: Haltia, T. / Brown, K. / Tegoni, M. / Cambillau, C. / Saraste, M. / Mattila, K. / Djinovic-Carugo, K.
History
DepositionSep 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 25, 2001Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Aug 9, 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 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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_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.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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)267,82627
Polymers265,5904
Non-polymers2,23623
Water47,5962642
1
A: NITROUS OXIDE REDUCTASE
B: NITROUS OXIDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,93314
Polymers132,7952
Non-polymers1,13812
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13740 Å2
ΔGint-173 kcal/mol
Surface area34700 Å2
MethodPISA, PQS
2
C: NITROUS OXIDE REDUCTASE
D: NITROUS OXIDE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,89313
Polymers132,7952
Non-polymers1,09811
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13570 Å2
ΔGint-169 kcal/mol
Surface area34810 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)102.595, 105.090, 116.696
Angle α, β, γ (deg.)90.00, 110.69, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is a dimer constructed from chains A and B, and C and D, related by the non-crystallographic two-fold.

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
NITROUS OXIDE REDUCTASE


Mass: 66397.500 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Paracoccus denitrificans (bacteria) / References: UniProt: Q51705, EC: 1.7.99.6

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Non-polymers , 5 types, 2665 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 40.078 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CUA / DINUCLEAR COPPER ION


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


Mass: 286.249 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu4S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2642 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailssequence Clear deltaF electron density map at position 291 suggests VAL rather than ALA. CLEAR ...sequence Clear deltaF electron density map at position 291 suggests VAL rather than ALA. CLEAR DELTAF ELECTRON DENSITY MAP AT POSITION 8 SUGGESTS ALA RATHER THAN GLY.

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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: 2.37 Å3/Da / Density % sol: 47.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG8000, Na cacodylate, Mg acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion / Details: Haltia, T., (2003) BIOCHEM.J., 369, 77.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
116 %(w/v)PEG80001reservoir
280 mMsodium cacodylate1reservoir
3160 mMmagnesium acetate1reservoir
414 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 17, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→40 Å / Num. all: 272421 / Num. obs: 272421 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.05 % / Biso Wilson estimate: 20.2 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 27.9
Reflection shellResolution: 1.63→1.65 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.252 / % possible all: 84.7
Reflection
*PLUS
Lowest resolution: 40 Å

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Processing

Software
NameVersionClassification
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
CNS0.9refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QNI

1qni


Resolution: 1.6→29.83 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1693812.71 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1331 0.5 %SHELLS
Rwork0.241 ---
all0.263 272421 --
obs0.263 272417 89.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.4278 Å2 / ksol: 0.372188 e/Å3
Displacement parametersBiso mean: 24.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.25 Å20 Å2-3.6 Å2
2--4.35 Å20 Å2
3----2.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.6→29.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18491 0 43 2642 21176
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_dihedral_angle_d26
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it0.311.5
X-RAY DIFFRACTIONc_mcangle_it0.522
X-RAY DIFFRACTIONc_scbond_it0.322
X-RAY DIFFRACTIONc_scangle_it0.542.5
LS refinement shellResolution: 1.6→1.7 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.389 193 0.5 %
Rwork0.322 41629 -
obs--82.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMION-WITHSULPHUR.TOP
X-RAY DIFFRACTION3ION-WITHSULPHUR.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 0.5 % / Rfactor obs: 0.241
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.3 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg2.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87
X-RAY DIFFRACTIONc_mcbond_it0.311.5
X-RAY DIFFRACTIONc_scbond_it0.322
X-RAY DIFFRACTIONc_mcangle_it0.522
X-RAY DIFFRACTIONc_scangle_it0.542.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.389 / % reflection Rfree: 0.5 % / Rfactor Rwork: 0.322

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