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- PDB-1nir: OXYDIZED NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA -

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Basic information

Entry
Database: PDB / ID: 1nir
TitleOXYDIZED NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA
ComponentsNITRITE REDUCTASE
KeywordsNITRITE REDUCTASE / PSEUDOMONAS AERUGINOSA / HEMOPROTEIN / DENITRIFICATION / DOMAIN SWAPPING
Function / homology
Function and homology information


hydroxylamine reductase / hydroxylamine reductase activity / nitrite reductase (NO-forming) / nitrite reductase (NO-forming) activity / electron transfer activity / periplasmic space / heme binding / metal ion binding
Similarity search - Function
C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase / Cytochrome cd1-nitrite reductase, C-terminal domain superfamily / Cytochrome D1 heme domain / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / 8 Propeller / Methanol Dehydrogenase; Chain A / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. ...C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase / Cytochrome cd1-nitrite reductase, C-terminal domain superfamily / Cytochrome D1 heme domain / Cytochrome cd1-nitrite reductase-like, haem d1 domain superfamily / 8 Propeller / Methanol Dehydrogenase; Chain A / Cytochrome C oxidase, cbb3-type, subunit III / Cytochrome c-like domain / Cytochrome Bc1 Complex; Chain D, domain 2 / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
HEME D / HEME C / HYDROXIDE ION / PHOSPHATE ION / Nitrite reductase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsNurizzo, D. / Tegoni, M. / Cambillau, C.
CitationJournal: Structure / Year: 1997
Title: N-terminal arm exchange is observed in the 2.15 A crystal structure of oxidized nitrite reductase from Pseudomonas aeruginosa.
Authors: Nurizzo, D. / Silvestrini, M.C. / Mathieu, M. / Cutruzzola, F. / Bourgeois, D. / Fulop, V. / Hajdu, J. / Brunori, M. / Tegoni, M. / Cambillau, C.
History
DepositionJun 17, 1997Processing site: BNL
Revision 1.0Dec 3, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 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_validate_chiral / refine / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_starting_model / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.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: NITRITE REDUCTASE
B: NITRITE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,47512
Polymers120,5182
Non-polymers2,95710
Water15,673870
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12730 Å2
ΔGint-167 kcal/mol
Surface area37800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.068, 90.072, 111.888
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.99989, -0.0065, -0.01349), (-0.00655, -0.99997, -0.00373), (-0.01347, 0.00382, -0.9999)
Vector: 0.46127, 22.48611, 56.85742)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein NITRITE REDUCTASE /


Mass: 60259.051 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: NCTC 6750 / Source: (natural) Pseudomonas aeruginosa (bacteria) / Cellular location: PERIPLASMIC SPACEPeriplasm / References: UniProt: P24474, EC: 1.9.3.2

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Non-polymers , 6 types, 880 molecules

#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-OH / HYDROXIDE ION / Hydroxide


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO
#5: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#6: Chemical ChemComp-DHE / HEME D / Heme


Mass: 712.484 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O10
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 870 / 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: 3.44 Å3/Da / Density % sol: 64.2 %
Crystal growpH: 8.4
Details: PROTEIN WAS CRYSTALLIZED FROM @M NA/K2 PHOSPHATE, 50MM TRIS-HCL, PH 8.4
Crystal grow
*PLUS
Method: unknown / PH range low: 8.5 / PH range high: 8.1
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 Mphosphate11
250 mMTris-HCl11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID09 / Wavelength: 0.76534
DetectorType: THOMPSON
Detector: X RAY IMAGE INTENSIFIER (THOMPSON) +PRINCETON CCD DETECTOR
Date: Jan 1, 1997 / Details: FOCUSED BEAM TOROIDAL MIRROR
RadiationMonochromator: LAUE BRAGG / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.76534 Å / Relative weight: 1
ReflectionResolution: 2.15→30 Å / Num. obs: 91663 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 36.18 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.063 / Net I/σ(I): 7.7
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 3.4 / Rsym value: 0.214 / % possible all: 96.9
Reflection
*PLUS
Num. measured all: 892032
Reflection shell
*PLUS
% possible obs: 96.9 %

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Processing

Software
NameVersionClassification
AMoREphasing
X-PLOR3.8refinement
DENZOdata reduction
PROWdata reduction
CCP4data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→30 Å / Rfactor Rfree error: 0.0045 / Data cutoff high absF: 4000 / Data cutoff low absF: 5 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2.5
RfactorNum. reflection% reflectionSelection details
Rfree0.242 2937 3.17 %RANDOM
Rwork0.209 ---
obs0.209 82362 89 %-
Displacement parametersBiso mean: 39.1 Å2
Baniso -1Baniso -2Baniso -3
1-3.2 Å20 Å20 Å2
2--3.416 Å20 Å2
3---3.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å-
Luzzati d res low-30 Å
Luzzati sigma a-0.32 Å
Refinement stepCycle: LAST / Resolution: 2.15→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8415 0 198 870 9483
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.857
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.59
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.342
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it3.2
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.15→2.25 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3235 341 2.99 %
Rwork0.2517 8554 -
obs--78.02 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.HEMETOPH19X.HEME
X-RAY DIFFRACTION2
X-RAY DIFFRACTION3PARHCSDX.PROTOPHCSDX.PRO
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.59
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.342
LS refinement shell
*PLUS
Rfactor obs: 0.2517

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