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- PDB-1gjq: Pseudomonas aeruginosa cd1 nitrite reductase reduced cyanide complex -

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Basic information

Entry
Database: PDB / ID: 1gjq
TitlePseudomonas aeruginosa cd1 nitrite reductase reduced cyanide complex
ComponentsNITRITE REDUCTASE
KeywordsOXIDOREDUCTASE / REDUCTASE / ELECTRON TRANSPORT / HEME
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
CYANIDE ION / HEME D / HEME C / Nitrite reductase
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsNurizzo, D. / Brown, K. / Tegoni, M. / Cambillau, C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2002
Title: Cyanide Binding to Cd(1) Nitrite Reductase from Pseudomonas Aeruginosa: Role of the Active-Site His369 in Ligand Stabilization.
Authors: Sun, W. / Arese, M. / Brunori, M. / Nurizzo, D. / Brown, K. / Cambillau, C. / Tegoni, M. / Cutruzzola, F.
History
DepositionAug 1, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_validate_chiral / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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_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)123,2328
Polymers120,5182
Non-polymers2,7146
Water10,791599
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)167.400, 88.600, 113.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-2047-

HOH

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Components

#1: Protein NITRITE REDUCTASE / / CYTOCHROME CD1 / CYTOCHROME OXIDASE


Mass: 60259.051 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) PSEUDOMONAS AERUGINOSA (bacteria) / References: UniProt: P24474, EC: 1.9.3.2
#2: Chemical ChemComp-HEC / HEME C / Heme C


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


Mass: 712.484 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O10
#4: Chemical ChemComp-CYN / CYANIDE ION / Cyanide


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 599 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCD1 IS A BIFUNCTIONAL ENZYME THAT CATALYSES THE REDUCTION OF NITRITE TO NITRIC OXIDE AND DIOXYGEN ...CD1 IS A BIFUNCTIONAL ENZYME THAT CATALYSES THE REDUCTION OF NITRITE TO NITRIC OXIDE AND DIOXYGEN TO WATER. N-TERMINAL DOMAIN SWAPPING OCCURS BETWEEN THE TWO CHAINS, WITH THE N_TERMINUS OF ONE CHAIN FORMING PART OF THE C-HEME BINDING SITE IN THE OTHER CHAIN.

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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: 3.47 Å3/Da / Density % sol: 64.6 %
Crystal growpH: 8 / Details: 2M NA/K2 PHOSPHATE, 50MM TRIS-HCL, PH 8.4
Crystal grow
*PLUS
pH: 8.4 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
12 Msodium potassium phosphate11
250 mMTris-HCl11pH8.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.907
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.907 Å / Relative weight: 1
ReflectionResolution: 2.7→18 Å / Num. obs: 42035 / % possible obs: 90.3 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / Biso Wilson estimate: 45.6 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 6.3
Reflection shellResolution: 2.7→2.77 Å / Rmerge(I) obs: 0.356 / Mean I/σ(I) obs: 2.1 / % possible all: 89.3
Reflection
*PLUS
Lowest resolution: 18 Å
Reflection shell
*PLUS
% possible obs: 89.3 %

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NNO

1nno


Resolution: 2.7→18 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1264 3 %RANDOM
Rwork0.204 ---
obs0.204 42035 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.31 e/Å3
Displacement parametersBiso mean: 33.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.5 Å20 Å20 Å2
2---0.57 Å20 Å2
3---0.07 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.38 Å
Refinement stepCycle: LAST / Resolution: 2.7→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8442 0 188 599 9229
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.319 217 3.2 %
Rwork0.288 6645 -
obs--89.1 %
Xplor fileSerial no: 1 / Param file: PARAM19X.PRO / Topol file: TOPH19X.PRO
Refinement
*PLUS
Lowest resolution: 18 Å / % reflection Rfree: 3 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.71

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