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- PDB-1n15: FOLLOWING THE C HEME REDUCTION IN NITRITE REDUCTASE FROM PSEUDOMO... -

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Basic information

Entry
Database: PDB / ID: 1n15
TitleFOLLOWING THE C HEME REDUCTION IN NITRITE REDUCTASE FROM PSEUDOMONAS AERUGINOSA
ComponentsNITRITE REDUCTASE
KeywordsOXIDOREDUCTASE / NITRITE REDUCTASE / PSEUDOMONAS AERUGINOSA / HEMOPROTEIN / DENITRIFICATION / CONFORMATIONAL CHANGE / MICROSPECTROPHOTOMETRY
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 / Nitrite reductase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsNurizzo, D. / Tegoni, M. / Cambillau, C.
CitationJournal: J.Biol.Chem. / Year: 1999
Title: Does the reduction of c heme trigger the conformational change of crystalline nitrite reductase?
Authors: Nurizzo, D. / Cutruzzola, F. / Arese, M. / Bourgeois, D. / Brunori, M. / Cambillau, C. / Tegoni, M.
History
DepositionSep 4, 1998Processing site: BNL
Revision 1.0Jun 15, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Apr 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 / 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 / _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

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Assembly

Deposited unit
A: NITRITE REDUCTASE
B: NITRITE REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,1806
Polymers120,5182
Non-polymers2,6624
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11760 Å2
ΔGint-125 kcal/mol
Surface area37940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.740, 89.910, 112.160
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein NITRITE REDUCTASE /


Mass: 60259.051 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: MODEL WITHOUT ION AND WATER / Source: (natural) Pseudomonas aeruginosa (bacteria) / Cellular location: PERIPLASMIC SPACEPeriplasm / 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
Nonpolymer detailsABOUT 15% OF THE C HEMES ARE REDUCED D1 HEMES ARE FULLY OXIDIZED DETERMINED BY ...ABOUT 15% OF THE C HEMES ARE REDUCED D1 HEMES ARE FULLY OXIDIZED DETERMINED BY MICROSPECTROPHOTOMETRY ON THE CRYSTAL.

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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: 3.46 Å3/Da / Density % sol: 64.29 %
Crystal growpH: 7.2 / Details: pH 7.2
Crystal grow
*PLUS
pH: 8.4 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12 MNa/K phosphate11
250 mMTris-HCl11

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.933
DetectorType: MARRESEARCH / Detector: CCD / Date: May 1, 1998
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.7→40 Å / Num. obs: 46310 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 53.22 Å2 / Rsym value: 0.052 / Net I/σ(I): 5.6
Reflection shellResolution: 2.7→2.77 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.24 / % possible all: 99.3
Reflection
*PLUS
Rmerge(I) obs: 0.052
Reflection shell
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.24

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Processing

Software
NameVersionClassification
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
PROWdata reduction
CCP4data scaling
X-PLOR3.8phasing
RefinementStarting model: OXIDIZED NITRITE REDUCTASE FROM PS. AERUGINOSA

Resolution: 2.9→12 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 40000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.247 1641 3.6 %RANDOM
Rwork0.203 ---
obs0.203 36937 99.6 %-
Displacement parametersBiso mean: 31.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.512 Å0.42 Å
Luzzati d res low-12 Å
Refinement stepCycle: LAST / Resolution: 2.9→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8417 0 184 0 8601
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.66
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d25.29
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.431
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.9→3.03 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.3647 85 1.86 %
Rwork0.2605 4459 -
obs--99.9 %
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_deg25.29
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.431

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