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- PDB-1jni: Structure of the NapB subunit of the periplasmic nitrate reductas... -

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Basic information

Entry
Database: PDB / ID: 1jni
TitleStructure of the NapB subunit of the periplasmic nitrate reductase from Haemophilus influenzae.
ComponentsDIHEME CYTOCHROME C NAPB
KeywordsOXIDOREDUCTASE / dihaem cytochrome c / proteolytic fragment / nitrate reductase subunit
Function / homology
Function and homology information


anaerobic respiration / molecular adaptor activity / periplasmic space / metal ion binding
Similarity search - Function
Nitrate reductase cytochrome c-type subunit NapB / Nitrate reductase cytochrome c-type subunit (NapB) / Flavocytochrome C3; Chain A / Flavocytochrome C3; Chain A, domain 2 / Multiheme cytochrome c family profile. / Multiheme cytochrome superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / Periplasmic nitrate reductase, electron transfer subunit
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.25 Å
AuthorsBrige, A. / Leys, D. / Meyer, T.E. / Cusanovich, M.A. / Van Beeumen, J.J.
CitationJournal: Biochemistry / Year: 2002
Title: The 1.25 A resolution structure of the diheme NapB subunit of soluble nitrate reductase reveals a novel cytochrome c fold with a stacked heme arrangement.
Authors: Brige, A. / Leys, D. / Meyer, T.E. / Cusanovich, M.A. / Van Beeumen, J.J.
History
DepositionJul 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 17, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Mar 3, 2021Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DIHEME CYTOCHROME C NAPB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6813
Polymers13,4441
Non-polymers1,2372
Water2,306128
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.752, 78.752, 29.047
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Cell settingtetragonal
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-136-

HOH

21A-145-

HOH

31A-160-

HOH

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Components

#1: Protein DIHEME CYTOCHROME C NAPB / periplasmic nitrate reductase / napB


Mass: 13444.035 Da / Num. of mol.: 1
Fragment: SMALL SUBUNIT OF THE PERIPLASMIC NITRATE REDUCTASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P44654
#2: Chemical ChemComp-HEC / HEME C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.67 Å3/Da / Density % sol: 26.57 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: ammonium sulphate, pH 5.5, VAPOR DIFFUSION, HANGING DROP at 296K
Crystal grow
*PLUS
Temperature: 277 K / pH: 6.5 / Details: Brige, A., (2001) Acta Crystallogr, D57, 418.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlprotein1drop
220 %PEG80001reservoir
30.2 Mmagnesium acetate tetrahydrate1reservoir
40.1 Msodium cacodylate1reservoirpH6.5
50.8 Mpotassium sodium tartrate tetrahydrate1reservoir
60.1 Msodium HEPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 173 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID13 / Wavelength: 0.964 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 14, 2000
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.964 Å / Relative weight: 1
ReflectionResolution: 1.24→10 Å / Num. obs: 22337 / % possible obs: 84.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 17
Reflection shellResolution: 1.24→1.3 Å / Rmerge(I) obs: 0.316 / Mean I/σ(I) obs: 1.37 / % possible all: 65.5
Reflection
*PLUS
Highest resolution: 1.25 Å / Lowest resolution: 10 Å / Num. measured all: 214619 / Rmerge(I) obs: 0.089
Reflection shell
*PLUS
Highest resolution: 1.25 Å / Lowest resolution: 1.26 Å / % possible obs: 65.47 % / Rmerge(I) obs: 0.316

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Processing

Software
NameClassification
MLPHAREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.25→10 Å / Isotropic thermal model: anisotropic model / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2141 1092 5 %RANDOM
Rwork0.1702 ---
all0.1596 20831 --
obs0.1596 20831 --
Displacement parametersBiso mean: 26.855 Å2
Refinement stepCycle: LAST / Resolution: 1.25→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms473 0 86 128 687
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_from_restr_planes0.0264
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.071
X-RAY DIFFRACTIONs_zero_chiral_vol0.077
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / Rfactor all: 0.16 / Rfactor obs: 0.1596 / Rfactor Rfree: 0.2165 / Rfactor Rwork: 0.1596
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.013
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.5
X-RAY DIFFRACTIONs_plane_restr0.026
X-RAY DIFFRACTIONs_chiral_restr0.077

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