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- PDB-2vr0: Crystal structure of cytochrome c nitrite reductase NrfHA complex... -

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Basic information

Entry
Database: PDB / ID: 2vr0
TitleCrystal structure of cytochrome c nitrite reductase NrfHA complex bound to the HQNO inhibitor
Components
  • CYTOCHROME C NITRITE REDUCTASE, CATALYTIC SUBUNIT NFRA
  • NAPC/NIRT CYTOCHROME C FAMILY PROTEIN
KeywordsOXIDOREDUCTASE / QUINOL DEHYDROGENASE / HQNO / NRFH / NRFHA / MEMBRANE COMPLEX
Function / homology
Function and homology information


nitrite reductase (cytochrome; ammonia-forming) / nitrite reductase (cytochrome, ammonia-forming) activity / denitrification pathway / : / periplasmic space / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Multiheme cytochrome fold / Di-heme elbow motif domain / NapC/NirT cytochrome c, N-terminal / Denitrification system component NapC/NirT/NrfH / NapC/NirT cytochrome c superfamily / NapC/NirT cytochrome c family, N-terminal region / Cytochrome c7 and related cytochrome c / Cytochrome c552 / Cytochrome c552 / Flavocytochrome C3; Chain A ...Multiheme cytochrome fold / Di-heme elbow motif domain / NapC/NirT cytochrome c, N-terminal / Denitrification system component NapC/NirT/NrfH / NapC/NirT cytochrome c superfamily / NapC/NirT cytochrome c family, N-terminal region / Cytochrome c7 and related cytochrome c / Cytochrome c552 / Cytochrome c552 / Flavocytochrome C3; Chain A / Flavocytochrome C3; Chain A, domain 2 / Multiheme cytochrome c family profile. / Butyryl-CoA Dehydrogenase, subunit A, domain 3 / Multiheme cytochrome superfamily / Butyryl-CoA Dehydrogenase, subunit A; domain 3 / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
HEME C / 2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE / Cytochrome c nitrite reductase subunit NrfA / Cytochrome c nitrite reductase subunit NrfH
Similarity search - Component
Biological speciesDESULFOVIBRIO VULGARIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsRodrigues, M.L. / Archer, M.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Quinol Oxidation by C-Type Cytochromes: Structural Characterization of the Menaquinol Binding Site of Nrfha.
Authors: Rodrigues, M.L. / Scott, K.A. / Sansom, M.S.P. / Pereira, I.A.C. / Archer, M.
History
DepositionMar 24, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 27, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_struct_conn_angle / pdbx_validate_close_contact ...pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _struct_conn_type.id
Revision 1.3Mar 6, 2019Group: Data collection / Experimental preparation
Category: database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.temp
Revision 2.0Sep 25, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_validate_close_contact / struct_conn / struct_site_gen
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 / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.name / _chem_comp.pdbx_synonyms / _entity.formula_weight / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Nov 20, 2019Group: Derived calculations / Category: pdbx_struct_conn_angle / struct_conn
Revision 2.2Dec 13, 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 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
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_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYTOCHROME C NITRITE REDUCTASE, CATALYTIC SUBUNIT NFRA
B: CYTOCHROME C NITRITE REDUCTASE, CATALYTIC SUBUNIT NFRA
C: NAPC/NIRT CYTOCHROME C FAMILY PROTEIN
D: CYTOCHROME C NITRITE REDUCTASE, CATALYTIC SUBUNIT NFRA
E: CYTOCHROME C NITRITE REDUCTASE, CATALYTIC SUBUNIT NFRA
F: NAPC/NIRT CYTOCHROME C FAMILY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)293,09944
Polymers274,9416
Non-polymers18,15738
Water2,054114
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26920 Å2
ΔGint-85.1 kcal/mol
Surface area104070 Å2
MethodPQS
Unit cell
Length a, b, c (Å)80.102, 189.115, 263.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21D
12B
22E
13C
23F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A2 - 519
2113D2 - 519
1123B26 - 519
2123E26 - 519
1133C1 - 158
2133F1 - 158

NCS ensembles :
ID
1
2
3

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Components

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Protein , 2 types, 6 molecules ABDECF

#1: Protein
CYTOCHROME C NITRITE REDUCTASE, CATALYTIC SUBUNIT NFRA / / CYTOCHROME C NITRITE REDUCTASE NRFA


Mass: 60090.277 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH
References: UniProt: Q72EF3, nitrite reductase (cytochrome; ammonia-forming)
#2: Protein NAPC/NIRT CYTOCHROME C FAMILY PROTEIN / CYTOCHROME C QUINOL DEHYDROGENASE NRFH


Mass: 17290.113 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH / References: UniProt: Q72EF4, EC: 1.10.2.-

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Non-polymers , 4 types, 152 molecules

#3: Chemical...
ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-HQO / 2-HEPTYL-4-HYDROXY QUINOLINE N-OXIDE / 2-HEPTYL-1-OXY-QUINOLIN-4-OL


Mass: 259.343 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H21NO2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 3.5 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: 277 K 9% PEG 4K 0.1 M HEPES PH 7.5 100 MM GLYCYL-GLYCYL-GLYCINE VAPOUR DIFFUSION METHOD.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Sep 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.8→29.77 Å / Num. obs: 92571 / % possible obs: 86.5 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 9.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2.5 / % possible all: 75.4

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Processing

Software
NameVersionClassification
REFMAC5.3.0013refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J7A

2j7a


Resolution: 2.8→154.3 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.842 / SU B: 25.484 / SU ML: 0.282 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.219 / ESU R Free: 0.374 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.261 2592 3 %RANDOM
Rwork0.22 ---
obs0.221 83976 87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.61 Å2
Baniso -1Baniso -2Baniso -3
1--2.5 Å20 Å20 Å2
2--0.88 Å20 Å2
3---1.62 Å2
Refinement stepCycle: LAST / Resolution: 2.8→154.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18217 0 1250 114 19581
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.02220169
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4212.13127692
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.87852268
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59924.169890
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.013153235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8261598
X-RAY DIFFRACTIONr_chiral_restr0.0940.22623
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215660
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2650.29518
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3050.213300
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2751
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1370.243
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.280.221
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0560.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3011.511581
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.508218323
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it0.961310042
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5064.59314
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A1976tight positional0.040.05
2B1972tight positional0.040.05
3C572tight positional0.040.05
1A2026loose positional0.055
2B2020loose positional0.055
3C497loose positional0.055
1A1976tight thermal0.070.5
2B1972tight thermal0.070.5
3C572tight thermal0.060.5
1A2026loose thermal0.0910
2B2020loose thermal0.0910
3C497loose thermal0.0810
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 182 -
Rwork0.311 5487 -
obs--77.81 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.27940.2167-0.12461.08510.26550.42690.0272-0.3627-0.0520.1581-0.06790.19730.1525-0.06090.0407-0.04690.00920.00350.08610.0576-0.140118.408724.541434.5853
21.1913-0.0001-0.3070.96560.21860.8318-0.0035-0.05840.0707-0.130.0078-0.0614-0.02390.07-0.0043-0.08260.0064-0.001-0.04780.0307-0.184855.12840.23816.9745
31.99270.762-0.07910.851-0.54580.8881-0.16730.3988-0.1051-0.4820.15350.01030.1468-0.17490.01380.228-0.0018-0.01530.06-0.0315-0.031735.82873.6242-5.6989
41.09520.1429-0.09510.7088-0.69371.44210.0364-0.11570.02040.0561-0.0823-0.0651-0.20270.13750.0459-0.0395-0.025-0.02170.01110.09720.028748.264-9.621148.1046
51.26230.1172-0.18770.6386-0.22881.7373-0.0155-0.003-0.254-0.11110.04350.1250.2552-0.1961-0.0279-0.0557-0.0368-0.0322-0.00430.14410.163611.6614-33.065746.3476
62.01290.6412-0.89241.112-0.78610.6731-0.12340.3745-0.4868-0.43210.1648-0.16180.4258-0.3033-0.04140.3096-0.0081-0.01760.1403-0.03990.121130.2765-22.13264.1421
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A26 - 520
2X-RAY DIFFRACTION2B25 - 522
3X-RAY DIFFRACTION3C14 - 158
4X-RAY DIFFRACTION4D26 - 519
5X-RAY DIFFRACTION5E25 - 519
6X-RAY DIFFRACTION6F14 - 159

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