PDB-2j7a: Crystal structure of cytochrome c nitrite reductase NrfHA complex...

ID or keywords:

Entry

Database: PDB / ID: 2j7a

Title

Crystal structure of cytochrome c nitrite reductase NrfHA complex from Desulfovibrio vulgaris

Components

(CYTOCHROME C ...) x 2

Keywords

OXIDOREDUCTASE / QUINOL DEHYDROGENASE / CYTOCHROME C NITRITE REDUCTASE / NRFA / NRFH / NAPC/NIRT FAMILY / MEMBRANE COMPLEX

Function / homology

Function and homology information

nitrite reductase (cytochrome; ammonia-forming) / nitrite reductase (cytochrome, ammonia-forming) activity / anaerobic electron transport chain / denitrification pathway / anaerobic respiration / outer membrane-bounded periplasmic space / electron transfer activity / heme binding / metal ion binding / plasma membrane
Similarity search - Function

Biological species

DESULFOVIBRIO VULGARIS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.3 Å

Authors

Rodrigues, M.L. / Oliveira, T.F. / Pereira, I.A.C. / Archer, M.

Citation

Journal: Embo J. / Year: 2006
Title: X-Ray Structure of the Membrane-Bound Cytochrome C Quinol Dehydrogenase Nrfh Reveals Novel Haem Coordination.
Authors: Rodrigues, M.L. / Oliveira, T.F. / Pereira, I.A.C. / Archer, M.

History

Deposition	Oct 6, 2006	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Dec 6, 2006	Provider: repository / Type: Initial release
Revision 2.0	Sep 25, 2019	Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Experimental preparation / Non-polymer description / Other / Structure summary Category: atom_site / chem_comp ...atom_site / chem_comp / entity / exptl_crystal_grow / 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 / _exptl_crystal_grow.method / _exptl_crystal_grow.temp / _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_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 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1	Nov 6, 2019	Group: Data collection / Refinement description / Category: software / Item: _software.name / _software.version

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2j7a.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb2j7a.ent.gz	1.2 MB	Display	PDB format
PDBx/mmJSON format	2j7a.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2j7a_validation.pdf.gz	28.2 MB	Display	wwPDB validaton report
Full document	2j7a_full_validation.pdf.gz	28.5 MB	Display
Data in XML	2j7a_validation.xml.gz	289.5 KB	Display
Data in CIF	2j7a_validation.cif.gz	382.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/j7/2j7a ftp://data.pdbj.org/pub/pdb/validation_reports/j7/2j7a	HTTPS FTP

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Related structure data

Similar structure data	5epi-2 5epi-4 6yj6-d 1urj-d 20550 6eny-d 5epi-1 5f4z-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#22 - Oct 2001 Photosystem I similarity (3) #36 - Dec 2002 Cytochrome c similarity (1) #111 - Mar 2009 Hydrogenase similarity (1) #137 - May 2011 Cytochrome bc1 similarity (1) #232 - Apr 2019 Proteins and Biominerals similarity (1) #59 - Nov 2004 Photosystem II similarity (1) #89 - May 2007 Aconitase and Iron Regulatory Protein 1 similarity (1)

Deposited unit

A: CYTOCHROME C NITRITE REDUCTASE NRFA

B: CYTOCHROME C NITRITE REDUCTASE NRFA

C: CYTOCHROME C QUINOL DEHYDROGENASE NRFH

D: CYTOCHROME C NITRITE REDUCTASE NRFA

E: CYTOCHROME C NITRITE REDUCTASE NRFA

F: CYTOCHROME C QUINOL DEHYDROGENASE NRFH

G: CYTOCHROME C NITRITE REDUCTASE NRFA

H: CYTOCHROME C NITRITE REDUCTASE NRFA

I: CYTOCHROME C QUINOL DEHYDROGENASE NRFH

J: CYTOCHROME C NITRITE REDUCTASE NRFA

K: CYTOCHROME C NITRITE REDUCTASE NRFA

L: CYTOCHROME C QUINOL DEHYDROGENASE NRFH

M: CYTOCHROME C NITRITE REDUCTASE NRFA

N: CYTOCHROME C NITRITE REDUCTASE NRFA

O: CYTOCHROME C QUINOL DEHYDROGENASE NRFH

P: CYTOCHROME C NITRITE REDUCTASE NRFA

Q: CYTOCHROME C NITRITE REDUCTASE NRFA

R: CYTOCHROME C QUINOL DEHYDROGENASE NRFH

hetero molecules

851 kDa, 18 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CYTOCHROME C NITRITE REDUCTASE NRFA

B: CYTOCHROME C NITRITE REDUCTASE NRFA

C: CYTOCHROME C QUINOL DEHYDROGENASE NRFH

D: CYTOCHROME C NITRITE REDUCTASE NRFA

E: CYTOCHROME C NITRITE REDUCTASE NRFA

F: CYTOCHROME C QUINOL DEHYDROGENASE NRFH

hetero molecules

defined by author&software
284 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

G: CYTOCHROME C NITRITE REDUCTASE NRFA

H: CYTOCHROME C NITRITE REDUCTASE NRFA

I: CYTOCHROME C QUINOL DEHYDROGENASE NRFH

J: CYTOCHROME C NITRITE REDUCTASE NRFA

K: CYTOCHROME C NITRITE REDUCTASE NRFA

L: CYTOCHROME C QUINOL DEHYDROGENASE NRFH

hetero molecules

defined by author&software
284 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

M: CYTOCHROME C NITRITE REDUCTASE NRFA

N: CYTOCHROME C NITRITE REDUCTASE NRFA

O: CYTOCHROME C QUINOL DEHYDROGENASE NRFH

P: CYTOCHROME C NITRITE REDUCTASE NRFA

Q: CYTOCHROME C NITRITE REDUCTASE NRFA

R: CYTOCHROME C QUINOL DEHYDROGENASE NRFH

hetero molecules

defined by author&software
284 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	79.664, 258.117, 580.742
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	5	A	26 - 519
2	1	1	5	G	26 - 519
3	1	1	5	M	26 - 519
1	1	2	5	D	26 - 519
2	1	2	5	J	26 - 519
3	1	2	5	P	26 - 519
1	1	3	5	B	26 - 519
2	1	3	5	H	26 - 519
3	1	3	5	N	26 - 519
1	1	4	5	E	26 - 519
2	1	4	5	K	26 - 519
3	1	4	5	Q	26 - 519
1	1	5	5	C	12 - 158
2	1	5	5	I	12 - 158
3	1	5	5	O	12 - 158
1	1	6	5	F	14 - 158
2	1	6	5	L	14 - 158
3	1	6	5	R	14 - 158

NCS ensembles :

ID
1
2
3
4
5
6

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CYTOCHROME C ... , 2 types, 18 molecules ABDEGHJKMNPQCFILOR

#1: Protein	CYTOCHROME C NITRITE REDUCTASE NRFA / NRFA / CYTOCHROME C NITRITE REDUCTASE CATALYTIC SUBUNIT Mass: 57570.242 Da / Num. of mol.: 12 / Fragment: RESIDUES 25-524 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH / References: UniProt: Q72EF3
#2: Protein	CYTOCHROME C QUINOL DEHYDROGENASE NRFH / NRFH / CYTOCHROME C NITRITE REDUCTASE ELECTRON DONOR SUBUNIT / NAPC/NIRT CYTOCHROME C Mass: 17290.113 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH / References: UniProt: Q72EF4

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Sugars , 1 types, 6 molecules

#5: Sugar	ChemComp-LMT / DODECYL-BETA-D-MALTOSIDE Type: D-saccharide / Mass: 510.615 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₂₄H₄₆O₁₁ / Comment: detergent*YM

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Non-polymers , 4 types, 2436 molecules

#3: Chemical	... ChemComp-HEC / HEME C Mass: 618.503 Da / Num. of mol.: 84 / Source method: obtained synthetically / Formula: C₃₄H₃₄FeN₄O₄
#4: Chemical	... ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Ca
#6: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₂H₃O₂
#7: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2325 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.6 Å³/Da / Density % sol: 65 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion / pH: 7.5 Details: 10% PEG 4K, 0.1 M HEPES PH 7.5, 30 MM GLYCYL-GLYCYL-GLYCINE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.7393
Detector	Type: MARRESEACH / Detector: CCD
Radiation	Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.7393 Å / Relative weight: 1
Reflection	Resolution: 2.3→53 Å / Num. obs: 443656 / % possible obs: 83.9 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / R_merge(I) obs: 0.1 / Net I/σ(I): 8.3
Reflection shell	Resolution: 2.3→2.42 Å / Redundancy: 2.1 % / R_merge(I) obs: 0.31 / Mean I/σ(I) obs: 3.1 / % possible all: 67.3

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MOSFLM		data reduction
SCALA		data scaling
SHARP		phasing

Refinement

Method to determine structure:

MAD / Resolution: 2.3→288.67 Å / Cor.coef. F_o:F_c: 0.92 / Cor.coef. F_o:F_c free: 0.886 / SU B: 6.055 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.292 / ESU R Free: 0.227 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24	22270	5 %	RANDOM
R_work	0.201	-	-	-
obs	0.203	421309	83.7 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 20.47 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.19 Å²	0 Å²	0 Å²
2-	-	0.84 Å²	0 Å²
3-	-	-	0.35 Å²

Refinement step

Cycle: LAST / Resolution: 2.3→288.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	54627	0	3858	2325	60810

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.022	60662
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.463	2.132	83298
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.479	5	6832
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.518	24.243	2670
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.264	15	9740
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.827	15	281
X-RAY DIFFRACTION	r_chiral_restr	0.103	0.2	7943
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	46923
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.254	0.2	28686
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.298	0.2	39648
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.16	0.2	3136
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.228	0.2	43
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.186	0.2	7
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	0.639	1.5	34767
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.084	2	55016
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.636	3	30079
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.519	4.5	28095
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1968	medium positional	0.07	0.5
1	2	G	1968	medium positional	0.07	0.5
1	3	M	1968	medium positional	0.07	0.5
2	1	D	1968	medium positional	0.08	0.5
2	2	J	1968	medium positional	0.07	0.5
2	3	P	1968	medium positional	0.08	0.5
3	1	B	1972	medium positional	0.08	0.5
3	2	H	1972	medium positional	0.08	0.5
3	3	N	1972	medium positional	0.1	0.5
4	1	E	1967	medium positional	0.12	0.5
4	2	K	1967	medium positional	0.11	0.5
4	3	Q	1967	medium positional	0.12	0.5
5	1	C	575	medium positional	0.16	0.5
5	2	I	575	medium positional	0.1	0.5
5	3	O	575	medium positional	0.1	0.5
6	1	F	579	medium positional	0.11	0.5
6	2	L	579	medium positional	0.14	0.5
6	3	R	579	medium positional	0.1	0.5
1	1	A	1996	loose positional	0.32	5
1	2	G	1996	loose positional	0.39	5
1	3	M	1996	loose positional	0.37	5
2	1	D	1996	loose positional	0.34	5
2	2	J	1996	loose positional	0.34	5
2	3	P	1996	loose positional	0.34	5
3	1	B	2004	loose positional	0.3	5
3	2	H	2004	loose positional	0.32	5
3	3	N	2004	loose positional	0.34	5
4	1	E	2011	loose positional	0.38	5
4	2	K	2011	loose positional	0.34	5
4	3	Q	2011	loose positional	0.42	5
5	1	C	496	loose positional	0.45	5
5	2	I	496	loose positional	0.33	5
5	3	O	496	loose positional	0.43	5
6	1	F	502	loose positional	0.53	5
6	2	L	502	loose positional	0.43	5
6	3	R	502	loose positional	0.46	5
1	1	A	1968	medium thermal	0.38	2
1	2	G	1968	medium thermal	0.36	2
1	3	M	1968	medium thermal	0.41	2
2	1	D	1968	medium thermal	0.53	2
2	2	J	1968	medium thermal	0.38	2
2	3	P	1968	medium thermal	0.58	2
3	1	B	1972	medium thermal	0.36	2
3	2	H	1972	medium thermal	0.41	2
3	3	N	1972	medium thermal	0.41	2
4	1	E	1967	medium thermal	0.51	2
4	2	K	1967	medium thermal	0.36	2
4	3	Q	1967	medium thermal	0.47	2
5	1	C	575	medium thermal	0.33	2
5	2	I	575	medium thermal	0.41	2
5	3	O	575	medium thermal	0.35	2
6	1	F	579	medium thermal	0.44	2
6	2	L	579	medium thermal	0.39	2
6	3	R	579	medium thermal	0.36	2
1	1	A	1996	loose thermal	1.2	10
1	2	G	1996	loose thermal	1.12	10
1	3	M	1996	loose thermal	1.23	10
2	1	D	1996	loose thermal	1.3	10
2	2	J	1996	loose thermal	1.11	10
2	3	P	1996	loose thermal	1.35	10
3	1	B	2004	loose thermal	1.13	10
3	2	H	2004	loose thermal	1.15	10
3	3	N	2004	loose thermal	1.09	10
4	1	E	2011	loose thermal	1.21	10
4	2	K	2011	loose thermal	1.12	10
4	3	Q	2011	loose thermal	1.21	10
5	1	C	496	loose thermal	1.09	10
5	2	I	496	loose thermal	1.13	10
5	3	O	496	loose thermal	1.05	10
6	1	F	502	loose thermal	1.21	10
6	2	L	502	loose thermal	1.06	10
6	3	R	502	loose thermal	1.04	10

LS refinement shell

Resolution: 2.3→2.36 Å / Total num. of bins used: 20 /

	R_factor	Num. reflection
R_free	0.321	1251
R_work	0.264	23494

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CYTOCHROME C ... , 2 types, 18 molecules ABDEGHJKMNPQCFILOR

-
Sugars , 1 types, 6 molecules

-
Non-polymers , 4 types, 2436 molecules

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Experimental details

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Experiment

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Sample preparation

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-CYTOCHROME C ... , 2 types, 18 molecules ABDEGHJKMNPQCFILOR

-Sugars , 1 types, 6 molecules

-Non-polymers , 4 types, 2436 molecules

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

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-Feb 9, 2022. New format data for meta-information of EMDB entries

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Open data

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Basic information

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Related structure data

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Links

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Assembly

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Components

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CYTOCHROME C ... , 2 types, 18 molecules ABDEGHJKMNPQCFILOR

-
Sugars , 1 types, 6 molecules

-
Non-polymers , 4 types, 2436 molecules

-
Experimental details

-
Experiment

-
Sample preparation

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Data collection

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Processing

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About Yorodumi

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News

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