PDB-1h29: Sulfate respiration in Desulfovibrio vulgaris Hildenborough: Stru...

ID or keywords:

Entry

Database: PDB / ID: 1h29

Title

Sulfate respiration in Desulfovibrio vulgaris Hildenborough: Structure of the 16-heme Cytochrome c HmcA at 2.5 A resolution and a view of its role in transmembrane electron transfer

Components

HIGH-MOLECULAR-WEIGHT CYTOCHROME C

Keywords

ELECTRON TRANSPORT / HIGH MOLECULAR MASS CYTOCHROME / SULFATE RESPIRATION / HYDROGEN CYCLE / TRANSMEMBRANE REDOX COMPLEX / ENERGY CONSERVATION / PROTON GRADIENT / TETRA-HEME / C3-LIKE DOMAIN

Function / homology

Function and homology information

periplasmic space / electron transfer activity / heme binding / metal ion binding
Similarity search - Function

Biological species

DESULFOVIBRIO VULGARIS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.51 Å

Authors

Matias, P.M. / Coelho, A.V. / Valente, F.M.A. / Placido, D. / Legall, J. / Xavier, A.V. / Pereira, I.A.C. / Carrondo, M.A.

Citation

Journal: J.Biol.Chem. / Year: 2002
Title: Sulfate Respiration in Desulfovibrio Vulgaris Hildenborough: Structure of the 16-Heme Cytochrome C Hmca at 2.5 A Resolution and a View of its Role in Transmembrane Electron Transfer
Authors: Matias, P.M. / Coelho, A.V. / Valente, F.M.A. / Placido, D. / Legall, J. / Xavier, A.V. / Pereira, I.A.C. / Carrondo, M.A.

History

Deposition	Aug 1, 2002	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Oct 2, 2002	Provider: repository / Type: Initial release
Revision 1.1	May 8, 2011	Group: Version format compliance
Revision 1.2	Jul 13, 2011	Group: Version format compliance
Revision 1.3	Aug 30, 2017	Group: Advisory / Data collection / Category: diffrn_detector / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_detector.type
Revision 1.4	May 15, 2019	Group: Data collection / Derived calculations / Experimental preparation Category: exptl_crystal_grow / struct_conn Item: _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5	Oct 16, 2024	Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_conn_type 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 / _pdbx_entry_details.has_protein_modification / _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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	1h29.cif.gz	473 KB	Display	PDBx/mmCIF format
PDB format	pdb1h29.ent.gz	397.2 KB	Display	PDB format
PDBx/mmJSON format	1h29.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	1h29_validation.pdf.gz	5 MB	Display	wwPDB validaton report
Full document	1h29_full_validation.pdf.gz	5.1 MB	Display
Data in XML	1h29_validation.xml.gz	56.4 KB	Display
Data in CIF	1h29_validation.cif.gz	79.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h2/1h29 ftp://data.pdbj.org/pub/pdb/validation_reports/h2/1h29	HTTPS FTP

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Related structure data

Related structure data	1gws
Similar structure data	1gws-d 2cvc-d 6efv-d 3tdz-d 2z0l-3 2z0l-2 6klt-d 4lqq-1 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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

1gws

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: HIGH-MOLECULAR-WEIGHT CYTOCHROME C

B: HIGH-MOLECULAR-WEIGHT CYTOCHROME C

C: HIGH-MOLECULAR-WEIGHT CYTOCHROME C

D: HIGH-MOLECULAR-WEIGHT CYTOCHROME C

hetero molecules

263 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: HIGH-MOLECULAR-WEIGHT CYTOCHROME C

hetero molecules

defined by author&software
65.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: HIGH-MOLECULAR-WEIGHT CYTOCHROME C

hetero molecules

defined by author&software
65.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: HIGH-MOLECULAR-WEIGHT CYTOCHROME C

hetero molecules

defined by author&software
65.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

D: HIGH-MOLECULAR-WEIGHT CYTOCHROME C

hetero molecules

defined by author&software
65.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	220.390, 220.390, 102.640
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	171
Space group name H-M	P6₂

#1: Protein	HIGH-MOLECULAR-WEIGHT CYTOCHROME C / CYTOCHROME CC3 / HMCA Mass: 55765.961 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) DESULFOVIBRIO VULGARIS (bacteria) / Strain: HILDENBOROUGH / References: UniProt: P24092
#2: Chemical	... ChemComp-HEC / HEME C Mass: 618.503 Da / Num. of mol.: 64 / Source method: obtained synthetically / Formula: C₃₄H₃₄FeN₄O₄
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 497 / Source method: isolated from a natural source / Formula: H₂O
Compound details	FORM TRANSMEMBRANE PROTEIN COMPLEX TO AID ELECTRON FLOW TO AID ENZYMES THAT ARE INVOLVED IN THE ...FORM TRANSMEMBRANE PROTEIN COMPLEX TO AID ELECTRON FLOW TO AID ENZYMES THAT ARE INVOLVED IN THE CATALYSIS OF SULFATES. BINDS 16 MOLECULES OF HEME C PER MONOMER. COMPRISED OF ONE INCOMPLETE AND THREE COMPLETE C3-CYTOCHROME-LIKE DOMAINS.
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal

Density Matthews: 2.8 Å³/Da / Density % sol: 55 %

Crystal grow

Temperature: 277 K / pH: 7.5
Details: EACH CRYSTALLIZATION ASSAY WAS PREPARED BY ADDING 5 UL OF THE PROTEIN SOLUTION (10 MG/ML) TO A DIALYSIS BUTTON WHICH WAS THEN COMPLETELY SOAKED IN THE CRYSTALLIZATION WAS THEN COMPLETELY ...

Crystal grow

*PLUS

Method: microdialysis

Components of the solutions

*PLUS

ID	Conc.	Common name	Crystal-ID	Sol-ID	Details
1	40 %(v/v)	2-propanol	1	reservoir
2	0.1 M	Tris-HCl	1	reservoir	pH7.5
3	10 mg/ml	protein	1	drop

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9179
Detector	Type: ADSC QUANTUM 4r / Detector: CCD / Date: Jun 15, 2001 / Details: MIRRORS
Radiation	Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9179 Å / Relative weight: 1
Reflection	Resolution: 2.5→25 Å / Num. obs: 89606 / % possible obs: 91.3 % / Redundancy: 6.5 % / R_merge(I) obs: 0.064 / Net I/σ(I): 11.9
Reflection shell	Resolution: 2.5→2.59 Å / R_merge(I) obs: 0.354 / Mean I/σ(I) obs: 3 / % possible all: 84
Reflection shell	PLUS % possible obs*: 84 %

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Processing

Software

Name	Version	Classification
REFMAC	5.1.24	refinement
DENZO		data reduction
SCALEPACK		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 2.51→30 Å / Cor.coef. F_o:F_c: 0.956 / Cor.coef. F_o:F_c free: 0.924 / SU B: 10.051 / SU ML: 0.226 / Cross valid method: THROUGHOUT / ESU R: 0.591 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: RESIDUE NUMBERING FOLLOWS THE COMPLET PRECURSOR SEQUENCE INCLUDING SIGNAL PEPTIDE. CHAIN A HAS MISSIN RESIDUES 32-37, 500-504 AND 544-545. CHAIN B HAS MISSING RESIDU 32-37, 500-504 AND 542- ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.258	4494	5 %	RANDOM
R_work	0.192	-	-	-
obs	0.195	85075	92.1 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 30.61 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.57 Å²	0.79 Å²	0 Å²
2-	-	1.57 Å²	0 Å²
3-	-	-	-2.36 Å²

Refinement step

Cycle: LAST / Resolution: 2.51→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	15038	0	2752	497	18287

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	18536
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.547	2.399	25611
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.751	5	1983
X-RAY DIFFRACTION	r_dihedral_angle_2_deg
X-RAY DIFFRACTION	r_dihedral_angle_3_deg
X-RAY DIFFRACTION	r_dihedral_angle_4_deg
X-RAY DIFFRACTION	r_chiral_restr	0.099	0.2	2215
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	14251
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.222	0.2	8149
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.152	0.2	678
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	0.2	0.2	101
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.214	0.2	20
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	0.515	1.5	9928
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.97	2	15851
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.647	3	8608
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.385	4.5	9760
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

LS refinement shell

Resolution: 2.51→2.59 Å / Total num. of bins used: 15 /

	R_factor	Num. reflection
R_free	0.317	446
R_work	0.226	8239

Refinement TLS params.

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

ID	L11 (°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)
1	5.9985	0.2852	-1.0254	2.5405	-0.4424	4.8708	0.1534	-0.4116	-0.15	0.0434	0.0586	0.1968	-0.1029	0.175	-0.2119	0.026	-0.0088	-0.0032	0.1849	-0.0265	0.0774	117.227	123.22	0.333
2	8.1072	0.5814	1.2102	2.5379	-1.0706	3.6815	0.1084	-0.3167	0.2423	-0.0124	0.0442	0.3155	-0.189	-0.3199	-0.1526	0.0546	0.0474	0.0531	0.2731	0.0994	0.2757	90.597	120.356	-0.642
3	0.9447	-1.101	0.3616	5.5014	-1.3157	0.9313	0.0806	0.1978	-0.0962	-0.1433	-0.1637	0.5715	0.1707	-0.1373	0.0832	0.092	-0.008	0.0663	0.3974	0.0264	0.3634	76.286	86.353	-5.648
4	6.9092	0.6168	-0.7168	2.6917	0.1278	4.3897	0.0438	0.3313	-0.283	-0.1631	0.141	0.1388	-0.0176	0.2398	-0.1847	0.0366	-0.0375	-0.0211	0.1135	-0.0359	0.0973	169.773	25.222	0.107
5	8.4287	1.9938	1.9537	4.1513	1.0709	3.2113	-0.3025	0.3261	0.1002	-0.2327	0.1476	0.1804	-0.2347	-0.1897	0.155	0.0572	-0.0462	-0.0201	0.1465	-0.0065	0.1546	143.419	21.021	-1.545
6	0.535	-0.6449	0.4741	4.129	-0.7882	1.2062	0.055	-0.1044	-0.0605	-0.06	-0.1025	0.4964	0.2347	-0.0603	0.0476	0.094	-0.0252	0.0438	0.2575	-0.0145	0.3516	131.13	-13.245	-7.298
7	5.6701	-0.0502	1.5666	2.5917	-0.7011	3.909	0.0063	0.1121	0.1154	0.1327	0.0729	-0.0122	0.0063	-0.0558	-0.0791	0.1846	-0.0095	0.0089	0.0432	0.021	0.0636	105.629	68.716	1.113
8	7.4596	0.852	-0.358	2.514	-1.0822	3.2942	-0.3209	0.5485	0.1649	-0.1128	-0.0139	-0.2276	0.0224	0.3926	0.3348	0.2285	-0.0527	-0.0315	0.2154	0.0846	0.1763	132.202	71.963	-0.801
9	0.7515	-0.3564	-0.1863	3.3355	1.3565	1.5669	0.0331	-0.2034	0.0097	-0.0225	-0.048	-0.2318	0.0474	-0.049	0.015	0.0089	-0.0435	-0.0237	0.3747	0.0465	0.1773	146.615	106.133	-6.851
10	7.2858	0.1004	0.6688	2.0398	0.2358	4.387	0.411	0.4443	0.2115	0.074	-0.1047	-0.0557	0.0323	-0.0425	-0.3062	0.3075	0.1513	0.0173	0.184	0.0048	0.1053	161.953	-29.15	0.112
11	5.5999	-0.115	-1.5345	2.508	0.2847	2.9273	0.1441	-0.0219	0.0828	0.1456	-0.0732	-0.0768	-0.1226	0.3005	-0.071	0.315	0.1	0.0109	0.2605	-0.0257	0.2107	188.369	-24.785	-1.484
12	0.7475	-0.6193	-0.2079	3.9337	1.6128	1.6403	0.0728	0.1139	-0.0211	-0.2157	-0.049	-0.3094	0.1132	0.249	-0.0237	0.1119	0.039	-0.0109	0.4696	-0.0099	0.2284	200.385	9.704	-6.565

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	38 - 148
2	X-RAY DIFFRACTION	1	A	1101 - 1103
3	X-RAY DIFFRACTION	2	A	149 - 260
4	X-RAY DIFFRACTION	2	A	1104 - 1107
5	X-RAY DIFFRACTION	3	A	261 - 543
6	X-RAY DIFFRACTION	3	A	1108 - 1116
7	X-RAY DIFFRACTION	4	B	38 - 148
8	X-RAY DIFFRACTION	4	B	1101 - 1103
9	X-RAY DIFFRACTION	5	B	149 - 260
10	X-RAY DIFFRACTION	5	B	1104 - 1107
11	X-RAY DIFFRACTION	6	B	261 - 541
12	X-RAY DIFFRACTION	6	B	1108 - 1116
13	X-RAY DIFFRACTION	7	C	38 - 148
14	X-RAY DIFFRACTION	7	C	1101 - 1103
15	X-RAY DIFFRACTION	8	C	149 - 260
16	X-RAY DIFFRACTION	8	C	1104 - 1107
17	X-RAY DIFFRACTION	9	C	261 - 544
18	X-RAY DIFFRACTION	9	C	1108 - 1116
19	X-RAY DIFFRACTION	10	D	38 - 148
20	X-RAY DIFFRACTION	10	D	1101 - 1103
21	X-RAY DIFFRACTION	11	D	149 - 260
22	X-RAY DIFFRACTION	11	D	1104 - 1107
23	X-RAY DIFFRACTION	12	D	261 - 542
24	X-RAY DIFFRACTION	12	D	1108 - 1116

Refinement

*PLUS

Lowest resolution: 25 Å / R_factor R_free: 0.258 / R_factor R_work: 0.192

Solvent computation

*PLUS

Displacement parameters

*PLUS

Refine LS restraints

*PLUS

Refine-ID	Type	Dev ideal
X-RAY DIFFRACTION	r_bond_d	0.014
X-RAY DIFFRACTION	r_angle_d
X-RAY DIFFRACTION	r_angle_deg	1.55
X-RAY DIFFRACTION	r_planar_d	0.005
X-RAY DIFFRACTION	r_plane_restr	0.099

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