PDB-6p5z: Cobalt-sirohydrochlorin-bound S. typhimurium siroheme synthase

ID or keywords:

Entry

Database: PDB / ID: 6p5z

Title

Cobalt-sirohydrochlorin-bound S. typhimurium siroheme synthase

Components

Siroheme synthase

Keywords

BIOSYNTHETIC PROTEIN / tetrapyrrole biosynthesis / CysG

Function / homology

Function and homology information

precorrin-2 dehydrogenase / precorrin-2 dehydrogenase activity / uroporphyrinogen-III C-methyltransferase / uroporphyrin-III C-methyltransferase activity / sirohydrochlorin ferrochelatase / sirohydrochlorin ferrochelatase activity / siroheme biosynthetic process / cobalamin biosynthetic process / NAD binding / methylation
Similarity search - Function

Biological species

Salmonella typhimurium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.26 Å

Authors

Pennington, J.M. / Stroupe, M.E.

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2020
Title: Siroheme synthase orients substrates for dehydrogenase and chelatase activities in a common active site.
Authors: Pennington, J.M. / Kemp, M. / McGarry, L. / Chen, Y. / Stroupe, M.E.

History

Deposition	May 31, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 16, 2021	Provider: repository / Type: Initial release
Revision 1.1	Dec 29, 2021	Group: Database references / Category: citation / citation_author / database_2 Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2	Oct 11, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	6p5z.cif.gz	441.5 KB	Display	PDBx/mmCIF format
PDB format	pdb6p5z.ent.gz	303.6 KB	Display	PDB format
PDBx/mmJSON format	6p5z.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	6p5z_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	6p5z_full_validation.pdf.gz	1.8 MB	Display
Data in XML	6p5z_validation.xml.gz	34.7 KB	Display
Data in CIF	6p5z_validation.cif.gz	47.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p5/6p5z ftp://data.pdbj.org/pub/pdb/validation_reports/p5/6p5z	HTTPS FTP

-
Related structure data

Related structure data	6p5xC 6p7cC 6p7dC 6pqzC 6pr0C 6pr1C 6pr2C 6pr3C 6pr4C 6uluC 6vebC 1pjsS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	1pjt-d 6pr0-d 1pjs-d 6p5x-d 6pr1-d 6ulu-d 6p7c-d 6pr4-d 1pjq-d 5vev-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Siroheme synthase

B: Siroheme synthase

hetero molecules

103 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	59.601, 100.446, 146.400
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab

#1: Protein	Siroheme synthase Mass: 50190.500 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Salmonella typhimurium (bacteria) Gene: cobA, cysG, C2253_19735, CET98_25025, D7F20_23535, D7H43_21790, DJ388_17225, NCTC13348_03825 Production host: Escherichia coli (E. coli) / Variant (production host): LMG194 References: UniProt: A0A3V0JC15, UniProt: A0A0F7JCI1*PLUS, uroporphyrinogen-III C-methyltransferase, precorrin-2 dehydrogenase, sirohydrochlorin ferrochelatase
#2: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#3: Chemical	ChemComp-F0X / cobalt-sirohydrochlorin Mass: 919.749 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₄₂H₄₄CoN₄O₁₆ / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.17 Å³/Da / Density % sol: 43.24 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 4-14% PEG 4000, 100 mM 2-(N-morpholino)ethanesulfonic acid (MES) pH 5.0, 500mM sodium chloride, 7 mM 2-Mercaptoethanol (BME), microseeded

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 10, 2017
Radiation	Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.26→50 Å / Num. obs: 41427 / % possible obs: 99 % / Redundancy: 7.1 % / B_iso Wilson estimate: 57.55 Å² / Net I/σ(I): 39
Reflection shell	Resolution: 2.26→2.3 Å / Num. unique obs: 1769

-
Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1PJS

1pjs

Resolution: 2.26→35.34 Å / SU ML: 0.2836 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4781

	R_factor	Num. reflection	% reflection
R_free	0.2416	1998	4.83 %
R_work	0.179	-	-
obs	0.1819	41335	98.9 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 77.88 Å²

Refinement step

Cycle: LAST / Resolution: 2.26→35.34 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6956	0	128	53	7137

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0073	7237
X-RAY DIFFRACTION	f_angle_d	1.3304	9838
X-RAY DIFFRACTION	f_chiral_restr	0.0569	1112
X-RAY DIFFRACTION	f_plane_restr	0.0055	1281
X-RAY DIFFRACTION	f_dihedral_angle_d	16.0542	4360

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.26-2.32	0.2828	125	0.2499	2458	X-RAY DIFFRACTION	87.77
2.32-2.38	0.3021	141	0.2382	2794	X-RAY DIFFRACTION	99.09
2.38-2.45	0.2882	141	0.2379	2766	X-RAY DIFFRACTION	99.9
2.45-2.53	0.3193	143	0.2251	2809	X-RAY DIFFRACTION	99.53
2.53-2.62	0.2857	141	0.2114	2777	X-RAY DIFFRACTION	99.66
2.62-2.73	0.2671	143	0.2139	2823	X-RAY DIFFRACTION	99.8
2.73-2.85	0.3	142	0.2181	2797	X-RAY DIFFRACTION	99.86
2.85-3	0.2885	144	0.2319	2827	X-RAY DIFFRACTION	99.87
3-3.19	0.3352	143	0.224	2822	X-RAY DIFFRACTION	100
3.19-3.44	0.264	145	0.207	2834	X-RAY DIFFRACTION	100
3.44-3.78	0.2467	145	0.1809	2844	X-RAY DIFFRACTION	100
3.78-4.33	0.2198	145	0.1549	2879	X-RAY DIFFRACTION	100
4.33-5.45	0.2188	148	0.1446	2889	X-RAY DIFFRACTION	99.97
5.45-35.34	0.1973	152	0.1566	3018	X-RAY DIFFRACTION	99.06

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	7.59741204303	2.28192068634	0.0124744647847	4.35413861489	-1.03689607522	3.72559136597	0.0591699782573	-0.476161988407	-0.828510032997	0.0957800779922	0.00490270872524	0.1707497113	0.48180760645	-0.22148955466	-0.0886131667938	0.408128219846	0.0274328495903	-0.0300029245058	0.386611621388	0.0261761713974	0.512332257945	-30.1114913443	-21.0932738688	48.2098916284
2	8.23656321631	2.77073962376	5.79138875888	1.90494448292	2.02738541348	7.83854873284	0.0258670698164	-0.719087963876	-0.243273561205	-0.12308021809	-0.0575838356477	-0.00579666943346	0.0826761512053	-0.289913480569	-0.00891668456825	0.432725178072	0.012484549327	0.0394639757235	0.625720523671	0.0541067859471	0.400468342477	1.14484077881	-17.3622572909	49.5281184836
3	2.77419144069	-0.237962072886	-1.3985574596	1.10596846715	-0.788638592831	3.40335484647	0.160024994965	-0.632879915813	0.525081093365	0.107917995666	-0.0376937326611	-0.124344654363	-0.522698681912	0.118649523174	-0.12938904111	0.507719979533	0.038045673012	0.0603235948164	0.468034033867	-0.0395973584666	0.418734874949	7.45180957702	-3.20462727192	34.220591839
4	4.88750350406	1.17979839489	0.227387164836	4.14556421967	0.0676754843464	5.2372328513	0.240616373437	-0.359171153849	1.12876719517	0.655336985041	-0.133479457251	0.2160166883	-1.14869654495	-0.167559210702	-0.0556115614864	0.76805418266	0.0575543402574	0.0906796472792	0.436994471117	-0.0523047774049	0.616149299858	7.61841552336	3.97743789295	28.2227427692
5	6.17063579168	2.46147313269	-2.25834443799	5.42793292019	-3.8841386591	7.07757286376	-0.028207945896	0.889950357368	0.458576346002	-0.435085093455	0.190248042161	0.309116993	-0.00452179694583	-0.160275081162	-0.131783314102	0.436286909052	0.0272628737811	-0.0755274769765	0.574035301662	0.0501461187522	0.362175798113	9.17765103161	0.614045275378	0.943506087546
6	0.8780081424	-0.772364100358	0.537296777562	9.19038417222	-2.59681385157	2.91024505452	-0.0113367658063	0.77275035605	-0.417855254685	-0.430206455795	0.364062029917	1.14852715445	0.243679154633	-0.817615519022	-0.251565988323	0.569469125928	0.00813402169022	-0.13539190441	0.839061461949	-0.0163868256094	0.586882812269	1.31139472458	-7.49058290387	3.8629072999
7	3.6901572108	2.53325124767	-0.591022922557	8.98551386322	0.113823173765	2.61315227833	0.113433121185	-0.118340542363	0.469627320481	-0.152222011812	0.0374162302274	0.197485764825	-0.338315481309	0.06588228855	-0.157128138266	0.319588601943	0.00921221529972	-0.0219114567664	0.384788989229	-0.0627252683281	0.499188013876	-19.883483514	2.73364218928	43.9111760711
8	5.8641405181	-3.55921238818	-4.6143332354	4.66456655484	1.45882435695	5.13320615659	0.00249281762952	-0.105270590808	0.423070322413	0.0755460613952	0.0436369088688	-0.093653185406	-0.184674590542	0.537073323959	-0.00285079667251	0.316837128824	-0.0460892149572	-0.0360366715562	0.49170629414	-0.0689394092816	0.469373207303	-13.2914677608	-9.32765891501	45.1603955608
9	3.26116369917	-2.14413739744	0.34957109933	3.73564416159	0.882989601491	6.82537650838	-0.166546699116	0.260781426606	-0.661657318375	-0.325396828888	-0.246486679159	0.83806003406	0.26277239862	-0.645408438979	0.385899705036	0.450566008389	-0.0590812888892	0.0180264169876	0.539066584931	0.0529319151644	0.690882977118	-11.9102706829	-21.8146737335	26.9681025787
10	2.61124648988	-2.11899732747	-1.06545045162	8.78515713666	0.628772678797	6.69004179528	0.467407644514	0.576685233027	-0.245469601484	-0.76317572095	-1.17364578696	-1.09512980808	1.20576663927	-0.223771550652	0.624716196088	0.80222824299	-0.0175780124738	-0.116853071303	0.771286924613	0.00799033644237	0.683817161679	-12.2147047636	-24.7668572158	15.55465425
11	4.71823472916	0.379416336583	1.39130803433	7.48565109438	1.47382877947	5.05421660262	-0.0340347496093	-0.196315279239	-0.832264415579	0.169666340655	0.00829069928312	0.245496608066	0.563609309847	0.0328801006988	-0.0305514806945	0.528273595948	0.0356911735877	0.0944549869029	0.392217168657	0.0677266459961	0.479601546092	8.03097109093	-25.7840798949	21.3647960296
12	3.58346037864	1.7798640301	-0.411995414688	5.01929758193	-1.59773756296	3.33882072583	-0.287697471231	0.723099761349	-0.610868474887	-1.02233999171	0.152340586636	-0.272580093655	0.694864980635	0.23093226218	0.0605051685924	0.668454891844	0.117688485568	0.0566604038677	0.533520176277	-0.0820189485729	0.444107152968	11.6887989058	-17.7427263825	12.1262655008
13	5.37685366932	0.479766303181	-1.45370806285	4.92569206464	-1.146547437	4.51698280187	-0.0139501182129	0.443276425265	-0.236369586499	-0.127252629608	-0.727717567883	-1.07350062103	-0.0863657742865	1.41036963372	0.606562966456	0.387145481937	0.0552176904623	-0.0251823016437	0.804120787129	0.182541750715	0.710571573759	30.005565646	-4.322432149	15.1438476492

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 114 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 115 through 209 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 210 through 247 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 248 through 339 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 340 through 432 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 433 through 457 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1 through 96 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 97 through 132 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 133 through 174 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 175 through 209 )
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 210 through 278 )
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 279 through 351 )
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 352 through 457 )

-
News

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

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

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

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi