PDB-6p7d: D104N S. typhimurium siroheme synthase

ID or keywords:

Entry

Database: PDB / ID: 6p7d

Title

D104N S. typhimurium siroheme synthase

Components

Siroheme synthase

Keywords

TRANSFERASE / sirohydrochlorin / precorrin-2 / 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 /

molecular replacement / Resolution: 2.4 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	Jun 5, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 26, 2020	Provider: repository / Type: Initial release
Revision 1.1	Mar 13, 2024	Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6p7d.cif.gz	440.2 KB	Display	PDBx/mmCIF format
PDB format	pdb6p7d.ent.gz	303.5 KB	Display	PDB format
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Validation report

Summary document	6p7d_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	6p7d_full_validation.pdf.gz	1.1 MB	Display
Data in XML	6p7d_validation.xml.gz	34.5 KB	Display
Data in CIF	6p7d_validation.cif.gz	47.6 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/p7/6p7d ftp://data.pdbj.org/pub/pdb/validation_reports/p7/6p7d	HTTPS FTP

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Related structure data

Related structure data	6p5xC 6p5zC 6p7cC 6pqzC 6pr0C 6pr1C 6pr2C 6pr3C 6pr4C 6uluC 6vebC 1pjs C: citing same article (ref.)
Similar structure data	6pr3-d 6lin-2 2q7q-d 6veb-d 6pr4-d 5fpd-d 2agx-d 4jn5-d 4jn3-d 2ojy-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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Siroheme synthase

B: Siroheme synthase

hetero molecules

101 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)	60.096, 99.329, 147.421
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: 50189.516 Da / Num. of mol.: 2 / Mutation: S128A, D104N 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) References: UniProt: A0A3V0JC15, UniProt: P25924*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-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 111 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.24 Å³/Da / Density % sol: 45.09 %
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

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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: Nov 20, 2017

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1 Å / Relative weight: 1

Reflection

Resolution: 2.11→50 Å / Num. obs: 44327 / % possible obs: 86.7 % / Redundancy: 10.5 % / B_iso Wilson estimate: 53.88 Å² / R_merge(I) obs: 0.233 / R_pim(I) all: 0.067 / R_rim(I) all: 0.243 / Χ²: 3.475 / Net I/σ(I): 6 / Num. measured all: 464961

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	Num. unique obs	CC_1/2	Χ²	% possible all	R_merge(I) obs	R_pim(I) all	R_rim(I) all
2.11-2.15	1.1	239	0.107	0.655	9.5
2.15-2.19	1.3	572	0.107	0.71	22.8	2.056	1.877	2.796
2.19-2.23	1.5	1117		0.549	43.8	2.272	1.891	2.975
2.23-2.27	2.1	1720	0.073	0.616	68.9	2.29	1.624	2.833
2.27-2.32	2.8	2210	0.165	0.608	88.4	1.948	1.232	2.328
2.32-2.38	4.1	2455	0.25	0.628	97.3	1.703	0.881	1.933
2.38-2.44	5.9	2502	0.352	0.641	99.8	1.627	0.712	1.784
2.44-2.5	7.4	2548	0.516	0.651	100	1.553	0.601	1.669
2.5-2.58	8.7	2527	0.683	0.668	100	1.402	0.498	1.49
2.58-2.66	10	2521	0.78	0.669	100	1.411	0.461	1.486
2.66-2.75	11.8	2554	0.843	0.699	100	1.509	0.451	1.576
2.75-2.86	13.3	2549	0.897	0.742	100	1.405	0.396	1.461
2.86-2.99	14.1	2542	0.948	0.822	100	1.12	0.309	1.162
2.99-3.15	14.3	2565	0.968	1.004	100	0.728	0.199	0.755
3.15-3.35	14.5	2541	0.977	1.435	100	0.471	0.128	0.488
3.35-3.61	14.5	2571	0.986	2.357	100	0.292	0.079	0.302
3.61-3.97	14.5	2593	0.989	4.215	100	0.211	0.057	0.219
3.97-4.54	14.5	2600	0.991	7.446	100	0.165	0.045	0.171
4.54-5.72	14.4	2632	0.994	8.269	100	0.133	0.036	0.137
5.72-50	13.6	2769	0.993	13.53	99.7	0.118	0.033	0.122

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	7.04 Å	42.17 Å
Translation	7.04 Å	42.17 Å

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Processing

Software

Name	Version	Classification
PHENIX	1.13_2998	refinement
HKL-2000		data scaling
PHASER	2.8.0	phasing
PDB_EXTRACT	3.25	data extraction
HKL-2000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.4→38.28 Å / SU ML: 0.3386 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.6692

	R_factor	Num. reflection	% reflection
R_free	0.2503	1614	4.57 %
R_work	0.1796	-	-
obs	0.1828	35284	99.96 %

Solvent computation

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

Displacement parameters

B_iso mean: 70.29 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→38.28 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6941	0	1	111	7053

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0086	7187
X-RAY DIFFRACTION	f_angle_d	1.0538	9751
X-RAY DIFFRACTION	f_chiral_restr	0.0575	1118
X-RAY DIFFRACTION	f_plane_restr	0.0057	1282
X-RAY DIFFRACTION	f_dihedral_angle_d	5.1731	5964

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 (%)
2.4-2.47	0.3582	132	0.2761	2771	X-RAY DIFFRACTION	99.9
2.47-2.55	0.2922	132	0.2462	2737	X-RAY DIFFRACTION	100
2.55-2.64	0.2796	133	0.2208	2788	X-RAY DIFFRACTION	100
2.64-2.75	0.3083	132	0.2233	2756	X-RAY DIFFRACTION	100
2.75-2.87	0.2945	133	0.2194	2762	X-RAY DIFFRACTION	100
2.87-3.02	0.2879	135	0.2237	2802	X-RAY DIFFRACTION	100
3.02-3.21	0.2801	133	0.199	2769	X-RAY DIFFRACTION	100
3.21-3.46	0.2602	133	0.1897	2799	X-RAY DIFFRACTION	100
3.46-3.81	0.2801	135	0.1736	2803	X-RAY DIFFRACTION	100
3.81-4.36	0.2255	136	0.1444	2833	X-RAY DIFFRACTION	99.97
4.36-5.49	0.2028	136	0.1527	2865	X-RAY DIFFRACTION	99.97
5.49-38.28	0.2325	144	0.1697	2985	X-RAY DIFFRACTION	99.74

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	7.25575617189	3.07675870273	-1.49963850504	6.23068731419	-1.66796379164	3.35695366272	-0.0531025758498	-0.298211149612	-0.302619818641	0.12852102563	0.0970148769588	-0.192640871637	0.354442017155	-0.0124446311363	-0.0457160081279	0.33396050437	0.0263077522324	-0.0524445212904	0.35498867715	-0.0549155618033	0.343170725063	-0.706019894299	-20.7962928677	47.7701228455
2	8.30968900504	4.5315280801	5.94631248176	3.37799510163	3.02744785495	8.52257058726	0.15788760779	-0.827644146738	0.0119894374037	-0.0999528065705	-0.291793997529	-0.0825785361952	0.0341874024733	-0.761504918754	0.101896587225	0.29531764196	0.0916236874891	0.0667102673957	0.405389751663	0.010530936903	0.353720390084	27.4691855649	-16.4388575641	46.4176657431
3	6.53648222648	3.37258866114	1.68007975245	3.22217389201	-1.00407386511	2.87106660468	-0.0574672264659	-0.498946763264	-0.989541799785	-0.117607975197	0.0682122665298	-0.227291875258	0.434647149842	0.411805859507	0.0662118970643	0.439664989422	-0.0242189452165	0.0128551532733	0.566015334211	-0.0164381676488	0.488714707722	41.0334722605	-19.7100998634	57.2229774696
4	0.558227618285	-0.504414969713	0.54772362286	0.708170341639	-1.46599255406	2.98768788218	-0.198938936748	-0.226316168186	0.253144583745	0.321860327261	-0.107189689694	0.0863087592612	-0.166334054945	-0.643020028541	0.329488428746	0.635297633794	0.0164708537989	0.111748568674	0.430463983287	-0.00830452578	0.470815826911	37.6057488164	-2.67295923433	34.2248294821
5	5.31639065534	-0.832994207847	0.763072965632	6.6371444179	1.91908661905	6.49758779443	-0.151447174534	0.00291607703788	0.551037942183	0.24474988545	-0.149815832007	0.543870925489	-1.03841185587	0.113455612244	0.22999703251	0.855831690269	0.0625167667012	0.0310438512783	0.416737302591	-0.0403388789463	0.577968700416	36.1735686405	6.83191689941	28.2406904514
6	5.01474059534	2.36343749824	2.65880065991	7.14072180141	0.244211114466	2.5469974373	0.0993281233591	0.33456485253	0.165968668082	-0.00725170762534	-0.106435647199	-0.111182123132	0.949383621634	-0.172515752906	-0.130922532955	0.331396318323	0.00956858285721	0.0152854812387	0.288911232064	0.0632507346602	0.367930623635	41.7033584574	-7.5349916244	13.0476845246
7	6.8124542382	2.30847494167	-0.491257141335	5.86612347271	-3.78625263029	7.58569790689	0.213343799894	0.327706724124	0.401203568968	-0.0972471535006	-0.141370933939	0.145443947025	-0.339895732541	0.139672964259	-0.122948963453	0.388959975542	0.0678222575365	-0.042026885921	0.415455426284	0.0445627941021	0.367513391938	40.6555186764	1.99740066909	0.184748565525
8	4.36053997403	-0.540873810424	0.0136620511444	2.5972748665	-0.801702701743	6.78428355516	0.0444710447266	0.299792608732	-0.299267340807	-0.815734985702	0.246939421135	0.793068084234	0.469479775509	-1.22884697049	-0.286558343555	0.448941312984	-0.162200724311	-0.076621104083	0.67732898566	0.0882258599835	0.546691411375	31.0484370249	-5.29625098615	0.118438600829
9	1.61544168388	-0.457777702377	-1.01597262394	3.38735885133	1.55002342245	2.76659548582	0.0250242019802	0.0103597620532	0.340498057567	-0.164376815089	0.0806781216274	0.12655439766	-0.332631097974	0.231674067912	-0.0964924441393	0.359741716584	-0.0694371915596	-0.00868321249571	0.465659208166	-0.00523604420482	0.432224900843	13.2890130538	-2.95879536641	41.5332200489
10	5.10887980625	1.66779880626	-0.371664946698	2.93917747204	-1.3253792624	2.7759588815	-0.0862054068974	0.0856085047646	-0.0902594976726	-0.229124328519	-0.173727136862	-0.306345274266	0.280145103811	0.261252170404	0.232377171717	0.502772305861	0.0696617587407	-0.0284405875417	0.383303922545	0.00536072691865	0.352209935601	42.6804338477	-16.6756945482	15.5218217774

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 184 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 185 through 208 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 209 through 247 )
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 248 through 319 )
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 320 through 351 )
7	X-RAY DIFFRACTION	7	chain 'A' and (resid 352 through 416 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 417 through 457 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 161 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 162 through 455 )

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