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- PDB-6pr1: R260A/S128A S. typhimurium siroheme synthase -

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Basic information

Entry
Database: PDB / ID: 6pr1
TitleR260A/S128A S. typhimurium siroheme synthase
ComponentsSiroheme synthaseSirohaem synthase
KeywordsTRANSFERASE / 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
Sirohaem synthase / Sirohaem synthase, dimerisation domain / Sirohaem synthase, dimerisation domain superfamily / Sirohaem synthase dimerisation region / Sirohaem synthase, N-terminal / Siroheme synthase, central domain / Putative NAD(P)-binding / Sirohaem biosynthesis protein central / Uroporphyrin-III C-methyltransferase / Uroporphyrin-III C-methyltransferase signature 2. ...Sirohaem synthase / Sirohaem synthase, dimerisation domain / Sirohaem synthase, dimerisation domain superfamily / Sirohaem synthase dimerisation region / Sirohaem synthase, N-terminal / Siroheme synthase, central domain / Putative NAD(P)-binding / Sirohaem biosynthesis protein central / Uroporphyrin-III C-methyltransferase / Uroporphyrin-III C-methyltransferase signature 2. / Uroporphyrin-III C-methyltransferase signature 1. / Uroporphiryn-III C-methyltransferase, conserved site / Tetrapyrrole methylase, subdomain 2 / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
S-ADENOSYL-L-HOMOCYSTEINE / Siroheme synthase / Siroheme synthase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsPennington, J.M. / Stroupe, M.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB1149763 United States
CitationJournal: 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
DepositionJul 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 26, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Siroheme synthase
B: Siroheme synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,0486
Polymers100,2092
Non-polymers8404
Water8,737485
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12500 Å2
ΔGint-97 kcal/mol
Surface area35940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.619, 99.553, 147.516
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Siroheme synthase / Sirohaem synthase


Mass: 50104.383 Da / Num. of mol.: 2 / Mutation: R260A, S128A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria)
Gene: cysG, cobA, AAP89_23165, ABO94_22995, AF480_23265, AF488_22710, AF489_21700, AIC76_23675, AXR84_23260, AXU58_22185, C2253_19735, CD48_22680, CE87_23070, CET98_25025, CVR97_13625, D7F20_23535, ...Gene: cysG, cobA, AAP89_23165, ABO94_22995, AF480_23265, AF488_22710, AF489_21700, AIC76_23675, AXR84_23260, AXU58_22185, C2253_19735, CD48_22680, CE87_23070, CET98_25025, CVR97_13625, D7F20_23535, D7H43_21790, DJ388_17225, E2F01_22980, FCJ89_03505, FGA22_01875, FGA24_01980, FGA25_01865, FGA26_01870, GW08_22845, JO10_22525, LZ63_24065, NCTC13348_03825, NG18_22490, NU83_22495, QA89_22165, QB40_24005, QD15_23475, RJ78_23420, SE14_03689, Y934_21155, YG50_22125, YI33_23225, YR17_23015, ZC54_23835
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0F7JCI1, UniProt: P25924*PLUS, uroporphyrinogen-III C-methyltransferase, precorrin-2 dehydrogenase, sirohydrochlorin ferrochelatase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 485 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.21 Å3/Da / Density % sol: 44.26 %
Crystal growTemperature: 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)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.82→47.16 Å / Num. obs: 79224 / % possible obs: 99.7 % / Redundancy: 13.8 % / Biso Wilson estimate: 30.41 Å2 / Rmerge(I) obs: 0.1322 / Rpim(I) all: 0.03647 / Net I/σ(I): 21.4
Reflection shellResolution: 1.82→1.885 Å / Num. unique obs: 7615 / Rpim(I) all: 0.4639 / % possible all: 97.34

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PJS

1pjs


Resolution: 1.82→47.16 Å / SU ML: 0.2372 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.952
RfactorNum. reflection% reflection
Rfree0.2101 2000 2.53 %
Rwork0.1761 --
obs0.177 79193 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.77 Å2
Refinement stepCycle: LAST / Resolution: 1.82→47.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6967 0 2 485 7454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00637250
X-RAY DIFFRACTIONf_angle_d0.87779847
X-RAY DIFFRACTIONf_chiral_restr0.05871127
X-RAY DIFFRACTIONf_plane_restr0.0051300
X-RAY DIFFRACTIONf_dihedral_angle_d5.54445985
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.870.37911360.31895248X-RAY DIFFRACTION96.28
1.87-1.920.29661430.26355490X-RAY DIFFRACTION100
1.92-1.970.26691400.21265428X-RAY DIFFRACTION99.98
1.97-2.040.23061420.20155489X-RAY DIFFRACTION100
2.04-2.110.21471420.19295482X-RAY DIFFRACTION100
2.11-2.190.21191420.19535453X-RAY DIFFRACTION100
2.19-2.290.25171420.19555512X-RAY DIFFRACTION100
2.29-2.410.26871420.19345495X-RAY DIFFRACTION100
2.41-2.570.2441430.18845510X-RAY DIFFRACTION99.98
2.57-2.760.21161430.19165521X-RAY DIFFRACTION100
2.76-3.040.25141440.19255547X-RAY DIFFRACTION100
3.04-3.480.19561440.17735575X-RAY DIFFRACTION100
3.48-4.390.16511450.14295604X-RAY DIFFRACTION99.5
4.39-47.160.18071520.15025839X-RAY DIFFRACTION99.53
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)
13.216959821451.47563537278-0.04251057584342.87534841263-0.3015152496691.81883345420.0521164816648-0.129888523069-0.463150620380.03566653032250.00801426863086-0.1591110036030.2591584657410.0735499069091-0.04741299824460.1611794917350.0190929606254-0.02886524494050.17617663267-0.02177541066720.2682542205829.4446472447-21.004717936647.7560676758
23.985137420491.048885729642.246400643890.9074684481930.364755338893.34815540630.0929157858429-0.478849698423-0.260166639383-0.02480927675-0.116800497394-0.02960049716830.0629612121034-0.3434956438840.0092328707960.1895122380550.0128721359770.03683857991260.291797081029-0.02310866850640.20647256009661.1098460184-16.952160851449.6783088516
31.533821320140.211684427966-0.7957756255911.20674602806-1.714258422683.907196631390.05651781534660.01552779883070.2523989398950.1078420323570.05968313627690.0919613941077-0.547076025886-0.0803066892018-0.05419476839080.2669607024280.02029445667640.005833313236440.143956022302-0.01959810809560.2351262274967.1170619680.21022091202315.3916900455
40.678850338427-0.0698421958594-0.3248405516251.386125924340.3666198868721.47410951665-0.06696031971370.09708421811740.0880278942611-0.1247198905540.03937800059680.134463194344-0.05323582700790.05909945349780.0416428926370.187817846051-0.0461254602239-0.04648033974650.265077634492-0.006325579047250.2765924280843.610927332-8.2497772587137.2071482909
51.979562916510.266420330317-0.2237095719012.48753714084-1.457854430863.06402839492-0.05224819524330.0608103868113-0.181781638381-0.246854396059-0.156419719064-0.3385138629390.3354324406220.3963781060050.1079656251220.2274786707210.05923062369230.03092308441110.2150111416540.004976331099420.20522803779576.6634733101-14.811728978715.2538427424
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 114 )
2X-RAY DIFFRACTION2chain 'A' and (resid 115 through 209 )
3X-RAY DIFFRACTION3chain 'A' and (resid 210 through 457 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 196 )
5X-RAY DIFFRACTION5chain 'B' and (resid 197 through 457 )

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