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- PDB-6p5x: Sirohydrochlorin-bound S. typhimurium siroheme synthase -

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Basic information

Entry
Database: PDB / ID: 6p5x
TitleSirohydrochlorin-bound S. typhimurium siroheme synthase
ComponentsSiroheme synthase
KeywordsBIOSYNTHETIC PROTEIN / 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
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 / Chem-SHN / Siroheme synthase / Siroheme synthase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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
DepositionMay 31, 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)102,0847
Polymers100,3812
Non-polymers1,7035
Water5,657314
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13020 Å2
ΔGint-85 kcal/mol
Surface area35290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.061, 99.784, 145.463
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Siroheme synthase


Mass: 50190.500 Da / Num. of mol.: 2 / Mutation: S128A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria)
Gene: cobA, C2253_19735, CET98_25025, D7F20_23535, D7H43_21790, DJ388_17225
Production host: Escherichia coli (E. coli) / Variant (production host): LMG194
References: UniProt: A0A3V0JC15, UniProt: P25924*PLUS, uroporphyrinogen-III C-methyltransferase
#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.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-SHN / 3,3',3'',3'''-[(7S,8S,12S,13S)-3,8,13,17-tetrakis(carboxymethyl)-8,13-dimethyl-7,8,12,13-tetrahydroporphyrin-2,7,12,18-tetrayl]tetrapropanoic acid


Mass: 862.832 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H46N4O16 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.16 Å3/Da / Density % sol: 43.03 %
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), microseeded

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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: Mar 10, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.97→50 Å / Num. obs: 62657 / % possible obs: 99.8 % / Redundancy: 14.5 % / Biso Wilson estimate: 36.97 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.1034 / Rpim(I) all: 0.02865 / Net I/σ(I): 60
Reflection shellResolution: 1.97→2 Å / Rmerge(I) obs: 0.5818 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 3107 / CC1/2: 0.917 / Rpim(I) all: 0.1729

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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: 1PJT

1pjt


Resolution: 1.97→38.38 Å / SU ML: 0.2268 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.8107 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.22 1444 2.31 %
Rwork0.1734 61061 -
obs0.1745 62505 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.92 Å2
Refinement stepCycle: LAST / Resolution: 1.97→38.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7050 0 2 314 7366
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00637436
X-RAY DIFFRACTIONf_angle_d0.88110123
X-RAY DIFFRACTIONf_chiral_restr0.05651151
X-RAY DIFFRACTIONf_plane_restr0.00481333
X-RAY DIFFRACTIONf_dihedral_angle_d18.02752827
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.040.28551420.22086000X-RAY DIFFRACTION99.47
2.04-2.120.29151430.21396063X-RAY DIFFRACTION100
2.12-2.220.27161430.20476047X-RAY DIFFRACTION99.98
2.22-2.340.26621420.19756027X-RAY DIFFRACTION100
2.34-2.480.24351450.26084X-RAY DIFFRACTION100
2.48-2.670.22451420.19516049X-RAY DIFFRACTION100
2.67-2.940.23881450.19856112X-RAY DIFFRACTION100
2.94-3.370.21011450.19226138X-RAY DIFFRACTION100
3.37-4.240.21671460.15036180X-RAY DIFFRACTION99.79
4.24-38.380.18981510.14826361X-RAY DIFFRACTION98.79
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)
16.826483914421.33002103792-0.0121028011571.55179135651-0.09707598975381.339130436710.0317200475128-0.154890393717-0.595329611010.02709711799420.007614453949560.09245125530540.1885430213180.00798592252657-0.02505159274350.29019938529-0.00106589148993-0.03487720110330.234462226404-0.01378093277490.3159677415881.88852336763-21.085162402146.5157617997
21.30763704980.348962723739-0.158705268835-0.189471346776-0.6717790555682.991096984040.0672699707397-0.1803442306890.1901664341850.0564341762562-0.015981543006-0.0420062430031-0.4603754486230.0441834429566-0.06859643749930.4223876336310.03882688408940.03960871904740.308755865367-0.06232465526810.35371045829636.530018445-5.4651626754938.0920077031
34.664825216741.37933669883-1.533266210674.4506049766-3.084320647445.57759293034-0.0147757914520.4523363844880.220759032192-0.2396627019180.1349917259890.09843749426880.0307354403424-0.167747107378-0.1091267463990.2424638492360.00361817622088-0.03769410159350.334115001570.01525414655890.17982146667837.8409831908-1.268747168321.31781490037
41.66917985986-0.590042909694-1.343240686421.082455099610.4085306199191.57017606386-0.01396054460580.181750644887-0.0100617729794-0.166918941502-0.08060920927020.2009679941570.0438631209592-0.1719341107630.08606140116630.27983054311-0.035419002651-0.07262731023750.294988794515-0.008162942676820.32727089655715.935895761-10.800970773433.4061843841
55.98183091111-1.770374929391.60933590868.160344933410.2926969054175.30633283001-0.06072167571630.0869871711761-0.8429804701040.2541124325150.118645923129-0.3240399372270.9518010223080.3293676069410.04136979987830.4643521529590.03936361783420.004632907702440.2233514590130.02128515792610.33109378979741.5848697457-26.785808957521.8521066829
62.717843431831.50955058649-0.6117769651013.08056913984-1.209744357552.257798338-0.0703389450720.257755316357-0.153376513186-0.139615619216-0.116024921859-0.4638136886110.1883905084480.4697041116470.1109724967010.2634197066380.0688469683870.02535142852770.3445854940490.007923961880790.34588066502252.5837103794-10.026163755313.5455113575
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 132 )
2X-RAY DIFFRACTION2chain 'A' and (resid 133 through 340 )
3X-RAY DIFFRACTION3chain 'A' and (resid 341 through 457 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 232 )
5X-RAY DIFFRACTION5chain 'B' and (resid 233 through 278 )
6X-RAY DIFFRACTION6chain 'B' and (resid 279 through 457 )

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