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- PDB-6pr0: P133H-S128A S. typhimurium siroheme synthase -

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Basic information

Entry
Database: PDB / ID: 6pr0
TitleP133H-S128A S. typhimurium siroheme synthase
ComponentsSiroheme 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: 1.9 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)101,2324
Polymers100,4632
Non-polymers7692
Water7,080393
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12370 Å2
ΔGint-76 kcal/mol
Surface area35300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.828, 99.882, 146.544
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


Mass: 50231.531 Da / Num. of mol.: 2 / Mutation: P133H
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-SAH / S-ADENOSYL-L-HOMOCYSTEINE


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


Mass: 18.015 Da / Num. of mol.: 393 / 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: 44.3 %
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: 1.9→47.27 Å / Num. obs: 69444 / % possible obs: 99.1 % / Redundancy: 12.8 % / Biso Wilson estimate: 34.13 Å2 / Rmerge(I) obs: 0.1881 / Rpim(I) all: 0.05325 / Net I/σ(I): 19.3
Reflection shellResolution: 1.9→1.968 Å / Num. unique obs: 6801 / Rpim(I) all: 0.3946 / % possible all: 98.5

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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: 1.9→47.27 Å / SU ML: 0.2389 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.131
RfactorNum. reflection% reflection
Rfree0.229 1785 2.57 %
Rwork0.1801 --
obs0.1814 69368 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 48.65 Å2
Refinement stepCycle: LAST / Resolution: 1.9→47.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6965 0 0 393 7358
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00697169
X-RAY DIFFRACTIONf_angle_d0.89059724
X-RAY DIFFRACTIONf_chiral_restr0.05791117
X-RAY DIFFRACTIONf_plane_restr0.00511277
X-RAY DIFFRACTIONf_dihedral_angle_d4.96885950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.33281350.31175100X-RAY DIFFRACTION98.33
1.95-2.010.36411360.2745146X-RAY DIFFRACTION99.23
2.01-2.070.22231360.21855146X-RAY DIFFRACTION99.7
2.07-2.150.28251370.20585166X-RAY DIFFRACTION99.76
2.15-2.230.25591370.20785189X-RAY DIFFRACTION99.81
2.23-2.340.26941370.22265176X-RAY DIFFRACTION99.35
2.34-2.460.27151360.19245192X-RAY DIFFRACTION100
2.46-2.610.22151380.1885222X-RAY DIFFRACTION100
2.61-2.810.24391390.19255238X-RAY DIFFRACTION100
2.81-3.10.24631380.19745246X-RAY DIFFRACTION100
3.1-3.550.22771400.18075304X-RAY DIFFRACTION99.89
3.55-4.470.20861310.14154946X-RAY DIFFRACTION92.97
4.47-47.270.18921450.15635512X-RAY DIFFRACTION99.25
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)
14.579835825081.403876494190.06614833977052.936508132210.3374517634731.894305331420.115900639058-0.29233264381-0.4774185018010.121477427343-0.0734733172971-0.03618182119590.185484678430.0254047754698-0.02126610859760.1700993306330.000113257221039-0.03792867915740.2011298241420.004169440699660.29983060725829.557430178-21.130890018947.6631442142
23.328586895890.08835792479882.228734131073.075706056981.488531654667.192321491930.416982213233-0.221594972896-0.814235035042-0.246290713689-0.159138495139-0.1916505453521.29419741287-0.61182483908-0.3022564198870.423130761015-0.0834593003450.002932022269610.417042235188-0.02077582714260.38668682716349.6298660062-24.146260132138.4067959623
34.574109187010.1686080491810.3315008892612.749150627880.6421958987153.30444523633-0.0115007081699-0.475400722977-0.186517237425-0.03320753524790.021333494760.118550604863-0.123644477897-0.38736373263-0.006358523211140.205604564791-0.02109396995350.001245265424540.410125313423-0.006750660637130.21326205567266.7736487909-14.275650036754.9320371318
40.402172531901-0.182566376368-0.3427568591481.14133434383-0.543038411421.034766260380.0158071604407-0.2636172852540.1055824441140.35502042921-0.00993983743544-0.0643787875831-0.2556742281440.0208854221468-0.03174004739590.3742907783760.002972924066710.05122642417720.294484461691-0.0490147595250.25093143525467.3594096488-3.3434952249233.9728691335
52.290920807810.314687695012-0.4860494852461.91114770409-0.4082300728842.539328278060.135291581518-0.2409061219480.5851598762650.27463156684-0.07772983536950.226330644699-0.6721426215190.0179109091506-0.03858788217740.4037816311730.007067870048750.05770231736510.212153523121-0.05049312788150.32560029369467.44261715633.7878718547227.7598198704
62.835459671751.10177840202-1.189458736222.9894193035-2.163180120824.57176611078-0.06994641747410.4128085378030.139980972739-0.3465705025480.1736256513530.1032419489770.115181787999-0.235458069638-0.08977326767440.3087439251430.0137081478283-0.02894505628620.309595043280.02757277562010.20498867213367.5784405192-1.403962774921.19030442812
71.40476237349-0.447963735642-0.5825228334732.211851691070.7957705988931.895229355720.03143865562040.08404405745940.0416171263013-0.256761375535-0.06118631435680.19565089835-0.08352481322520.05328590114790.04459121679990.223350999687-0.0386997449089-0.06188061394590.2508069136870.006350973901480.29871302242343.9529602034-9.3030227020735.4350636692
81.918621872030.652848389313-0.3991325273362.64077433255-1.232429356412.7365774949-0.05872617030680.0690017208708-0.260517992708-0.191933351313-0.144498922462-0.3441362098360.4093070788880.4008012267860.1094917329810.2600779349990.1087422007210.03882711591820.259665291702-0.003988627118510.24308108771178.5764735549-14.290646655315.5514658286
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 148 )
3X-RAY DIFFRACTION3chain 'A' and (resid 149 through 209 )
4X-RAY DIFFRACTION4chain 'A' and (resid 210 through 247 )
5X-RAY DIFFRACTION5chain 'A' and (resid 248 through 340 )
6X-RAY DIFFRACTION6chain 'A' and (resid 341 through 457 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 209 )
8X-RAY DIFFRACTION8chain 'B' and (resid 210 through 457 )

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