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- PDB-6pr2: R261A/S128A S. typhimurium siroheme synthase -

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Basic information

Entry
Database: PDB / ID: 6pr2
TitleR261A/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: 2.16 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)101,2798
Polymers100,2092
Non-polymers1,0706
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13200 Å2
ΔGint-98 kcal/mol
Surface area34790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.438, 99.758, 146.587
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: 50104.383 Da / Num. of mol.: 2 / Mutation: R261A, 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


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / 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: Nov 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.16→41.24 Å / Num. obs: 47523 / % possible obs: 99.8 % / Redundancy: 11.6 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.2836 / Rpim(I) all: 0.087 / Net I/σ(I): 25.8
Reflection shellResolution: 2.16→2.237 Å / Num. unique obs: 4664 / Rpim(I) all: 0.696

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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: 2.16→41.24 Å / SU ML: 0.2265 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5583
RfactorNum. reflection% reflection
Rfree0.216 1254 2.64 %
Rwork0.1656 --
obs0.1669 47501 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 55.99 Å2
Refinement stepCycle: LAST / Resolution: 2.16→41.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6910 0 15 311 7236
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00777115
X-RAY DIFFRACTIONf_angle_d0.96929650
X-RAY DIFFRACTIONf_chiral_restr0.05931111
X-RAY DIFFRACTIONf_plane_restr0.00581263
X-RAY DIFFRACTIONf_dihedral_angle_d5.20875912
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.16-2.250.27891380.2215052X-RAY DIFFRACTION99.77
2.25-2.350.24641370.21535081X-RAY DIFFRACTION99.85
2.35-2.470.26741380.19375086X-RAY DIFFRACTION99.94
2.47-2.630.24591370.18125080X-RAY DIFFRACTION99.89
2.63-2.830.23411400.17755120X-RAY DIFFRACTION99.98
2.83-3.120.23931380.18095113X-RAY DIFFRACTION99.92
3.12-3.570.23711390.16765137X-RAY DIFFRACTION100
3.57-4.490.17121410.1395203X-RAY DIFFRACTION99.91
4.49-41.240.20041460.15475375X-RAY DIFFRACTION99.14
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)
14.484794481531.519692598460.008241999219823.2740307416-0.2334506616031.980785119770.0747674363841-0.134789491643-0.2955471704380.0112107912246-0.0277202504841-0.04978455895290.2528009534780.0154246974102-0.02339552961830.1986743841320.0110998878806-0.01701251623930.220001926034-0.02993532101370.25192170242459.0810788678-20.982868819347.6140959999
23.945635967731.399734393632.405491622380.7839126952440.3221563951674.64506990556-0.0282437041579-0.476259618580.0206286366306-0.0891549093764-0.1600195735860.05656327912160.0876814677546-0.4510297619990.08438740248150.2345971458710.06314724283690.02643763217570.320962016697-0.03567204950740.2680526239186.7449043911-16.442031718946.4199705146
33.411986452110.8973141007470.263421488624.32616276946-0.007542782554132.732869656850.0320100695854-0.745889556263-0.4428575766390.162737277587-0.1559905503980.1147905516910.431388736808-0.07172233965610.1173591836610.31488906867-0.05782611250930.02142725097290.4719288990270.007073625052040.331815679386100.533305188-19.48725951357.0930140476
40.900651367487-0.451089280384-0.07813150484281.01915674525-0.8612700431111.08902997016-0.0410899889601-0.3105925758870.1663162389910.3182346711730.0660644897732-0.0205518957911-0.630406513791-0.0499701766539-0.03284682975370.568554049821-0.01579374698780.09486068976990.35052261855-0.05705101260590.32621002034896.0878711218-3.3169070785333.4636790348
51.97087715463-0.4340298662380.3810615035121.753115772010.8209040775013.072874439740.0585464319418-0.1739423371670.8888360434060.2218688887070.01264180144680.372353436732-1.11127636595-0.01839845527720.01025442123580.838484822374-0.009361019760450.1374969234750.365477474949-0.09221268249360.67193830832996.18516705025.4193777465528.703222974
64.344709080412.605532482120.1251935235283.3393029886-1.323251959942.82292170015-0.2505535450480.333407330470.451942627349-0.6484334982050.1153794924510.1769686359380.1709771149360.306963256630.06758625723890.357901747480.003890778469390.0304394901180.3342887444920.05974672907630.291149152151101.70246496-3.97955350674.79084042775
71.970131856610.474057137156-0.5496175572742.93582479857-2.488569886734.06274622183-0.02206372216880.5128904917510.197466218687-0.3709170995150.228602116790.2860878215210.1827138258-0.393478071686-0.152087852320.326649174448-0.00292210126202-0.03256254121450.3707852341290.07804174928560.30197031782994.7262423873-1.69884095158-0.127942529024
82.634434876711.86605925224-0.1685521902834.590363190750.8460448598372.41329601679-0.01856528193580.1175969292050.46025065284-0.3840327305810.1473330337990.216840227215-0.3689205939470.08889908055-0.1034739586260.285787843611-0.02207131530430.01663846068110.221063449438-0.01205701613210.37916517139869.08253909732.6862231877143.538129679
91.07189587361-0.661103654126-0.9120840529131.69042077530.6704048642851.170473337710.0192649705122-0.2157415535740.1764185337260.05237951406670.128844278551-0.170200442049-0.2178970588110.468246539711-0.06699889687640.244602152129-0.0548019872512-0.001535405642570.380477169526-0.08148391807360.34889059339175.7699293214-9.2602776752744.5233771916
101.90925681924-0.2633880386341.08026298972.37841033331-0.7555583771313.70178184245-0.07121978931060.464796697344-0.0942739090563-0.6388261315270.2358714195420.274836471260.4785067371560.0274360314067-0.09246677293170.389114510909-0.0933269791655-0.01178801660740.4299362034770.02069243102730.32671558895977.2290410121-23.686554759621.5161488599
112.24925616114-0.08402293107790.04283971018443.559149767880.4339719659183.22853441160.0406394245703-0.280076430785-0.5418278401340.006258383376430.02805562466390.09798169199460.6956962449690.0116516218198-0.02281584012510.399613216775-0.00537274306875-0.0009822565491370.2122280654850.05391684707220.31107828213697.236102026-26.022163430120.5662893633
122.72251254770.781211971407-0.5005994939963.17994906328-2.232013457463.1927159863-0.05350103348420.133631760039-0.0415612202479-0.234430662897-0.303582452625-0.6370748562180.0861257993530.6324393799360.2108619233870.2827810319710.05784898531130.03048653945820.3722683769120.05715638321870.383442586602111.42927944-9.7509486778613.2747452653
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 184 )
3X-RAY DIFFRACTION3chain 'A' and (resid 185 through 209 )
4X-RAY DIFFRACTION4chain 'A' and (resid 210 through 247 )
5X-RAY DIFFRACTION5chain 'A' and (resid 248 through 331 )
6X-RAY DIFFRACTION6chain 'A' and (resid 332 through 367 )
7X-RAY DIFFRACTION7chain 'A' and (resid 368 through 456 )
8X-RAY DIFFRACTION8chain 'B' and (resid 1 through 96 )
9X-RAY DIFFRACTION9chain 'B' and (resid 97 through 132 )
10X-RAY DIFFRACTION10chain 'B' and (resid 133 through 209 )
11X-RAY DIFFRACTION11chain 'B' and (resid 210 through 278 )
12X-RAY DIFFRACTION12chain 'B' and (resid 279 through 455 )

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