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- PDB-6ulu: D104A/S128A S. typhimurium siroheme synthase -

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Basic information

Entry
Database: PDB / ID: 6ulu
TitleD104A/S128A S. typhimurium siroheme synthase
ComponentsSiroheme synthase
KeywordsBIOSYNTHETIC PROTEIN / 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: 2.76 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
DepositionOct 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 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)101,0975
Polymers100,2932
Non-polymers8043
Water86548
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12770 Å2
ΔGint-90 kcal/mol
Surface area36820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.940, 99.913, 147.545
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: 50146.488 Da / Num. of mol.: 2
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, DM376_19045, E2F01_22980, FCJ89_03505, FG594_22565, FG605_22440, FG608_22845, FG609_22120, FG610_23420, FG612_22925, FG614_17700, FG736_21980, FJV50_24115, FJV51_21965, FJV53_21305, FJV54_21440, FJV55_23340, FJV56_23845, FJV57_21575, FJV58_21460, FJV59_22630, FJV60_22895, FJV61_22810, FJV62_21845, FJV63_22695, FJV64_21465, FJV65_22650, FJV66_23645, FJV67_23240, FJV68_22685, FJV69_23140, FJV70_23085, FJV71_22715, FJV73_22540, FJV74_23150, FJV75_23690, FJV78_22515, FJV79_22055, 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: 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.: 48 / 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: 44.41 %
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: Nov 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.76→42.2 Å / Num. obs: 23510 / % possible obs: 99.5 % / Redundancy: 12.5 % / Biso Wilson estimate: 51.78 Å2 / CC1/2: 0.962 / Rrim(I) all: 0.511 / Net I/σ(I): 0.11
Reflection shellResolution: 2.76→2.85 Å / Num. unique obs: 2263 / CC1/2: 0.608 / Rrim(I) all: 0.5

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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: 2.76→42.17 Å / SU ML: 0.4382 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.4939
RfactorNum. reflection% reflection
Rfree0.2851 1997 8.49 %
Rwork0.1843 --
obs0.1929 23510 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 59.16 Å2
Refinement stepCycle: LAST / Resolution: 2.76→42.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6963 0 1 48 7012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00787155
X-RAY DIFFRACTIONf_angle_d1.039701
X-RAY DIFFRACTIONf_chiral_restr0.0581117
X-RAY DIFFRACTIONf_plane_restr0.00531271
X-RAY DIFFRACTIONf_dihedral_angle_d16.01724338
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.76-2.820.40111350.26731455X-RAY DIFFRACTION96.54
2.82-2.90.37981400.24591503X-RAY DIFFRACTION98.38
2.9-2.990.36311410.25521518X-RAY DIFFRACTION100
2.99-3.080.40361390.22891505X-RAY DIFFRACTION100
3.08-3.190.35261420.21321525X-RAY DIFFRACTION100
3.19-3.320.31751430.20741545X-RAY DIFFRACTION100
3.32-3.470.29421410.18391512X-RAY DIFFRACTION100
3.47-3.650.28721400.1761515X-RAY DIFFRACTION100
3.65-3.880.27031460.17941558X-RAY DIFFRACTION100
3.88-4.180.26431410.15681528X-RAY DIFFRACTION100
4.18-4.60.25251450.14641558X-RAY DIFFRACTION100
4.6-5.270.25021440.15341557X-RAY DIFFRACTION99.88
5.27-6.630.27081480.18881587X-RAY DIFFRACTION100
6.63-42.170.24481520.18291647X-RAY DIFFRACTION98.63
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)
10.963391150990.330625337517-0.6838305990350.204399088967-0.3792917768730.9922016393190.0559974949416-0.02258683344210.0982500263715-0.0487066587179-0.03344858545270.0590772722514-0.0745341962810.0871298776989-0.02996438820740.3988103711150.0378783527393-0.01168495105760.293069973554-0.04746657789410.33197680608986.4148406092-8.8820679138930.9048283927
21.54240494990.0497522078511-1.015076106190.640889425399-0.4533622765811.72526923359-0.06990644472090.06995127680270.022410139318-0.144679032634-0.0150466633621-0.07235105409840.2160062292710.09691805574930.0918717445260.312665224805-0.025169887425-0.07059940496170.2415113419240.02721633754570.31437859641792.2555346951-11.954436690224.9920457724
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 501)
2X-RAY DIFFRACTION2(chain 'B' and resid 1 through 502)

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