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- PDB-6pqz: P133G/S128A S. typhimurium siroheme synthase -

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Basic information

Entry
Database: PDB / ID: 6pqz
TitleP133G/S128A S. typhimurium siroheme synthase
ComponentsSiroheme synthaseSirohaem synthase
KeywordsBIOSYNTHETIC PROTEIN / 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: 2.23 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)101,0704
Polymers100,3012
Non-polymers7692
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12240 Å2
ΔGint-73 kcal/mol
Surface area35280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.308, 98.284, 143.229
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: 50150.434 Da / Num. of mol.: 2 / Mutation: P133G, 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-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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.11 Å3/Da / Density % sol: 41.71 %
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: Oct 24, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.23→37.2 Å / Num. obs: 40963 / % possible obs: 98.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 43.44 Å2 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.08 / Net I/σ(I): 19.1
Reflection shellResolution: 2.23→2.31 Å / Num. unique obs: 3755

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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: 2.23→37.19 Å / SU ML: 0.2801 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.3546
RfactorNum. reflection% reflection
Rfree0.245 1999 4.88 %
Rwork0.1811 --
obs0.1842 40941 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 59.11 Å2
Refinement stepCycle: LAST / Resolution: 2.23→37.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6947 0 0 187 7134
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00717120
X-RAY DIFFRACTIONf_angle_d0.95069650
X-RAY DIFFRACTIONf_chiral_restr0.05321111
X-RAY DIFFRACTIONf_plane_restr0.00591265
X-RAY DIFFRACTIONf_dihedral_angle_d16.85524312
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.290.35161260.24892487X-RAY DIFFRACTION89.58
2.29-2.350.27131420.24572740X-RAY DIFFRACTION99.14
2.35-2.420.3411400.23412728X-RAY DIFFRACTION99.45
2.42-2.50.30651420.21872771X-RAY DIFFRACTION99.69
2.5-2.590.27291430.21762787X-RAY DIFFRACTION99.63
2.59-2.690.27651410.21982755X-RAY DIFFRACTION99.62
2.69-2.810.24821440.20192798X-RAY DIFFRACTION99.7
2.81-2.960.27341430.20472779X-RAY DIFFRACTION99.83
2.96-3.150.27311420.19642791X-RAY DIFFRACTION99.8
3.15-3.390.25661450.1932808X-RAY DIFFRACTION99.93
3.39-3.730.2351440.17152811X-RAY DIFFRACTION99.9
3.73-4.270.21241470.1522860X-RAY DIFFRACTION100
4.27-5.380.21271460.15212859X-RAY DIFFRACTION100
5.38-37.190.22991540.17012968X-RAY DIFFRACTION98.52
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)
14.576691267872.00800059702-1.582483715392.67977907312-0.3048355109921.6125472417-0.1004711150350.118218889446-0.319774199435-0.0418968090308-0.00247531852087-0.1613033274440.3343569327910.06661279820710.1059257158480.3194133794670.0571289770529-0.0264808041830.293228963083-0.02498353325170.27767483979733.3994918212-21.383768731244.4975425312
25.3355443833-1.080197830020.8415051061677.64889111913-1.190692487274.48426960097-0.157150393632-0.200664265676-0.0446090143421-0.08032230550840.1973772034020.377883233063-0.07081498238-0.480476117577-0.02227670724760.274535881697-0.01571580382910.03870549895960.525237979365-0.03256758023940.21927344446665.9985312582-14.074299516353.3643245147
32.84446878215-0.2020632003810.008629947709841.99907532761-0.07039585883263.879883591340.0338114123795-0.2259358200070.6108485759350.163042573950.0809528601520.00149067256427-0.8461131070910.104167221314-0.07749943427080.462802859029-0.02526738668650.08706113938740.292855756224-0.04706751956950.42783596852566.09809279142.1979539054328.1991964786
45.577460823761.45441776985-1.688500790415.14323972553-3.420871467687.128794533780.01128729629840.461874915170.218486539438-0.465519985790.03589836970520.145435107140.20747359088-0.162226775154-0.04428622188760.3638768912610.0333394829988-0.03095603214490.3811329361420.0177733207760.26046146930366.9768903225-1.291568215920.640271864114
52.60162897965-0.2940237907-1.021637179732.950207363480.6617164283311.990354378880.05859062770420.1444398319920.328831678726-0.1454826811640.01819884233260.208599411721-0.1554736594380.074189975128-0.07574140730630.247579685539-0.0175342905515-0.004157336444960.2763092128960.02777557265050.26932744456842.7919704241-1.5161574579742.3824703458
63.574047752210.948605140603-0.6454012207512.97157412684-1.606438786092.57011741878-0.1449951420410.119802946-0.267826326114-0.414633640422-0.075667488304-0.2626865286530.4228519943730.09721268638250.1840559434120.3907654669510.0538250892050.03983994881780.295510317052-0.01672497733790.25037184333270.3477181867-16.425740310915.4320313808
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 148 )
2X-RAY DIFFRACTION2chain 'A' and (resid 149 through 209 )
3X-RAY DIFFRACTION3chain 'A' and (resid 210 through 340 )
4X-RAY DIFFRACTION4chain 'A' and (resid 341 through 457 )
5X-RAY DIFFRACTION5chain 'B' and (resid 1 through 146 )
6X-RAY DIFFRACTION6chain 'B' and (resid 147 through 455 )

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