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- PDB-6pr3: D262A/S128A S. typhimurium siroheme synthase -

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Basic information

Entry
Database: PDB / ID: 6pr3
TitleD262A/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: 1.96 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)101,1336
Polymers100,2932
Non-polymers8404
Water8,323462
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12500 Å2
ΔGint-105 kcal/mol
Surface area35520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.276, 98.944, 146.312
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: 50146.492 Da / Num. of mol.: 2 / Mutation: D262A, 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.: 2 / Source method: obtained synthetically / Formula: Cl
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 462 / 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: 2.16 Å3/Da / Density % sol: 43.13 %
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: 1.96→35.2 Å / Num. obs: 61240 / % possible obs: 98.2 % / Redundancy: 7 % / Biso Wilson estimate: 34.73 Å2 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.05876 / Net I/σ(I): 20.7
Reflection shellResolution: 1.96→2.03 Å / Num. unique obs: 5525 / Rpim(I) all: 0.452

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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: 1.96→35.2 Å / SU ML: 0.2019 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.5715
RfactorNum. reflection% reflection
Rfree0.2146 1999 3.27 %
Rwork0.1672 --
obs0.1687 61185 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 47.81 Å2
Refinement stepCycle: LAST / Resolution: 1.96→35.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6965 0 2 462 7429
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077177
X-RAY DIFFRACTIONf_angle_d0.89619734
X-RAY DIFFRACTIONf_chiral_restr0.05661119
X-RAY DIFFRACTIONf_plane_restr0.00511277
X-RAY DIFFRACTIONf_dihedral_angle_d5.90945968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-2.010.30481210.24273589X-RAY DIFFRACTION84.99
2.01-2.070.27611410.21134168X-RAY DIFFRACTION97.53
2.07-2.130.22851420.19614198X-RAY DIFFRACTION98.79
2.13-2.20.26981420.19444217X-RAY DIFFRACTION98.6
2.2-2.270.22161420.18594205X-RAY DIFFRACTION99.2
2.27-2.370.26641430.18374236X-RAY DIFFRACTION98.96
2.37-2.470.24181430.17934222X-RAY DIFFRACTION99.23
2.47-2.60.20981430.17264243X-RAY DIFFRACTION99.28
2.6-2.770.21481440.17484267X-RAY DIFFRACTION99.55
2.77-2.980.22741460.17964307X-RAY DIFFRACTION99.71
2.98-3.280.24171450.17434314X-RAY DIFFRACTION99.8
3.28-3.750.19361460.15574330X-RAY DIFFRACTION99.91
3.75-4.730.1871480.13444382X-RAY DIFFRACTION99.98
4.73-35.20.1991530.16634508X-RAY DIFFRACTION98.48
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)
12.723080083361.49941166198-0.701165428922.43227389882-0.5842162515061.96245927731-0.05718918129210.0384278062914-0.154551338312-0.02574926272080.00162031587152-0.02326903493410.2119901382070.06917987508460.05386413282610.1693309203570.0350668344341-0.009681942016340.202976971544-0.04155549813810.21703584021858.4769585221-20.984249437747.4173886168
22.804150175770.2617993654741.864599082082.141159131350.4527212799255.830530339820.156372923535-0.337547572254-0.392264100566-0.1571117174190.114772208917-0.1808355448760.869155458576-0.525063779173-0.1885518208360.309425216719-0.01903075138530.002780370143170.3821894919310.01970955761490.34489831708678.5007559626-23.998240289138.3813738138
33.67429343766-0.4174855041290.6015735047223.360509780030.01518950867373.34803488442-0.0875096378505-0.292698906423-0.094464711299-0.05398311923520.02567918646610.0992201672366-0.15694185853-0.2950922282370.05887218649290.210922547792-0.0001262062801470.01007682110180.369602371082-0.03713271592660.20042466675395.6250416107-13.94138666254.5123732978
41.05778812059-0.526924843318-0.162704273931.14966859551-0.6960666714910.758740273805-0.0122169073167-0.3157194909260.2141625890690.36138851419-0.005704191570570.0425846756243-0.179808180892-0.01704183133550.02166853688680.343874253459-0.04591677056910.08449854347190.254069896601-0.07528748535690.25202149940495.7044999722-3.1036252667533.1963855727
51.88589707098-0.7430221923960.2702506725141.635833335280.373250562373.007405770960.0898125219963-0.1250144831320.7790505755720.189232655316-0.06117393840710.171381836177-0.938623013698-0.06659217517990.03654267691180.536266455724-0.03002907129550.1149451309310.307988063497-0.08437601549380.52246161730695.98194466795.5991526381328.3222933687
64.171940132721.94429404597-0.003856197963953.66737527888-1.277644634623.04898944505-0.1717771351320.3553604778260.259640166513-0.4665390220220.115822060332-0.06346861435640.1223616582770.2907333926190.06001712287890.2711961875590.006876130258860.01645797645980.260387481640.03463904573550.235205444714101.55288761-3.514075124174.84849123477
71.577391421680.760697078735-0.1271310919182.65278442949-1.659489615863.17081085238-0.03508111184210.4725557771870.299002240035-0.3054451874770.1963993125810.2271638946420.0241947232933-0.243697597504-0.17230267330.2884665683490.0127325495563-0.008474317471890.3149086371830.07241334741840.26042914508895.74038577471.07854983765-1.34864794013
80.4336927023760.557662803004-0.1224637218843.0201074934-0.5961350655760.8136097182980.08852490763350.3612322413640.0458124297027-0.3906435627360.09743235325490.801032110080.373899916926-0.596719520151-0.08186378003270.403512411491-0.0608495872543-0.0534200231330.4127552159290.05521130691560.37551135415890.3739697615-8.331691485462.68398652571
91.108051799830.0814545834541-0.3722427566491.961640273970.7569820789052.1620929073-0.07772128397490.1326840973040.129492054471-0.2543489495880.1272382610170.0809749032921-0.09199560836040.0464781739808-0.03199984784460.172437855242-0.0568515201917-0.03353690078080.2078398518930.04733410883950.21349208480273.0376158665-9.2021034191135.4621432935
102.703549277460.813622803216-0.2997837084913.3616495329-1.382249829672.67565755643-0.0347559595456-0.011747970038-0.121236960472-0.33608843186-0.224971960484-0.4408340042670.3684613573140.3608073971090.1231942588850.2617804383930.06569855509950.0692285129790.2247252036130.01076297282420.248160790066107.636363653-14.12167382815.1601019918
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 331 )
6X-RAY DIFFRACTION6chain 'A' and (resid 332 through 367 )
7X-RAY DIFFRACTION7chain 'A' and (resid 368 through 432 )
8X-RAY DIFFRACTION8chain 'A' and (resid 433 through 457 )
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 209 )
10X-RAY DIFFRACTION10chain 'B' and (resid 210 through 457 )

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