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- PDB-6p5z: Cobalt-sirohydrochlorin-bound S. typhimurium siroheme synthase -

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Basic information

Entry
Database: PDB / ID: 6p5z
TitleCobalt-sirohydrochlorin-bound 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
cobalt-sirohydrochlorin / S-ADENOSYL-L-HOMOCYSTEINE / Siroheme synthase / Siroheme synthase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 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
DepositionMay 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 29, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Dec 25, 2024Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / pdbx_entry_details / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Item: _chem_comp.mon_nstd_flag / _chem_comp.type / _pdbx_entry_details.has_protein_modification

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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)103,0608
Polymers100,3812
Non-polymers2,6796
Water95553
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12810 Å2
ΔGint-103 kcal/mol
Surface area35980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.601, 100.446, 146.400
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: 50190.500 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria)
Gene: cobA, cysG, C2253_19735, CET98_25025, D7F20_23535, D7H43_21790, DJ388_17225, NCTC13348_03825
Production host: Escherichia coli (E. coli) / Variant (production host): LMG194
References: UniProt: A0A3V0JC15, UniProt: A0A0F7JCI1*PLUS, uroporphyrinogen-III C-methyltransferase, precorrin-2 dehydrogenase, sirohydrochlorin ferrochelatase
#2: Chemical ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H20N6O5S
#3: Chemical ChemComp-F0X / cobalt-sirohydrochlorin


Mass: 919.749 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C42H44CoN4O16 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.17 Å3/Da / Density % sol: 43.24 %
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: Mar 10, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 41427 / % possible obs: 99 % / Redundancy: 7.1 % / Biso Wilson estimate: 57.55 Å2 / Net I/σ(I): 39
Reflection shellResolution: 2.26→2.3 Å / Num. unique obs: 1769

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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: 2.26→35.34 Å / SU ML: 0.2836 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4781
RfactorNum. reflection% reflection
Rfree0.2416 1998 4.83 %
Rwork0.179 --
obs0.1819 41335 98.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 77.88 Å2
Refinement stepCycle: LAST / Resolution: 2.26→35.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6956 0 128 53 7137
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00737237
X-RAY DIFFRACTIONf_angle_d1.33049838
X-RAY DIFFRACTIONf_chiral_restr0.05691112
X-RAY DIFFRACTIONf_plane_restr0.00551281
X-RAY DIFFRACTIONf_dihedral_angle_d16.05424360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.320.28281250.24992458X-RAY DIFFRACTION87.77
2.32-2.380.30211410.23822794X-RAY DIFFRACTION99.09
2.38-2.450.28821410.23792766X-RAY DIFFRACTION99.9
2.45-2.530.31931430.22512809X-RAY DIFFRACTION99.53
2.53-2.620.28571410.21142777X-RAY DIFFRACTION99.66
2.62-2.730.26711430.21392823X-RAY DIFFRACTION99.8
2.73-2.850.31420.21812797X-RAY DIFFRACTION99.86
2.85-30.28851440.23192827X-RAY DIFFRACTION99.87
3-3.190.33521430.2242822X-RAY DIFFRACTION100
3.19-3.440.2641450.2072834X-RAY DIFFRACTION100
3.44-3.780.24671450.18092844X-RAY DIFFRACTION100
3.78-4.330.21981450.15492879X-RAY DIFFRACTION100
4.33-5.450.21881480.14462889X-RAY DIFFRACTION99.97
5.45-35.340.19731520.15663018X-RAY DIFFRACTION99.06
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)
17.597412043032.281920686340.01247446478474.35413861489-1.036896075223.725591365970.0591699782573-0.476161988407-0.8285100329970.09578007799220.004902708725240.17074971130.48180760645-0.22148955466-0.08861316679380.4081282198460.0274328495903-0.03000292450580.3866116213880.02617617139740.512332257945-30.1114913443-21.093273868848.2098916284
28.236563216312.770739623765.791388758881.904944482922.027385413487.838548732840.0258670698164-0.719087963876-0.243273561205-0.12308021809-0.0575838356477-0.005796669433460.0826761512053-0.289913480569-0.008916684568250.4327251780720.0124845493270.03946397572350.6257205236710.05410678594710.4004683424771.14484077881-17.362257290949.5281184836
32.77419144069-0.237962072886-1.39855745961.10596846715-0.7886385928313.403354846470.160024994965-0.6328799158130.5250810933650.107917995666-0.0376937326611-0.124344654363-0.5226986819120.118649523174-0.129389041110.5077199795330.0380456730120.06032359481640.468034033867-0.03959735846660.4187348749497.45180957702-3.2046272719234.220591839
44.887503504061.179798394890.2273871648364.145564219670.06767548434645.23723285130.240616373437-0.3591711538491.128767195170.655336985041-0.1334794572510.2160166883-1.14869654495-0.167559210702-0.05561156148640.768054182660.05755434025740.09067964727920.436994471117-0.05230477740490.6161492998587.618415523363.9774378929528.2227427692
56.170635791682.46147313269-2.258344437995.42793292019-3.88413865917.07757286376-0.0282079458960.8899503573680.458576346002-0.4350850934550.1902480421610.309116993-0.00452179694583-0.160275081162-0.1317833141020.4362869090520.0272628737811-0.07552747697650.5740353016620.05014611875220.3621757981139.177651031610.6140452753780.943506087546
60.8780081424-0.7723641003580.5372967775629.19038417222-2.596813851572.91024505452-0.01133676580630.77275035605-0.417855254685-0.4302064557950.3640620299171.148527154450.243679154633-0.817615519022-0.2515659883230.5694691259280.00813402169022-0.135391904410.839061461949-0.01638682560940.5868828122691.31139472458-7.490582903873.8629072999
73.69015721082.53325124767-0.5910229225578.985513863220.1138231737652.613152278330.113433121185-0.1183405423630.469627320481-0.1522220118120.03741623022740.197485764825-0.3383154813090.06588228855-0.1571281382660.3195886019430.00921221529972-0.02191145676640.384788989229-0.06272526832810.499188013876-19.8834835142.7336421892843.9111760711
85.8641405181-3.55921238818-4.61433323544.664566554841.458824356955.133206156590.00249281762952-0.1052705908080.4230703224130.07554606139520.0436369088688-0.093653185406-0.1846745905420.537073323959-0.002850796672510.316837128824-0.0460892149572-0.03603667155620.49170629414-0.06893940928160.469373207303-13.2914677608-9.3276589150145.1603955608
93.26116369917-2.144137397440.349571099333.735644161590.8829896014916.82537650838-0.1665466991160.260781426606-0.661657318375-0.325396828888-0.2464866791590.838060034060.26277239862-0.6454084389790.3858997050360.450566008389-0.05908128888920.01802641698760.5390665849310.05293191516440.690882977118-11.9102706829-21.814673733526.9681025787
102.61124648988-2.11899732747-1.065450451628.785157136660.6287726787976.690041795280.4674076445140.576685233027-0.245469601484-0.76317572095-1.17364578696-1.095129808081.20576663927-0.2237715506520.6247161960880.80222824299-0.0175780124738-0.1168530713030.7712869246130.007990336442370.683817161679-12.2147047636-24.766857215815.55465425
114.718234729160.3794163365831.391308034337.485651094381.473828779475.05421660262-0.0340347496093-0.196315279239-0.8322644155790.1696663406550.008290699283120.2454966080660.5636093098470.0328801006988-0.03055148069450.5282735959480.03569117358770.09445498690290.3922171686570.06772664599610.4796015460928.03097109093-25.784079894921.3647960296
123.583460378641.7798640301-0.4119954146885.01929758193-1.597737562963.33882072583-0.2876974712310.723099761349-0.610868474887-1.022339991710.152340586636-0.2725800936550.6948649806350.230932262180.06050516859240.6684548918440.1176884855680.05666040386770.533520176277-0.08201894857290.44410715296811.6887989058-17.742726382512.1262655008
135.376853669320.479766303181-1.453708062854.92569206464-1.1465474374.51698280187-0.01395011821290.443276425265-0.236369586499-0.127252629608-0.727717567883-1.07350062103-0.08636577428651.410369633720.6065629664560.3871454819370.0552176904623-0.02518230164370.8041207871290.1825417507150.71057157375930.005565646-4.32243214915.1438476492
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 209 )
3X-RAY DIFFRACTION3chain 'A' and (resid 210 through 247 )
4X-RAY DIFFRACTION4chain 'A' and (resid 248 through 339 )
5X-RAY DIFFRACTION5chain 'A' and (resid 340 through 432 )
6X-RAY DIFFRACTION6chain 'A' and (resid 433 through 457 )
7X-RAY DIFFRACTION7chain 'B' and (resid 1 through 96 )
8X-RAY DIFFRACTION8chain 'B' and (resid 97 through 132 )
9X-RAY DIFFRACTION9chain 'B' and (resid 133 through 174 )
10X-RAY DIFFRACTION10chain 'B' and (resid 175 through 209 )
11X-RAY DIFFRACTION11chain 'B' and (resid 210 through 278 )
12X-RAY DIFFRACTION12chain 'B' and (resid 279 through 351 )
13X-RAY DIFFRACTION13chain 'B' and (resid 352 through 457 )

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