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- PDB-6veb: Precorrin-2-bound S128A S. typhimurium siroheme synthase -

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Basic information

Entry
Database: PDB / ID: 6veb
TitlePrecorrin-2-bound S128A S. typhimurium siroheme synthase
ComponentsSiroheme synthaseSirohaem synthase
KeywordsTRANSFERASE / 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 ...: / 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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Chem-PQ2 / S-ADENOSYL-L-HOMOCYSTEINE / Siroheme synthase / Siroheme synthase
Similarity search - Component
Biological speciesSalmonella enterica I (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 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
DepositionDec 31, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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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)102,92613
Polymers100,3812
Non-polymers2,54511
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14830 Å2
ΔGint-160 kcal/mol
Surface area34880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.682, 99.489, 146.037
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

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Protein , 1 types, 2 molecules AB

#1: Protein Siroheme synthase / Sirohaem synthase


Mass: 50190.500 Da / Num. of mol.: 2 / Mutation: S128A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica I (bacteria)
Gene: cobA, cysG, A4O23_22680, A4O45_23495, A5895_10260, ACK40_21915, AH543_24340, AL864_13490, B9C63_23695, CC394_23355, CC828_23245, CPY04_23335, CQF73_24090, CQH69_23770, CQM83_24035, CQM91_23950, ...Gene: cobA, cysG, A4O23_22680, A4O45_23495, A5895_10260, ACK40_21915, AH543_24340, AL864_13490, B9C63_23695, CC394_23355, CC828_23245, CPY04_23335, CQF73_24090, CQH69_23770, CQM83_24035, CQM91_23950, CWG97_04420, D4392_23335, D4408_24080, D4427_23490, D4428_23600, D4507_23395, D4515_23795, D4E09_23835, D4E59_23545, D4E64_23910, D4E70_23615, D4E75_22760, D4F17_23250, D4F20_23570, D4F29_23000, D4F49_23820, D4F54_21825, D4F87_23560, D4G07_23810, D4G50_23805, D4X67_23945, D4Y38_22995, D4Y42_23265, D4Y96_23470, D4Z75_23120, D5782_23070, D5836_24310, D5881_23125, D5A65_24210, D5B23_24060, D5C00_23760, D5C21_23840, D5O45_24060, D5O48_24255, D5P09_24125, D5P22_23765, D5P36_21245, D5P54_19825, D5P71_21870, D5Q05_23505, D5X20_22850, D5Y01_23010, D5Y08_23660, D6379_23290, D6429_21865, D6J55_23675, D6J74_23505, D6P41_23695, D6Q63_23855, D6R58_22975, D6R98_23865, D6S02_23370, D6S45_23570, D6S74_23640, D6S82_23760, D6T18_23595, D7N15_23195, D7N26_23945, D7N30_23525, D7N52_23575, D7O25_23820, D7O77_23450, D8Q64_21745, D8S35_24215, D8S62_23725, D8S66_24520, D9O71_23255, D9P12_23260, D9P13_23305, D9P51_22965, DFQ85_08280, DK030_07475, DK113_22975, DK687_23375, DKT04_23460, DKT40_22680, DKU65_22440, DKV20_24340, DL110_23435, DL115_21645, DL130_23925, DL146_23455, DL163_23880, DLB18_22580, DLB43_23490, DLC24_22825, DLF22_23220, DLF29_24400, DLF33_23155, DLF36_23470, DLM10_23710, DLM26_23890, DLQ73_23465, DLQ92_22925, DLR05_23380, DM006_23485, DM323_23285, DM367_24075, DM371_23830, DM705_23905, DMA96_24030, DMB04_23395, DML85_20570, DMM43_23865, DMO61_22925, DMO65_23235, DMV32_23255, DN092_21835, DN096_17090, DN123_18420, DN182_24420, DN282_24210, DN317_23660, DN319_23985, DN362_23995, DNI00_21425, DNI67_22410, DNI82_24175, DNJ17_23520, DNM80_24185, DNU17_23255, DNU67_23755, DNU84_23130, DNV04_23575, DNV18_24435, DNV28_23830, DNV55_23115, DNV59_23205, DNV93_24240, DNY86_24000, DNZ02_24100, DNZ29_23620, DO557_23340, DO565_23090, DO591_24015, DO596_23880, DO617_23890, DO630_23685, DO638_23100, DO681_24120, DO731_24105, DO981_16865, DOA55_23120, DOA87_24295, DOA98_24055, DOB00_23930, DOC25_23595, DOC31_12165, DOH04_23240, DOH41_23555, DOH63_23205, DOH69_23565, DOH81_23800, DOI78_23195, DOJ02_24430, DOJ11_19160, DOR51_23145, DOV77_22745, DOV78_22375, DOW52_23180, DOX30_23900, DP688_24205, DP693_23150, DP698_23535, DP703_24195, DP713_24390, DP736_24050, DP778_23450, DP800_23450, DP859_23875, DPA01_22585, DPA36_23285, DPB61_23630, DPD61_23230, DPE40_23250, DPE76_21335, DPE98_22330, DPP34_22980, DPP41_24295, DPP49_23850, DPP70_23140, DPS71_23220, DPT22_23580, DPT74_23805, DPU13_22980, DPY81_22995, DPZ65_20145, DQ076_23430, DQ082_23395, DQ880_23785, DQ933_23705, DQC12_20050, DQC81_21240, DQC88_22075, DQD11_23435, DQD59_15735, DQE08_19980, DQE20_22815, DQE42_23995, DQJ22_22855, DQK43_23325, DQQ27_23480, DQR39_23575, DQR74_22755, DQS55_23550, DQS89_23430, DQT21_24150, DQT40_20085, DQT67_24145, DQZ89_22730, DRA21_23780, DRA26_23910, DRA37_23360, DRD40_23755, DRD55_22850, DRE12_23690, DRE69_22130, DRE92_22615, DRK49_23400, DRL53_23670, DRL65_24040, DRL96_23465, DRM39_23520, DRM43_23115, DRT45_23760, DRT76_23250, DRU07_22490, DRV17_23930, DRV44_23300, DRY30_24240, DS168_23130, DS336_23415, DS372_23280, DS485_23475, DS493_23550, DS572_23890, DS605_22630, DS651_22985, DS666_23240, DS688_24580, DS708_23885, DSA90_23105, DSB20_24505, DSB26_23530, DSB29_23215, DSB36_23820, DSF03_22695, DSF23_12440, DSF57_23350, DSF93_23505, DSG69_23455, DSM73_23875, DSM81_23920, DSM96_23930, DSN18_23205, DSR78_24250, DSR92_21190, DSS12_22290, DSS37_23620, DSS62_22775, DSS75_23430, DSS77_24315, DST25_23085, DT168_23620, DTE69_22625, DTG45_23495, DTG68_22565, DTG80_23765, DTT99_19805, DTV63_23440, DTW19_23225, DU084_22390, DU129_23835, DU131_22825, DU159_23825, DU165_23925, DU205_24120, DU207_23795, DU257_24320, DU750_19160, DU762_23420, DU854_22090, DU873_23310, DU916_20895, DU947_24440, DUB79_23050, DUB80_23255, DUB82_23235, DUP91_23210, DUQ41_22935, DUQ55_23840, DUQ58_20775, DUR69_18130, DUR90_22210, DUU54_20070, DUU71_24500, DUU80_23985, DUU92_23505, DUV51_23775, DV01_23265, DVF71_23695, DVG21_22945, E5N87_17725, EBJ71_23145, EBJ89_23915, EBK43_23020, EBK48_23810, EBO89_23265, EBO94_22695, EBP12_23765, EC422_22620, EC429_22615, EC434_22830, EC491_23745, EC492_18880, ECA94_23540, ECD30_24635, ED477_23805, EDK87_23895, EDL36_23455, EDL46_24280, EEA59_23510, EEA93_23330, EER72_21930, EES08_23010, EF649_23005, EGM25_23675, EH130_23450, EHB46_23510, EHB61_21570, EHD20_23630, EIE60_23400, EIL32_22805, EIW55_23130, EIW93_23605, FD75_21980, PK95_22395, S639_25165
Production host: Escherichia coli (E. coli)
References: UniProt: A0A3U8X2F7, UniProt: P25924*PLUS, uroporphyrinogen-III C-methyltransferase, precorrin-2 dehydrogenase, sirohydrochlorin ferrochelatase

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Non-polymers , 5 types, 218 molecules

#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: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-PQ2 / 3,3',3'',3'''-[(7S,8S,12S,13S)-3,8,13,17-tetrakis(carboxymethyl)-8,13-dimethyl-7,8,12,13,20,24-hexahydroporphyrin-2,7,1 2,18-tetrayl]tetrapropanoic acid / Precorrin-2


Mass: 864.848 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H48N4O16 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.14 Å3/Da / Density % sol: 42.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
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: 2.55→49.74 Å / Num. obs: 29098 / % possible obs: 99.9 % / Redundancy: 12.9 % / Biso Wilson estimate: 39.77 Å2 / CC1/2: 0.988 / Rmerge(I) obs: 0.268 / Net I/σ(I): 11.8
Reflection shellResolution: 2.55→2.64 Å / Rmerge(I) obs: 0.802 / Num. unique obs: 17561 / CC1/2: 0.663

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PJQ

1pjq


Resolution: 2.55→49.74 Å / SU ML: 0.3258 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.4339
RfactorNum. reflection% reflection
Rfree0.245 1547 5.32 %
Rwork0.1644 --
obs0.1687 29094 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 50.85 Å2
Refinement stepCycle: LAST / Resolution: 2.55→49.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6989 0 113 207 7309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00887425
X-RAY DIFFRACTIONf_angle_d1.124710098
X-RAY DIFFRACTIONf_chiral_restr0.05821148
X-RAY DIFFRACTIONf_plane_restr0.00581319
X-RAY DIFFRACTIONf_dihedral_angle_d5.91126095
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.55-2.630.30511380.21382468X-RAY DIFFRACTION99.73
2.63-2.730.32921380.21312446X-RAY DIFFRACTION99.92
2.73-2.840.33621380.21122474X-RAY DIFFRACTION99.92
2.84-2.960.30771390.21652467X-RAY DIFFRACTION99.92
2.96-3.120.31551390.19372477X-RAY DIFFRACTION100
3.12-3.320.27291400.18352492X-RAY DIFFRACTION100
3.32-3.570.26211390.17032474X-RAY DIFFRACTION100
3.57-3.930.21851410.14112503X-RAY DIFFRACTION100
3.93-4.50.1941410.1232522X-RAY DIFFRACTION100
4.5-5.670.18911430.13392540X-RAY DIFFRACTION100
5.67-49.740.23341510.1662684X-RAY DIFFRACTION99.68
Refinement TLS params.Method: refined / Origin x: 58.9518717231 Å / Origin y: -10.4295408637 Å / Origin z: 28.411776428 Å
111213212223313233
T0.222447760564 Å2-0.00233576640003 Å2-0.0469925694359 Å2-0.196883192574 Å2-0.019766391723 Å2--0.252746652939 Å2
L1.2906773934 °20.144664242341 °2-0.817812016181 °2-0.334916343355 °2-0.293958246487 °2--1.02303700244 °2
S0.00294322003366 Å °0.01471180445 Å °0.0895101774648 Å °-0.0433196837384 Å °0.00106736175422 Å °0.0109018893637 Å °0.0272689356876 Å °0.0371828038537 Å °0.00262737872028 Å °
Refinement TLS groupSelection details: all

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