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- PDB-1pjs: The co-crystal structure of CysG, the multifunctional methyltrans... -

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Basic information

Entry
Database: PDB / ID: 1pjs
TitleThe co-crystal structure of CysG, the multifunctional methyltransferase/dehydrogenase/ferrochelatase for siroheme synthesis, in complex with it NAD cofactor
ComponentsSiroheme synthase
KeywordsTRANSFERASE/OXIDOREDUCTASE/LYASE / rossmann fold / nucleotide binding motif / SAH / SAM / NAD / phosphoserine / TRANSFERASE-OXIDOREDUCTASE-LYASE COMPLEX
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, dimerisation domain / Sirohaem synthase, central domain / 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 ...Sirohaem synthase, dimerisation domain / Sirohaem synthase, central domain / 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, N-terminal domain / Tetrapyrrole methylase, C-terminal domain / Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 / Tetrapyrrole methylase, subdomain 2 / Cobalt-precorrin-4 Transmethylase; domain 1 / Tetrapyrrole methylase / Tetrapyrrole (Corrin/Porphyrin) Methylases / Tetrapyrrole methylase, subdomain 1 / Tetrapyrrole methylase superfamily / Double Stranded RNA Binding Domain / Helicase, Ruva Protein; domain 3 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / TRIETHYLENE GLYCOL / PHOSPHATE ION / S-ADENOSYL-L-HOMOCYSTEINE / Siroheme synthase
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsStroupe, M.E. / Leech, H.K. / Daniels, D.S. / Warren, M.J. / Getzoff, E.D.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: CysG structure reveals tetrapyrrole-binding features and novel regulation of siroheme biosynthesis.
Authors: Stroupe, M.E. / Leech, H.K. / Daniels, D.S. / Warren, M.J. / Getzoff, E.D.
History
DepositionJun 3, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.mon_nstd_flag / _chem_comp.type

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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)103,0649
Polymers100,5732
Non-polymers2,4917
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15430 Å2
ΔGint-75 kcal/mol
Surface area35780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.124, 120.686, 130.178
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit contains a single homodimer. Each of CysG's modules (CysGB, residues 1-212, and CysGA, residues 213-457) are homodimers. Each subunit contains half of CysGB and half of CysGA, each of which is related to its dimer partner by a unique non-crystallographic two-fold symmetry axis. CysG has two distinct non-crystallographic two-fold symmetry axes, one for each homodimeric module.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Siroheme synthase / CysG


Mass: 50286.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: RESIDUES 1-212 (CYSGB) ARE A DEHYDROGENASE/FERROCHELATASE, RESIDUES 213-457 (CYSGA) ARE A BISMETHYLTRANSFERASE
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Gene: CYSG OR STM3477 / Plasmid: PBAD-HIS-MYC (INVITROGEN) / Production host: Escherichia coli (E. coli) / Strain (production host): LMG194
References: UniProt: P25924, uroporphyrinogen-III C-methyltransferase, Oxidoreductases, EC: 4.99.1.-

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Non-polymers , 5 types, 219 molecules

#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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 212 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: PEG400, phosphate/citrate, sodium chloride, 2-mercaptoethanol, NAD, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 4.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mg/mlprotein1drop
230 %(v/v)PEG2001reservoir
3200 mMsodium acetate1reservoirpH4.5
4200 mM1reservoirNaCl
51 %(v/v)beta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 10, 2002 / Details: double crystal monochromator
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→22.58 Å / Num. obs: 36207 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 31.5 Å2 / Rsym value: 0.079 / Net I/σ(I): 14.3
Reflection shellResolution: 2.4→2.49 Å / Mean I/σ(I) obs: 2.8 / Num. unique all: 3583 / Rsym value: 0.415 / % possible all: 97
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / % possible obs: 97 % / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 95.5 % / Rmerge(I) obs: 0.415

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1PJQ

1pjq


Resolution: 2.4→22.58 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.281 3603 10 %RANDOM
Rwork0.2388 ---
obs-36154 95.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.3105 Å2 / ksol: 0.340922 e/Å3
Displacement parametersBiso mean: 41.2 Å2
Baniso -1Baniso -2Baniso -3
1-3.27 Å20 Å20 Å2
2---7.47 Å20 Å2
3---4.19 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.4→22.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6933 0 165 212 7310
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.9
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d1.05
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.369 584 9.7 %
Rwork0.321 5424 -
obs--97 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3CONAD-OTHER.PARCONAD-OTHER.TOP
X-RAY DIFFRACTION4TMP.PARAMTMP.TOP
X-RAY DIFFRACTION5ION.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 10 % / Rfactor Rwork: 0.239
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0095
X-RAY DIFFRACTIONc_angle_deg1.91
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.05

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