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- PDB-4qdj: Crystal structure of magnesium protoporphyrin IX methyltransferas... -

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Basic information

Entry
Database: PDB / ID: 4qdj
TitleCrystal structure of magnesium protoporphyrin IX methyltransferase (ChlM) from Synechocystis PCC 6803 with bound SAM
ComponentsMagnesium-protoporphyrin O-methyltransferase
KeywordsTRANSFERASE / Methyltransferase / Magnesium protoporphyrin IX / S-adenosyl methionine
Function / homology
Function and homology information


magnesium protoporphyrin IX methyltransferase / magnesium protoporphyrin IX methyltransferase activity / light-independent chlorophyll biosynthetic process / photosynthesis / methyltransferase activity / methylation
Similarity search - Function
Magnesium-protoporphyrin IX methyltransferase / Magnesium-protoporphyrin IX methyltransferase, C-terminal / Magnesium-protoporphyrin IX methyltransferase C-terminus / Magnesium protoporphyrin IX methyltransferase (EC 2.1.1.11) family profile. / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
S-ADENOSYLMETHIONINE / Magnesium-protoporphyrin O-methyltransferase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsChen, X. / Wang, X. / Liu, L.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: Structural insights into the catalytic mechanism of Synechocystis magnesium protoporphyrin IX O-methyltransferase (ChlM).
Authors: Chen, X. / Wang, X. / Feng, J. / Chen, Y. / Fang, Y. / Zhao, S. / Zhao, A. / Zhang, M. / Liu, L.
History
DepositionMay 14, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Magnesium-protoporphyrin O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6703
Polymers26,1801
Non-polymers4912
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.319, 61.026, 68.892
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Magnesium-protoporphyrin O-methyltransferase / Magnesium-protoporphyrin IX methyltransferase


Mass: 26179.801 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: chlM, slr0525 / Production host: Escherichia coli (E. coli)
References: UniProt: Q55467, magnesium protoporphyrin IX methyltransferase
#2: Chemical ChemComp-SAM / S-ADENOSYLMETHIONINE / S-Adenosyl methionine


Mass: 398.437 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H22N6O5S
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 1.98 Å3/Da / Density % sol: 37.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 0.1M MES pH 6.7, 10% PEG 3350, 200mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRF BL17U10.9793
SYNCHROTRONSSRF BL17U20.9793
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDApr 10, 2013
ADSC QUANTUM 315r2CCDJun 28, 2013
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystalSINGLE WAVELENGTHMx-ray1
2double crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 27515 / % possible obs: 97.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.6→1.66 Å / % possible all: 84.3

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIX(phenix.refine: 1.8.1_1168)model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.8.1_1168phasing
RefinementMethod to determine structure: SAD / Resolution: 1.6→33.514 Å / SU ML: 0.13 / σ(F): 1.41 / Phase error: 16.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1797 1383 5.04 %RANDOM
Rwork0.1415 ---
all0.1434 28069 --
obs0.1434 27466 97.85 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6→33.514 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1598 0 33 177 1808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0031708
X-RAY DIFFRACTIONf_angle_d0.842329
X-RAY DIFFRACTIONf_dihedral_angle_d10.513635
X-RAY DIFFRACTIONf_chiral_restr0.055266
X-RAY DIFFRACTIONf_plane_restr0.003300
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.6002-1.65740.20891090.1176218784
1.6574-1.72380.17731240.1218253497
1.7238-1.80220.1941340.11782660100
1.8022-1.89730.17091410.12162623100
1.8973-2.01610.17631520.1252620100
2.0161-2.17170.16041610.11892638100
2.1717-2.39020.17451470.12722638100
2.3902-2.7360.17911430.14372684100
2.736-3.44650.20091300.15332721100
3.4465-33.52110.17581420.1653277898

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