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

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Basic information

Entry
Database: PDB / ID: 4qdk
TitleCrystal structure of magnesium protoporphyrin IX methyltransferase (ChlM) from Synechocystis PCC 6803 with bound SAH
ComponentsMagnesium-protoporphyrin O-methyltransferase
KeywordsTRANSFERASE / Methyltransferase / Magnesium protoporphyrin IX / S-adenosyl Homocysteine
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-ADENOSYL-L-HOMOCYSTEINE / Magnesium-protoporphyrin O-methyltransferase
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.2Nov 8, 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_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
B: Magnesium-protoporphyrin O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3136
Polymers52,3602
Non-polymers9534
Water6,702372
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Magnesium-protoporphyrin O-methyltransferase
hetero molecules

B: Magnesium-protoporphyrin O-methyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3136
Polymers52,3602
Non-polymers9534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area2530 Å2
ΔGint-25 kcal/mol
Surface area18560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.059, 98.876, 52.935
Angle α, β, γ (deg.)90.00, 95.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 26179.801 Da / Num. of mol.: 2
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-SAH / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.1M citrate sodium pH 5.8, 10% PEG 4000, 20% isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2013
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 54547 / Num. obs: 54275 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.7→1.76 Å / % possible all: 98.9

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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: MOLECULAR REPLACEMENT
Starting model: 4QDJ

4qdj


Resolution: 1.7→36.043 Å / SU ML: 0.17 / σ(F): 1.38 / Phase error: 23.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2242 2561 5.07 %RANDOM
Rwork0.1881 ---
all0.1899 55113 --
obs0.1899 50545 91.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→36.043 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3343 0 64 372 3779
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033487
X-RAY DIFFRACTIONf_angle_d0.7454724
X-RAY DIFFRACTIONf_dihedral_angle_d11.2421272
X-RAY DIFFRACTIONf_chiral_restr0.047540
X-RAY DIFFRACTIONf_plane_restr0.003599
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7001-1.73280.238720.1639142250
1.7328-1.76810.2557870.1917182962
1.7681-1.80660.2626840.202217074
1.8066-1.84860.25721160.1953238983
1.8486-1.89480.28121410.1904264990
1.8948-1.94610.24351330.1909279296
1.9461-2.00330.24261570.186285399
2.0033-2.0680.21721830.1777285099
2.068-2.14190.2331710.1721287099
2.1419-2.22760.21651370.1746291499
2.2276-2.3290.22151640.16982851100
2.329-2.45180.21321800.1852903100
2.4518-2.60530.21551390.19662919100
2.6053-2.80640.25791600.19582885100
2.8064-3.08870.23361730.19462907100
3.0887-3.53530.22291570.19392922100
3.5353-4.45280.18671640.17482907100
4.4528-36.05140.21661430.2074295299

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