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- PDB-1m5s: Formylmethanofuran:tetrahydromethanopterin fromyltransferase from... -

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Basic information

Entry
Database: PDB / ID: 1m5s
TitleFormylmethanofuran:tetrahydromethanopterin fromyltransferase from Methanosarcina barkeri
ComponentsFormylmethanofuran--tetrahydromethanopterin formyltransferase
KeywordsTRANSFERASE / ALPHA/BETA SANDWICH
Function / homology
Function and homology information


formylmethanofuran-tetrahydromethanopterin N-formyltransferase / formylmethanofuran-tetrahydromethanopterin N-formyltransferase activity / methanogenesis, from carbon dioxide / one-carbon metabolic process / cytoplasm
Similarity search - Function
Alpha-Beta Plaits - #520 / Formylmethanofuran: tetrahydromethanopterin formyltransferase Ftr, C-terminal / Formylmethanofuran: tetrahydromethanopterin formyltransferase Ftr / Formylmethanofuran: tetrahydromethanopterin formyltransferase Ftr, N-terminal / Formylmethanofuran: tetrahydromethanopterin formyltransferase Ftr, ferredoxin-like superfamily / Formylmethanofuran-tetrahydromethanopterin formyltransferase / FTR, proximal lobe / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Formylmethanofuran--tetrahydromethanopterin formyltransferase
Similarity search - Component
Biological speciesMethanosarcina barkeri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsMamat, B. / Roth, A. / Grimm, C. / Ermler, U. / Tziatzios, C. / Schubert, D. / Thauer, R.K. / Shima, S.
CitationJournal: Protein Sci. / Year: 2002
Title: Crystal structures and enzymatic properties of three formyltransferases from archaea: environmental adaptation and evolutionary relationship.
Authors: Mamat, B. / Roth, A. / Grimm, C. / Ermler, U. / Tziatzios, C. / Schubert, D. / Thauer, R.K. / Shima, S.
History
DepositionJul 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Formylmethanofuran--tetrahydromethanopterin formyltransferase
B: Formylmethanofuran--tetrahydromethanopterin formyltransferase
C: Formylmethanofuran--tetrahydromethanopterin formyltransferase
D: Formylmethanofuran--tetrahydromethanopterin formyltransferase


Theoretical massNumber of molelcules
Total (without water)126,7814
Polymers126,7814
Non-polymers00
Water13,115728
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15630 Å2
ΔGint-125 kcal/mol
Surface area39560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.100, 83.800, 126.400
Angle α, β, γ (deg.)90.00, 108.40, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein
Formylmethanofuran--tetrahydromethanopterin formyltransferase / E.C.2.3.1.101 / Formylmethanofuran:Tetrahydromethanopterin formyltransferase / ftr-2 / ftr-2 AF2207


Mass: 31695.168 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanosarcina barkeri (archaea) / Plasmid: pET24b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P55301, formylmethanofuran-tetrahydromethanopterin N-formyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 728 / 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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: MPD, sodium citrate, ammonium acetate, HEPES, formylmethanofuran, pH 6.7, VAPOR DIFFUSION, HANGING DROP at 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
210 mMMOPS1droppH7.0
30.1 Msodium citrate1reservoir
40.2 Mammonium acetate1reservoir
531 %MPD1reservoir
60.1 MHEPES1reservoirpH6.7
75.0 mMformylmethanofuran1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.85→30 Å / Num. all: 106340 / Num. obs: 99960 / % possible obs: 94 % / Observed criterion σ(I): 1 / Biso Wilson estimate: 19.3 Å2 / Rsym value: 0.037
Reflection shellResolution: 1.85→1.92 Å / Rsym value: 0.081 / % possible all: 84.4
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / % possible obs: 94 % / Num. measured all: 215926 / Rmerge(I) obs: 0.037
Reflection shell
*PLUS
Highest resolution: 1.88 Å / % possible obs: 84.4 % / Rmerge(I) obs: 0.081

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Formylmethanofuran:tetrahydromethanopterin formyltransferase from Methanopyrus kandleri

Resolution: 1.85→19.78 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.248 4913 5 %RANDOM
Rwork0.197 ---
all0.197 107467 --
obs0.197 97795 91 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.317 Å2 / ksol: 0.339322 e/Å3
Displacement parametersBiso mean: 32.9 Å2
Baniso -1Baniso -2Baniso -3
1--9.44 Å20 Å2-5.18 Å2
2--7.1 Å20 Å2
3---2.34 Å2
Refine analyzeLuzzati coordinate error free: 0.29 Å / Luzzati sigma a free: 0.26 Å
Refinement stepCycle: LAST / Resolution: 1.85→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8914 0 0 728 9642
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d26.4
X-RAY DIFFRACTIONc_improper_angle_d1.49
X-RAY DIFFRACTIONc_mcbond_it4.041.5
X-RAY DIFFRACTIONc_mcangle_it4.762
X-RAY DIFFRACTIONc_scbond_it5.512
X-RAY DIFFRACTIONc_scangle_it7.142.5
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 674 5.3 %
Rwork0.285 12063 -
obs--71.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
Rfactor all: 0.197 / Rfactor Rfree: 0.248 / Rfactor Rwork: 0.197 / Highest resolution: 1.9 Å / Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.49
LS refinement shell
*PLUS
Rfactor Rfree: 0.325 / Rfactor Rwork: 0.285

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