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- PDB-1ftr: FORMYLMETHANOFURAN:TETRAHYDROMETHANOPTERIN FORMYLTRANSFERASE FROM... -

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Basic information

Entry
Database: PDB / ID: 1ftr
TitleFORMYLMETHANOFURAN:TETRAHYDROMETHANOPTERIN FORMYLTRANSFERASE FROM METHANOPYRUS KANDLERI
ComponentsFORMYLMETHANOFURAN\:TETRAHYDROMETHANOPTERIN FORMYLTRANSFERASE
KeywordsFORMYLTRANSFERASE / METHANOGENESIS / ARCHAE / ACYLTRANSFERASE / HYPERTHERMOPHILIC / HALOPHILIC
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 speciesMethanopyrus kandleri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.7 Å
AuthorsErmler, U. / Merckel, M.C. / Thauer, R.K. / Shima, S.
CitationJournal: Structure / Year: 1997
Title: Formylmethanofuran: tetrahydromethanopterin formyltransferase from Methanopyrus kandleri - new insights into salt-dependence and thermostability.
Authors: Ermler, U. / Merckel, M. / Thauer, R. / Shima, S.
History
DepositionSep 21, 1997Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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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)126,7464
Polymers126,7464
Non-polymers00
Water12,719706
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16240 Å2
ΔGint-102 kcal/mol
Surface area38400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)157.500, 157.500, 242.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.2364, 0.0086, 0.9716), (0.0038, -1, 0.008), (0.9716, 0.0018, -0.2365)5.0198, 155.0376, -7.4627
2given(-1, 0.0027, 0.0001), (0.0027, 1, -0.0086), (-0.0001, -0.0086, -1)78.7205, 0.0918, 50.8724
3given(-0.2373, 0.0007, -0.9714), (-0.0053, -1, 0.0006), (-0.9714, 0.0053, 0.2373)73.1203, 155.576, 57.0284

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Components

#1: Protein
FORMYLMETHANOFURAN\:TETRAHYDROMETHANOPTERIN FORMYLTRANSFERASE / FTR


Mass: 31686.449 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanopyrus kandleri (archaea) / Cell line: BL21 / Cellular location: CYTOPLASM / Gene: FTR / Plasmid: PFTR1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q49610, formylmethanofuran-tetrahydromethanopterin N-formyltransferase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 706 / 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: 3 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 277 K / pH: 7
Details: 22% PEG 8000 0.3M (NH4)2SO4 0.1M MOPS (PH 7.0) 4 DEG C, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Details: Shima, S., (1996) Proteins Struct.Funct.Genet., 26, 118.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
150 mMMOPS1drop
22 mMdithiothreitol1drop
312-16 mg/mlenzyme1drop
422 %PEG80001reservoir
50.3 Mammonium sulfate1reservoir
60.1 MMOPS1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 1, 1995 / Details: MIRRORS
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→8 Å / Num. obs: 135354 / % possible obs: 87.8 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Rmerge(I) obs: 0.054 / Rsym value: 0.054 / Net I/σ(I): 8
Reflection shellResolution: 1.73→1.87 Å / Redundancy: 2 % / Rmerge(I) obs: 0.054 / Mean I/σ(I) obs: 2 / Rsym value: 0.245 / % possible all: 66

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Processing

Software
NameVersionClassification
MLPHAREphasing
SHELXSphasing
MOSFLMdata reduction
CCP4(ROTAVATAdata scaling
Agrovatadata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.7→10 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.248 13520 10 %RANDOM
Rwork0.198 ---
obs0.198 135354 87.8 %-
Displacement parametersBiso mean: 11.03 Å2
Refine analyzeLuzzati coordinate error obs: 0.25 Å / Luzzati d res low obs: 10 Å
Refinement stepCycle: LAST / Resolution: 1.7→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1184 0 0 706 1890
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg0.94
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.48
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.656
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: UNRESTRAINED
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOLTOPH19.SOL
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.488
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.656

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