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- PDB-1f07: STRUCTURE OF COENZYME F420 DEPENDENT TETRAHYDROMETHANOPTERIN REDU... -

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Basic information

Entry
Database: PDB / ID: 1f07
TitleSTRUCTURE OF COENZYME F420 DEPENDENT TETRAHYDROMETHANOPTERIN REDUCTASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM
ComponentsCOENZYME F420-DEPENDENT N5,N10-METHYLENETETRAHYDROMETHANOPTERIN REDUCTASE
KeywordsOXIDOREDUCTASE / (beta / alpha)8 barrel / TIM barrel
Function / homology
Function and homology information


5,10-methylenetetrahydromethanopterin reductase / coenzyme F420-dependent N5,N10-methenyltetrahydromethanopterin reductase activity / methanogenesis, from carbon dioxide / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen / one-carbon metabolic process / cytoplasm
Similarity search - Function
5,10-methylenetetrahydromethanopterin reductase / : / Luciferase-like domain / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
5,10-methylenetetrahydromethanopterin reductase
Similarity search - Component
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsShima, S. / Warkentin, E. / Grabarse, W. / Thauer, R.K. / Ermler, U.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: Structure of coenzyme F(420) dependent methylenetetrahydromethanopterin reductase from two methanogenic archaea.
Authors: Shima, S. / Warkentin, E. / Grabarse, W. / Sordel, M. / Wicke, M. / Thauer, R.K. / Ermler, U.
History
DepositionMay 15, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: COENZYME F420-DEPENDENT N5,N10-METHYLENETETRAHYDROMETHANOPTERIN REDUCTASE
B: COENZYME F420-DEPENDENT N5,N10-METHYLENETETRAHYDROMETHANOPTERIN REDUCTASE
C: COENZYME F420-DEPENDENT N5,N10-METHYLENETETRAHYDROMETHANOPTERIN REDUCTASE
D: COENZYME F420-DEPENDENT N5,N10-METHYLENETETRAHYDROMETHANOPTERIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,45414
Polymers134,0734
Non-polymers1,38110
Water9,098505
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: COENZYME F420-DEPENDENT N5,N10-METHYLENETETRAHYDROMETHANOPTERIN REDUCTASE
B: COENZYME F420-DEPENDENT N5,N10-METHYLENETETRAHYDROMETHANOPTERIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7277
Polymers67,0372
Non-polymers6905
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-42 kcal/mol
Surface area23880 Å2
MethodPISA, PQS
3
C: COENZYME F420-DEPENDENT N5,N10-METHYLENETETRAHYDROMETHANOPTERIN REDUCTASE
D: COENZYME F420-DEPENDENT N5,N10-METHYLENETETRAHYDROMETHANOPTERIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,7277
Polymers67,0372
Non-polymers6905
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4750 Å2
ΔGint-40 kcal/mol
Surface area23920 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)162.800, 128.200, 109.200
Angle α, β, γ (deg.)90.00, 131.40, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a homodimer, constructed from chains A and B, and from chains C and D

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Components

#1: Protein
COENZYME F420-DEPENDENT N5,N10-METHYLENETETRAHYDROMETHANOPTERIN REDUCTASE


Mass: 33518.324 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Methanothermobacter thermautotrophicus (archaea)
References: UniProt: Q50744
#2: Chemical
ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID


Mass: 209.263 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H15NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / 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: 3.19 Å3/Da / Density % sol: 61.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: MPD, Na(Ac), CaCl2, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal
*PLUS
Density % sol: 59 %
Crystal grow
*PLUS
Method: vapor diffusion
Details: drop consists of equal amounts of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
130 %MPD1reservoir
20.1 M1reservoirNaAc
30.02 M1reservoirCaCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.045
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 7, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.045 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 107409 / Num. obs: 107409 / % possible obs: 95 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Biso Wilson estimate: 24.9 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 14
Reflection shellResolution: 2→2.02 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.29 / Num. unique all: 3705 / % possible all: 88
Reflection shell
*PLUS
% possible obs: 88 %

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Processing

Software
NameVersionClassification
AMoREphasing
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2→30 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1596043.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.237 5402 5 %RANDOM
Rwork0.208 ---
all0.209 107409 --
obs0.209 107409 95 %-
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.24 Å20 Å2-0.95 Å2
2---1.26 Å20 Å2
3----0.98 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9412 0 86 505 10003
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_mcbond_it1.061.5
X-RAY DIFFRACTIONc_mcangle_it1.662
X-RAY DIFFRACTIONc_scbond_it6.782
X-RAY DIFFRACTIONc_scangle_it6.142.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.296 805 4.9 %
Rwork0.275 15691 -
obs--87.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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