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

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Basic information

Entry
Database: PDB / ID: 1ezw
TitleSTRUCTURE OF COENZYME F420 DEPENDENT TETRAHYDROMETHANOPTERIN REDUCTASE FROM METHANOPYRUS KANDLERI
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 speciesMethanopyrus kandleri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.65 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 12, 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 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

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Assembly

Deposited unit
A: COENZYME F420-DEPENDENT N5,N10-METHYLENETETRAHYDROMETHANOPTERIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,6103
Polymers37,5511
Non-polymers602
Water3,963220
1
A: COENZYME F420-DEPENDENT N5,N10-METHYLENETETRAHYDROMETHANOPTERIN REDUCTASE
hetero molecules

A: COENZYME F420-DEPENDENT N5,N10-METHYLENETETRAHYDROMETHANOPTERIN REDUCTASE
hetero molecules

A: COENZYME F420-DEPENDENT N5,N10-METHYLENETETRAHYDROMETHANOPTERIN REDUCTASE
hetero molecules

A: COENZYME F420-DEPENDENT N5,N10-METHYLENETETRAHYDROMETHANOPTERIN REDUCTASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,44212
Polymers150,2034
Non-polymers2398
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x,-y+1/2,-z+1/21
crystal symmetry operation11_455-x-1/2,y,-z+1/21
crystal symmetry operation14_455-x-1/2,-y+1/2,z1
Buried area11740 Å2
ΔGint-88 kcal/mol
Surface area47840 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)90.200, 144.100, 152.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Components on special symmetry positions
IDModelComponents
11A-361-

MG

21A-362-

CL

31A-401-

HOH

DetailsThe biological assembly is a homodimer or a dimer of dimers, i.e., a tetramer generated by the 222 axes

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Components

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


Mass: 37550.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Methanopyrus kandleri (archaea) / References: UniProt: Q8TXY4
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 220 / 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: 3.29 Å3/Da / Density % sol: 62.6 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 400, HEPES, Mg(ac)2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal
*PLUS
Density % sol: 64 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Details: used macroseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
115 mg/mlprotein1drop
328 %PEG4001reservoir
40.1 MHEPES1reservoir
50.38 M1reservoirMgAc2
2MOPS-KOH1drop

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. all: 58481 / Num. obs: 58481 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 16
Reflection shellResolution: 1.65→1.67 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.234 / Num. unique all: 2004 / % possible all: 99
Reflection
*PLUS
Lowest resolution: 30 Å

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.65→20 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 3491786.42 / 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
Rfree0.212 2963 5.1 %RANDOM
Rwork0.198 ---
all0.198 58481 --
obs0.198 58481 98.8 %-
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1--7.28 Å20 Å20 Å2
2--2.76 Å20 Å2
3---4.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2621 0 2 220 2843
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
X-RAY DIFFRACTIONc_angle_deg1.86
X-RAY DIFFRACTIONc_dihedral_angle_d22.6
X-RAY DIFFRACTIONc_improper_angle_d1.14
LS refinement shellResolution: 1.65→1.75 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.292 467 4.8 %
Rwork0.266 9265 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.1 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.14
LS refinement shell
*PLUS
Rfactor Rfree: 0.292 / % reflection Rfree: 4.8 % / Rfactor Rwork: 0.266

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