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- PDB-1z69: Crystal structure of methylenetetrahydromethanopterin reductase (... -

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Basic information

Entry
Database: PDB / ID: 1z69
TitleCrystal structure of methylenetetrahydromethanopterin reductase (Mer) in complex with coenzyme F420
ComponentsCoenzyme F420-dependent N(5),N(10)-methylenetetrahydromethanopterin reductase
KeywordsOXIDOREDUCTASE / (alpha / beta)8 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
Chem-1PG / COENZYME F420 / : / 5,10-methylenetetrahydromethanopterin reductase
Similarity search - Component
Biological speciesMethanosarcina barkeri (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsAufhammer, S.W. / Warkentin, E. / Ermler, U. / Hagemeier, C.H. / Thauer, R.K. / Shima, S.
CitationJournal: Protein Sci. / Year: 2005
Title: Crystal structure of methylenetetrahydromethanopterin reductase (Mer) in complex with coenzyme F420: Architecture of the F420/FMN binding site of enzymes within the nonprolyl cis-peptide ...Title: Crystal structure of methylenetetrahydromethanopterin reductase (Mer) in complex with coenzyme F420: Architecture of the F420/FMN binding site of enzymes within the nonprolyl cis-peptide containing bacterial luciferase family
Authors: Aufhammer, S.W. / Warkentin, E. / Ermler, U. / Hagemeier, C.H. / Thauer, R.K. / Shima, S.
History
DepositionMar 22, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 21, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_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 N(5),N(10)-methylenetetrahydromethanopterin reductase
B: Coenzyme F420-dependent N(5),N(10)-methylenetetrahydromethanopterin reductase
C: Coenzyme F420-dependent N(5),N(10)-methylenetetrahydromethanopterin reductase
D: Coenzyme F420-dependent N(5),N(10)-methylenetetrahydromethanopterin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,42511
Polymers138,0084
Non-polymers3,4187
Water4,306239
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14480 Å2
ΔGint-68 kcal/mol
Surface area46340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.81, 83.41, 99.17
Angle α, β, γ (deg.)90.00, 91.15, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein
Coenzyme F420-dependent N(5),N(10)-methylenetetrahydromethanopterin reductase / E.C.1.5.99.11 / COG2141 / Methylene-H(4)MPT reductase


Mass: 34501.938 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Methanosarcina barkeri (archaea) / Strain: Fusaro (DSMZ 804)
References: GenBank: 48840204, UniProt: Q46FV4*PLUS, EC: 1.5.99.11
#2: Chemical
ChemComp-F42 / COENZYME F420


Mass: 773.593 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C29H36N5O18P
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL


Mass: 252.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H24O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.38 Å3/Da / Density % sol: 46.7 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris/HCl, PEG 4000, Isopropanol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 9, 2004
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. all: 40607 / Num. obs: 40607 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.96 % / Biso Wilson estimate: 37.7 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 14.2
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.214 / Mean I/σ(I) obs: 6.8 / Num. unique all: 5785 / % possible all: 86.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
XDSdata reduction
EPMRphasing
CNS1.1refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1F07

1f07


Resolution: 2.61→19.95 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 208649.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: SEE REMARK 11 NCS RESTRAINTS NCS RESTRAINTS WERE USED FOR ALL FOUR CHAINS EXCEPT FOR RESIDUES 214 - 283 OF CHAIN D. DIFFERENT WEIGHTS WERE APPLIED TO MAIN CHAIN AND SIDE CHAINS. MAIN CHAIN ...Details: SEE REMARK 11 NCS RESTRAINTS NCS RESTRAINTS WERE USED FOR ALL FOUR CHAINS EXCEPT FOR RESIDUES 214 - 283 OF CHAIN D. DIFFERENT WEIGHTS WERE APPLIED TO MAIN CHAIN AND SIDE CHAINS. MAIN CHAIN ATOMS, EXCEPT FOR RESIDUES 214-285 CHAIN A CHAIN B CHAIN D RMSD 0.058 0.057 0.066 (A) REFERENCE MC ATOMS OF CHAIN C SIDE CHAIN ATOMS, EXCEPT FOR RESIDUES 214-285 CHAIN A CHAIN B CHAIN D RMSD 0.12 0.12 0.13 (A) REFERENCE SC ATOMS OF CHAIN C MAIN CHAIN ATOMS, RESIDUES 214-285 CHAIN A CHAIN B CHAIN D RMSD 0.056 0.054 --- (A) REFERENCE MC ATOMS OF CHAIN C SIDE CHAIN ATOMS, RESIDUES 214-285 CHAIN A CHAIN B CHAIN D RMSD 0.14 0.15 --- (A) REFERENCE SC ATOMS OF CHAIN C
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2011 5 %RANDOM
Rwork0.185 ---
all0.19 40216 --
obs0.1851 40216 98.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.7686 Å2 / ksol: 0.36323 e/Å3
Displacement parametersBiso mean: 28.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å2-1.57 Å2
2--3 Å20 Å2
3----2.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.61→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9684 0 231 239 10154
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_improper_angle_d1.28
X-RAY DIFFRACTIONc_mcbond_it1.671.5
X-RAY DIFFRACTIONc_mcangle_it2.632
X-RAY DIFFRACTIONc_scbond_it3.042
X-RAY DIFFRACTIONc_scangle_it4.392.5
LS refinement shellResolution: 2.61→2.76 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.315 295 5 %
Rwork0.241 5601 -
obs-5921 86.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2BMER_CIS.PARWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION4ION.PARAMNAP_F42.TOP
X-RAY DIFFRACTION5NAP_F42.PAR

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