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- PDB-1y60: Structure of the tetrahydromethanopterin dependent formaldehyde-a... -

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Basic information

Entry
Database: PDB / ID: 1y60
TitleStructure of the tetrahydromethanopterin dependent formaldehyde-activating enzyme (Fae) from Methylobacterium extorquens AM1 with bound 5,10-methylene tetrahydromethanopterin
ComponentsFormaldehyde-activating enzyme fae
KeywordsLYASE / Pentamer / beta-alpha-beta left handed crossover / TETRAHYDROMETHANOPTERIN-BINDING
Function / homology
Function and homology information


5,6,7,8-tetrahydromethanopterin hydro-lyase / carbon-nitrogen lyase activity / formaldehyde catabolic process / carbohydrate biosynthetic process / one-carbon metabolic process / cytoplasm
Similarity search - Function
Formaldehyde-activating enzyme / Formaldehyde-activating enzyme / Formaldehyde-activating enzyme superfamily / Formaldehyde-activating enzyme (Fae) / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN / 5,6,7,8-tetrahydromethanopterin hydro-lyase
Similarity search - Component
Biological speciesMethylobacterium extorquens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsAcharya, P. / Goenrich, M. / Hagemeier, C.H. / Demmer, U. / Vorholt, J.A. / Thauer, R.K. / Ermler, U.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: How an enzyme binds the C1-carrier tetrahydromethanopterin: Structure of the tetrahydromethanopterin dependent formaldehyde-activating enzyme (Fae) from Methylobacterium extorquens AM1
Authors: Acharya, P. / Goenrich, M. / Hagemeier, C.H. / Demmer, U. / Vorholt, J.A. / Thauer, R.K. / Ermler, U.
History
DepositionDec 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / 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

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Assembly

Deposited unit
A: Formaldehyde-activating enzyme fae
B: Formaldehyde-activating enzyme fae
C: Formaldehyde-activating enzyme fae
D: Formaldehyde-activating enzyme fae
E: Formaldehyde-activating enzyme fae
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,83510
Polymers89,8925
Non-polymers3,9435
Water8,863492
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24880 Å2
ΔGint-137 kcal/mol
Surface area24710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.860, 112.590, 72.010
Angle α, β, γ (deg.)90.00, 91.00, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein
Formaldehyde-activating enzyme fae


Mass: 17978.391 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Details: complexed with pterin-related cofactor / Source: (gene. exp.) Methylobacterium extorquens (bacteria) / Strain: AM1 / Gene: fae / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q9FA38
#2: Chemical
ChemComp-H4M / 5,10-DIMETHYLENE TETRAHYDROMETHANOPTERIN


Mass: 788.693 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C31H45N6O16P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 492 / 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 Å3/Da / Density % sol: 38 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES/NaOH pH 7.5, 20% (w/v) polyethyleneglycol 10,000, 5 mM tetrahydromethanopterin (H4MPT), VAPOR DIFFUSION, HANGING DROP, temperature 281.0K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93927 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Dec 7, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93927 Å / Relative weight: 1
ReflectionResolution: 1.9→44.82 Å / Num. all: 59516 / Num. obs: 57191 / % possible obs: 93.5 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 20.9 Å2 / Rmerge(I) obs: 0.144 / Rsym value: 0.082 / Net I/σ(I): 12.15
Reflection shellResolution: 1.9→2.01 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.03 / Num. unique all: 8288 / Rsym value: 0.4 / % possible all: 76.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
XDSdata reduction
EPMRphasing
CNS1.1refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Formaldehyde-activating enzyme from Methylobacterium extorquens AM1 PDB ID 1Y5Y

1y5y


Resolution: 1.9→44.82 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 108436.21 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 2967 5 %RANDOM
Rwork0.209 ---
all0.225 57191 --
obs0.225 57191 96.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.4963 Å2 / ksol: 0.390567 e/Å3
Displacement parametersBiso mean: 29 Å2
Baniso -1Baniso -2Baniso -3
1-18.76 Å20 Å26.46 Å2
2---9.77 Å20 Å2
3----8.99 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-50 Å
Luzzati sigma a0.46 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 1.9→44.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6293 0 225 492 7010
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d1.07
X-RAY DIFFRACTIONc_mcbond_it2.321.5
X-RAY DIFFRACTIONc_mcangle_it2.972
X-RAY DIFFRACTIONc_scbond_it3.532
X-RAY DIFFRACTIONc_scangle_it4.662.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.387 424 5 %
Rwork0.391 8083 -
obs-8507 83.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
X-RAY DIFFRACTION5H4M.PARH4M.TOP

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