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- PDB-1y5y: Structure of the tetrahydromethanopterin dependent formaldehyde-a... -

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Basic information

Entry
Database: PDB / ID: 1y5y
TitleStructure of the tetrahydromethanopterin dependent formaldehyde-activating enzyme (Fae) from Methylobacterium extorquens AM1
ComponentsFormaldehyde-activating enzyme fae
KeywordsLYASE / Pentamer / beta-alpha-beta left handed crossover / flexible C-terminus
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
5,6,7,8-tetrahydromethanopterin hydro-lyase
Similarity search - Component
Biological speciesMethylobacterium extorquens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 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 1.3Feb 14, 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _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.ptnr2_auth_asym_id / _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_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)89,9788
Polymers89,8925
Non-polymers863
Water10,052558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14800 Å2
ΔGint-104 kcal/mol
Surface area26460 Å2
MethodPISA
2
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

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)179,95616
Polymers179,78410
Non-polymers1726
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area31870 Å2
ΔGint-195 kcal/mol
Surface area50490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.659, 120.659, 205.947
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Cell settingtetragonal
Space group name H-MP43212
DetailsThe biological assembly is a pentamer. The asymmetric unit contains a pentamer.

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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
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 558 / 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: 3.9 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.2 M calciumchloride x 2H2O, 0.1 M sodium acetate x 3H2O pH 4.6 and 10-20% (v/v) isopropanol, VAPOR DIFFUSION, HANGING DROP, temperature 277K'

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9790, 0.9792, 0.9501
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Jul 14, 2002
RadiationMonochromator: DOUBLE CRYSTAL, SI(311) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.97921
30.95011
ReflectionResolution: 2→19.89 Å / Num. all: 100903 / Num. obs: 100903 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 34.1 Å2 / Rsym value: 0.054 / Net I/σ(I): 19.3
Reflection shellResolution: 2→2.07 Å / % possible obs: 95.4 % / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.88 / Rsym value: 0.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXSphasing
CNS1.1refinement
RefinementMethod to determine structure: MAD / Resolution: 2→19.89 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3482207.85 / 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
Rfree0.239 5112 5.1 %RANDOM
Rwork0.204 ---
all0.221 100903 --
obs0.221 100903 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 63.9159 Å2 / ksol: 0.390391 e/Å3
Displacement parametersBiso mean: 40.5 Å2
Baniso -1Baniso -2Baniso -3
1-4.21 Å20 Å20 Å2
2--4.21 Å20 Å2
3----8.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.25 Å
Luzzati d res low-50 Å
Luzzati sigma a0.3 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2→19.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5974 0 3 558 6535
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d1.12
X-RAY DIFFRACTIONc_mcbond_it2.991.5
X-RAY DIFFRACTIONc_mcangle_it3.742
X-RAY DIFFRACTIONc_scbond_it4.632
X-RAY DIFFRACTIONc_scangle_it6.242.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.345 868 5.3 %
Rwork0.298 15481 -
obs--96.5 %
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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