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- PDB-1lu9: Structure of methylene-tetrahydromethanopterin dehydrogenase from... -

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Basic information

Entry
Database: PDB / ID: 1lu9
TitleStructure of methylene-tetrahydromethanopterin dehydrogenase from Methylobacterium extorquens AM1
ComponentsMethylene Tetrahydromethanopterin Dehydrogenase
KeywordsOXIDOREDUCTASE / alpha/beta twisted open sheet structure
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-NH group of donors; With NAD+ or NADP+ as acceptor / methylenetetrahydrofolate dehydrogenase (NADP+) / methylenetetrahydrofolate dehydrogenase (NADP+) activity / formaldehyde catabolic process / one-carbon metabolic process / cytoplasm
Similarity search - Function
Methylene-tetrahydromethanopterin dehydrogenase, N-terminal domain / Methylene-tetrahydromethanopterin dehydrogenase, N-terminal / Methylene tetrahydromethanopterin dehydrogenase, NADP-binding domain / Methylene-tetrahydromethanopterin dehydrogenase, N-terminal domain superfamily / Methylene-tetrahydromethanopterin dehydrogenase, N-terminal / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Bifunctional protein MdtA
Similarity search - Component
Biological speciesMethylobacterium extorquens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsErmler, U. / Hagemeier, C.H. / Roth, A. / Demmer, U. / Grabarse, W. / Warkentin, E. / Vorholt, J.A.
Citation
Journal: Structure / Year: 2002
Title: Structure of methylene-tetrahydromethanopterin dehydrogenase from methylobacterium extorquens AM1.
Authors: Ermler, U. / Hagemeier, C.H. / Roth, A. / Demmer, U. / Grabarse, W. / Warkentin, E. / Vorholt, J.A.
#1: Journal: J.BACTERIOL. / Year: 1998
Title: The NADP-Dependent Methylene Tetrahydromethanopterin Dehydrogenase in Methylobacterium extorquens AM1
Authors: Vorholt, J.A. / Chistoserdova, L. / Lidstrom, M.E. / Thauer, R.K.
History
DepositionMay 22, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Methylene Tetrahydromethanopterin Dehydrogenase
B: Methylene Tetrahydromethanopterin Dehydrogenase
C: Methylene Tetrahydromethanopterin Dehydrogenase


Theoretical massNumber of molelcules
Total (without water)88,9223
Polymers88,9223
Non-polymers00
Water10,052558
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3410 Å2
ΔGint-20 kcal/mol
Surface area32840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.130, 85.240, 92.370
Angle α, β, γ (deg.)90.00, 113.81, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Methylene Tetrahydromethanopterin Dehydrogenase / Methylenetetrahydrofolate dehydrogenase


Mass: 29640.609 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methylobacterium extorquens (bacteria) / Strain: AM1 / Gene: mtdA / Plasmid: pET 17b CH1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS
References: UniProt: P55818, methylenetetrahydrofolate dehydrogenase (NADP+)
#2: 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: 2.7 Å3/Da / Density % sol: 54.37 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Hepes, PEG1500, Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1drop
2100 mMHEPES1droppH7.5
320 %PEG15001reservoir
420 mMTris1reservoirpH8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 30, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 69818 / Num. obs: 69818 / % possible obs: 93.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 20.3
Reflection shellResolution: 1.9→1.99 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 3 / Num. unique all: 8261 / % possible all: 84
Reflection
*PLUS
Lowest resolution: 30 Å / Redundancy: 3 % / Rmerge(I) obs: 0.064

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Processing

Software
NameVersionClassification
SOLVEphasing
SHARPphasing
DMmodel building
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: MIR / Resolution: 1.9→29.89 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.229 3331 5.1 %RANDOM
Rwork0.189 ---
all0.189 65187 --
obs0.189 65187 87.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.9865 Å2 / ksol: 0.317233 e/Å3
Displacement parametersBiso mean: 27.3 Å2
Baniso -1Baniso -2Baniso -3
1--5.25 Å20 Å2-0.48 Å2
2--2.38 Å20 Å2
3---2.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6252 0 0 558 6810
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.97
X-RAY DIFFRACTIONc_mcbond_it1.61.5
X-RAY DIFFRACTIONc_mcangle_it2.162
X-RAY DIFFRACTIONc_scbond_it2.532
X-RAY DIFFRACTIONc_scangle_it3.562.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 457 5.1 %
Rwork0.237 8501 -
obs--72.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4MTDAP21_CIS.PARAMION.TOP
X-RAY DIFFRACTION5ION.PARAM
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor all: 0.189 / Rfactor Rfree: 0.229 / Rfactor Rwork: 0.19
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.97
LS refinement shell
*PLUS
Rfactor Rfree: 0.294 / Rfactor Rwork: 0.237

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