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

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Basic information

Entry
Database: PDB / ID: 1lua
TitleStructure of methylene-tetrahydromethanopterin dehydrogenase from Methylobacterium extorquens AM1 complexed with NADP
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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Bifunctional protein MdtA
Similarity search - Component
Biological speciesMethylobacterium extorquens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)91,1526
Polymers88,9223
Non-polymers2,2303
Water12,827712
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6920 Å2
ΔGint-26 kcal/mol
Surface area32860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.9, 79.86, 154.29
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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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: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 712 / 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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG8000, MES, pH 6.5, 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
317 %PEG80001reservoir
450 mMMES1reservoirpH6.5
55 mMNADP+1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 30, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.81 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. all: 82475 / Num. obs: 82475 / % possible obs: 95.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.4 % / Biso Wilson estimate: 17.6 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 19
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.7 / Num. unique all: 9753 / % possible all: 97.4
Reflection
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 30 Å / Rmerge(I) obs: 0.091
Reflection shell
*PLUS
Rmerge(I) obs: 0.27

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Methylene Tetrahydromethanopterin Dehydrogenase

Resolution: 1.9→29.13 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 931083.76 / 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
Rfree0.222 3446 5.1 %RANDOM
Rwork0.185 ---
all0.185 68017 --
obs0.185 68017 91.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.4155 Å2 / ksol: 0.324197 e/Å3
Displacement parametersBiso mean: 28.1 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20 Å20 Å2
2---2.36 Å20 Å2
3---1.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.18 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→29.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6252 0 144 712 7108
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.263 462 4.6 %
Rwork0.213 9487 -
obs-9482 81.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3NAP_F42.PARAMNAP_F42.TOP
X-RAY DIFFRACTION4MTDAP21_CIS.PARAMION.TOP
X-RAY DIFFRACTION5ION.PARAM
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.222 / Rfactor Rwork: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.31
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91
LS refinement shell
*PLUS
Rfactor Rfree: 0.263 / Rfactor Rwork: 0.213

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