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- PDB-3apy: Properties and crystal structure of methylenetetrahydrofolate red... -

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Basic information

Entry
Database: PDB / ID: 3apy
TitleProperties and crystal structure of methylenetetrahydrofolate reductase from Thermus thermophilus HB8
ComponentsMethylenetetrahydrofolate reductase
KeywordsOXIDOREDUCTASE / TIM BARREL / FLAVIN
Function / homology
Function and homology information


methylenetetrahydrofolate reductase (NADH) / methylenetetrahydrofolate reductase (NADH) activity / methionine biosynthetic process / tetrahydrofolate interconversion / FAD binding / cytosol
Similarity search - Function
5,10-methylenetetrahydrofolate reductase / Methylenetetrahydrofolate reductase-like / Methylenetetrahydrofolate reductase / TIM Barrel - #220 / FAD-linked oxidoreductase-like / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Methylenetetrahydrofolate reductase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYamada, K.
CitationJournal: Plos One / Year: 2011
Title: Properties and Crystal Structure of Methylenetetrahydrofolate Reductase from Thermus thermophilus HB8.
Authors: Igari, S. / Ohtaki, A. / Yamanaka, Y. / Sato, Y. / Yohda, M. / Odaka, M. / Noguchi, K. / Yamada, K.
History
DepositionOct 21, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 14, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 1, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Methylenetetrahydrofolate reductase
B: Methylenetetrahydrofolate reductase
C: Methylenetetrahydrofolate reductase
D: Methylenetetrahydrofolate reductase
E: Methylenetetrahydrofolate reductase
F: Methylenetetrahydrofolate reductase
G: Methylenetetrahydrofolate reductase
H: Methylenetetrahydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,68722
Polymers277,1898
Non-polymers6,49714
Water16,376909
1
A: Methylenetetrahydrofolate reductase
B: Methylenetetrahydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9045
Polymers69,2972
Non-polymers1,6073
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-9 kcal/mol
Surface area25950 Å2
MethodPISA
2
C: Methylenetetrahydrofolate reductase
D: Methylenetetrahydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9045
Polymers69,2972
Non-polymers1,6073
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-9 kcal/mol
Surface area25840 Å2
MethodPISA
3
E: Methylenetetrahydrofolate reductase
F: Methylenetetrahydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9396
Polymers69,2972
Non-polymers1,6424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2380 Å2
ΔGint-11 kcal/mol
Surface area26180 Å2
MethodPISA
4
G: Methylenetetrahydrofolate reductase
H: Methylenetetrahydrofolate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,9396
Polymers69,2972
Non-polymers1,6424
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2360 Å2
ΔGint-8 kcal/mol
Surface area25770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.588, 90.930, 125.152
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Methylenetetrahydrofolate reductase


Mass: 34648.680 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Details: pET(tMRwt) / Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0327 / Plasmid: pET23, pET(tMRwt) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q5SLG6, methylenetetrahydrofolate reductase [NAD(P)H]
#2: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 909 / 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: 2.39 Å3/Da / Density % sol: 48.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris-HCl, 0.2M Ammonium Sulfate, 20-25% PEG 4000, 5% GLYCEROL , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 29, 2010
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.57→19.96 Å / Num. obs: 72447 / % possible obs: 91.54 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREP10.2.31phasing
REFMAC5.5.0102refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V93

1v93


Resolution: 2.8→19.96 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.873 / Rfactor Rfree error: 0.29767 / SU B: 17.619 / SU ML: 0.356 / Cross valid method: THROUGHOUT / ESU R Free: 0.508 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30586 3050 5 %RANDOM
Rwork0.2039 ---
obs0.20869 57531 93.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.499 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å2-0.03 Å2
2---0.05 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18416 0 430 909 19755
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02219320
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5722.00326192
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25652320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.40221.667912
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.35153152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.74215240
X-RAY DIFFRACTIONr_chiral_restr0.1030.22776
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02114888
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6181.511592
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.218218568
X-RAY DIFFRACTIONr_scbond_it1.85137728
X-RAY DIFFRACTIONr_scangle_it3.2624.57624
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.344 231 -
Rwork0.244 3951 -
obs--89.68 %

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