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- PDB-3w7b: Crystal structure of formyltetrahydrofolate deformylase from Ther... -

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Basic information

Entry
Database: PDB / ID: 3w7b
TitleCrystal structure of formyltetrahydrofolate deformylase from Thermus thermophilus HB8
ComponentsFormyltetrahydrofolate deformylase
KeywordsHYDROLASE / formyltetrahydrofolate deformylase / formyltetrahydrofolate
Function / homology
Function and homology information


formyltetrahydrofolate deformylase / formyltetrahydrofolate deformylase activity / hydroxymethyl-, formyl- and related transferase activity / 'de novo' IMP biosynthetic process / one-carbon metabolic process
Similarity search - Function
Formyltetrahydrofolate deformylase / Formyltetrahydrofolate deformylase, C-terminal hydrolase domain / Formyl transferase, N-terminal domain / ACT domain / ACT domain / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / ACT domain profile. / ACT domain ...Formyltetrahydrofolate deformylase / Formyltetrahydrofolate deformylase, C-terminal hydrolase domain / Formyl transferase, N-terminal domain / ACT domain / ACT domain / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / ACT domain profile. / ACT domain / Alpha-Beta Plaits / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Formyltetrahydrofolate deformylase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.71 Å
AuthorsSampei, G. / Yanagida, Y. / Ogata, N. / Kusano, M. / Terao, K. / Kawai, H. / Fukai, Y. / Kanagawa, M. / Inoue, Y. / Baba, S. / Kawai, G.
CitationJournal: J.Biochem. / Year: 2013
Title: Structures and reaction mechanisms of the two related enzymes, PurN and PurU
Authors: Sampei, G. / Kanagawa, M. / Baba, S. / Shimasaki, T. / Taka, H. / Mitsui, S. / Fujiwara, S. / Yanagida, Y. / Kusano, M. / Suzuki, S. / Terao, K. / Kawai, H. / Fukai, Y. / Nakagawa, N. / ...Authors: Sampei, G. / Kanagawa, M. / Baba, S. / Shimasaki, T. / Taka, H. / Mitsui, S. / Fujiwara, S. / Yanagida, Y. / Kusano, M. / Suzuki, S. / Terao, K. / Kawai, H. / Fukai, Y. / Nakagawa, N. / Ebihara, A. / Kuramitsu, S. / Yokoyama, S. / Kawai, G.
History
DepositionFeb 28, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 8, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Formyltetrahydrofolate deformylase
B: Formyltetrahydrofolate deformylase


Theoretical massNumber of molelcules
Total (without water)65,6762
Polymers65,6762
Non-polymers00
Water1,63991
1
A: Formyltetrahydrofolate deformylase
B: Formyltetrahydrofolate deformylase

A: Formyltetrahydrofolate deformylase
B: Formyltetrahydrofolate deformylase


Theoretical massNumber of molelcules
Total (without water)131,3514
Polymers131,3514
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Buried area11350 Å2
ΔGint0 kcal/mol
Surface area48510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.592, 90.726, 87.483
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-349-

HOH

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Components

#1: Protein Formyltetrahydrofolate deformylase /


Mass: 32837.789 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA1321 / Production host: Escherichia coli (E. coli)
References: UniProt: Q5SIP8, formyltetrahydrofolate deformylase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 91 / 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: 2.4 Å3/Da / Density % sol: 48.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 10
Details: 50% 2-methyl-2,4-pentanediol, 0.1M CAPS, pH 10.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 18, 2008 / Details: Toroidal Mirror
RadiationMonochromator: Fixed exit 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: 2.5→50 Å / Num. all: 17794 / Num. obs: 17779 / % possible obs: 99.9 % / Redundancy: 7.3 % / Biso Wilson estimate: 48.3 Å2 / Rmerge(I) obs: 0.122 / Net I/σ(I): 28.9
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.335 / Mean I/σ(I) obs: 5.9 / % possible all: 100

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Processing

Software
NameVersionClassification
BSSdata collection
AMoREphasing
CNS1.3refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LOU

3lou


Resolution: 2.71→29.92 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 182748.13 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.261 1689 9.8 %RANDOM
Rwork0.208 ---
obs0.208 17171 96.5 %-
all-17171 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.0609 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 36.7 Å2
Baniso -1Baniso -2Baniso -3
1-12.81 Å20 Å20 Å2
2---8.31 Å20 Å2
3----4.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.71→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4630 0 0 91 4721
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.791.5
X-RAY DIFFRACTIONc_mcangle_it3.192
X-RAY DIFFRACTIONc_scbond_it2.362
X-RAY DIFFRACTIONc_scangle_it3.782.5
LS refinement shellResolution: 2.71→2.88 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.35 264 9.8 %
Rwork0.261 2425 -
obs--92.6 %
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 DIFFRACTION5carbohydrate.paramcarbohydrate.top

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