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- PDB-1s3i: Crystal structure of the N terminal hydrolase domain of 10-formyl... -

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Basic information

Entry
Database: PDB / ID: 1s3i
TitleCrystal structure of the N terminal hydrolase domain of 10-formyltetrahydrofolate dehydrogenase
Components10-formyltetrahydrofolate dehydrogenase
KeywordsHYDROLASE / OXIDOREDUCTASE / Rossmann fold
Function / homology
Function and homology information


Metabolism of folate and pterines / aldehyde dehydrogenase (NADP+) activity / formyltetrahydrofolate dehydrogenase / formyltetrahydrofolate dehydrogenase activity / 10-formyltetrahydrofolate catabolic process / aldehyde dehydrogenase [NAD(P)+] activity / NADPH regeneration / aldehyde dehydrogenase (NAD+) activity / bile acid signaling pathway / folic acid metabolic process ...Metabolism of folate and pterines / aldehyde dehydrogenase (NADP+) activity / formyltetrahydrofolate dehydrogenase / formyltetrahydrofolate dehydrogenase activity / 10-formyltetrahydrofolate catabolic process / aldehyde dehydrogenase [NAD(P)+] activity / NADPH regeneration / aldehyde dehydrogenase (NAD+) activity / bile acid signaling pathway / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / protein-containing complex binding / protein-containing complex / cytosol
Similarity search - Function
Formyl transferase, C-terminal domain / Methionyl-tRNA Fmet Formyltransferase; Chain A, domain 2 / 10-formyltetrahydrofolate dehydrogenase / Formyl transferase, C-terminal domain superfamily / Formyl transferase, C-terminal / Formyl transferase, C-terminal domain / Formyl transferase-like, C-terminal domain superfamily / Formyl transferase, N-terminal domain / Phosphoribosylglycinamide formyltransferase, active site / Phosphoribosylglycinamide formyltransferase active site. ...Formyl transferase, C-terminal domain / Methionyl-tRNA Fmet Formyltransferase; Chain A, domain 2 / 10-formyltetrahydrofolate dehydrogenase / Formyl transferase, C-terminal domain superfamily / Formyl transferase, C-terminal / Formyl transferase, C-terminal domain / Formyl transferase-like, C-terminal domain superfamily / Formyl transferase, N-terminal domain / Phosphoribosylglycinamide formyltransferase, active site / Phosphoribosylglycinamide formyltransferase active site. / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Aldehyde dehydrogenase, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / ACP-like superfamily / Carrier protein (CP) domain profile. / Phosphopantetheine binding ACP domain / Roll / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Cytosolic 10-formyltetrahydrofolate dehydrogenase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MIR / Resolution: 2.3 Å
AuthorsChumanevich, A.A. / Krupenko, S.A. / Davies, C.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: The crystal structure of the hydrolase domain of 10-formyltetrahydrofolate dehydrogenase: mechanism of hydrolysis and its interplay with the dehydrogenase domain.
Authors: Chumanevich, A.A. / Krupenko, S.A. / Davies, C.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallization and preliminary X-ray diffraction analysis of recombinant hydrolase domain of 10-formyltetrahydrofolate dehydrogenase
Authors: Chumanevich, A.A. / Davies, C. / Krupenko, S.A.
History
DepositionJan 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE AMINO ACIDS AT POSITIONS 42, 51, 52, 283, AND 284 CONFLICT WITH THE PUBLISHED SEQUENCE. ...SEQUENCE THE AMINO ACIDS AT POSITIONS 42, 51, 52, 283, AND 284 CONFLICT WITH THE PUBLISHED SEQUENCE. THE ASPARTATE AT POSITION 310 IS NON-NATIVE AND RESULTS FROM THE CLONING.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 10-formyltetrahydrofolate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4736
Polymers34,0821
Non-polymers3915
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)100.00, 64.63, 64.59
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein 10-formyltetrahydrofolate dehydrogenase / 10-FTHFDH / FBP-CI


Mass: 34081.836 Da / Num. of mol.: 1 / Fragment: Nt-FDH,residues 1-310 / Mutation: none
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: FTHFD / Plasmid: pVL1393 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): HIGH FIVE
References: UniProt: P28037, formyltetrahydrofolate dehydrogenase
#2: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.11 Å3/Da / Density % sol: 60.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1.3 M ammonium sulphate, 0.1M sodium acetate pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: Chumanevich, A.A., (2002) Acta Cryst., D58, 1841. / PH range low: 5.1 / PH range high: 4.9
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
11.2-1.4 Mammonium sulfate1reservoirpH4.9-5.1
25 %glycerol1reservoir
310 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 2, 2001 / Details: mirrors
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.3→45.7 Å / Num. all: 19201 / Num. obs: 19201 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 32.9 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 5.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.346 / Mean I/σ(I) obs: 2 / Num. unique all: 1863 / Rsym value: 0.346 / % possible all: 100
Reflection
*PLUS
Num. measured all: 80514 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 1863 / Num. measured obs: 7894

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
CrystalClear(MSC/RIGAKU)data reduction
d*TREKdata scaling
PHASESphasing
RefinementMethod to determine structure: MIR / Resolution: 2.3→15 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.859 / SU B: 9.584 / SU ML: 0.226 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.309 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.30527 978 5.1 %RANDOM
Rwork0.24205 ---
all0.2453 19056 --
obs0.24532 19056 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.745 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.71 Å2
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2380 0 20 53 2453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212457
X-RAY DIFFRACTIONr_angle_refined_deg1.4811.9563314
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6375306
X-RAY DIFFRACTIONr_chiral_restr0.1180.2356
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021868
X-RAY DIFFRACTIONr_nbd_refined0.2070.21098
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.130.295
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.26
X-RAY DIFFRACTIONr_mcbond_it0.5771.51523
X-RAY DIFFRACTIONr_mcangle_it1.10722448
X-RAY DIFFRACTIONr_scbond_it1.6583934
X-RAY DIFFRACTIONr_scangle_it2.5764.5866
LS refinement shellResolution: 2.3→2.358 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.362 66
Rwork0.299 1278
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 15 Å / Num. reflection obs: 18079 / % reflection Rfree: 5 % / Rfactor Rfree: 0.305 / Rfactor Rwork: 0.242
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.01
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.48
LS refinement shell
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 2.36 Å

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