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- PDB-4tts: Crystal structure of the hydrolase domain of 10-formyltetrahydrof... -

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Basic information

Entry
Database: PDB / ID: 4tts
TitleCrystal structure of the hydrolase domain of 10-formyltetrahydrofolate dehydrogenase (Y200A) complex with 10-formyl-5,8-dideazafolate
Components10-formyltetrahydrofolate dehydrogenase
KeywordsOXIDOREDUCTASE / 10-Formyltetrahydrofolate dehydrogenase / hydrolase domain / catalysis
Function / homology
Function and homology information


neuromast deposition / Metabolism of folate and pterines / formyltetrahydrofolate dehydrogenase / formyltetrahydrofolate dehydrogenase activity / 10-formyltetrahydrofolate catabolic process / embryonic viscerocranium morphogenesis / aldehyde dehydrogenase (NAD+) activity / neural crest cell migration / biosynthetic process / gastrulation ...neuromast deposition / Metabolism of folate and pterines / formyltetrahydrofolate dehydrogenase / formyltetrahydrofolate dehydrogenase activity / 10-formyltetrahydrofolate catabolic process / embryonic viscerocranium morphogenesis / aldehyde dehydrogenase (NAD+) activity / neural crest cell migration / biosynthetic process / gastrulation / one-carbon metabolic process / heart development / hydrolase activity / 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, C-terminal / Aldehyde dehydrogenase, N-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
Chem-6DD / 10-formyltetrahydrofolate dehydrogenase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLin, C.C. / Chen, C.J. / Fu, T.F. / Chuankhayan, P. / Kao, T.T. / Chang, W.N.
Funding support Taiwan, Saudi Arabia, 7items
OrganizationGrant numberCountry
National Science Council (NSC)98-2313-B-009-001-MY3 Taiwan
National Science Council (NSC)101-2628-B-213-001-MY4 Taiwan
National Science Council (NSC)102-2627-M-213-001-MY3 Taiwan
National Synchrotron Radiation Center (NSRRC)1013RSB02 Taiwan
National Synchrotron Radiation Center (NSRRC)1023RSB02 Taiwan
National Science Council (NSC)99-2320-B-006-013-MY3 Taiwan
Deanship of Scientific Research at King Saud UniversityRGP-VPP-207 Saudi Arabia
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structures of the hydrolase domain of zebrafish 10-formyltetrahydrofolate dehydrogenase and its complexes reveal a complete set of key residues for hydrolysis and product inhibition.
Authors: Lin, C.C. / Chuankhayan, P. / Chang, W.N. / Kao, T.T. / Guan, H.H. / Fun, H.K. / Nakagawa, A. / Fu, T.F. / Chen, C.J.
History
DepositionJun 23, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 2.0Dec 18, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / citation_author / diffrn_source / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / struct_keywords
Item: _atom_site.occupancy / _citation.pdbx_database_id_PubMed ..._atom_site.occupancy / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.text
Revision 2.1Nov 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 / refine_hist
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: 10-formyltetrahydrofolate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8322
Polymers35,3641
Non-polymers4671
Water5,188288
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area14890 Å2
Unit cell
Length a, b, c (Å)103.636, 54.378, 61.009
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
11A-584-

HOH

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Components

#1: Protein 10-formyltetrahydrofolate dehydrogenase


Mass: 35364.344 Da / Num. of mol.: 1 / Fragment: UNP residues 1-311
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: aldh1l1 / Production host: Escherichia coli (E. coli)
References: UniProt: E3NZ06, formyltetrahydrofolate dehydrogenase
#2: Chemical ChemComp-6DD / N-(4-{[(2-amino-4-hydroxyquinazolin-6-yl)methyl](formyl)amino}benzoyl)-L-glutamic acid


Mass: 467.431 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C22H21N5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Bis-Tris (0.1~0.2 M, pH 5.5) and PEG3350 (25~29%, w/v)

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 23485 / % possible obs: 97.4 % / Redundancy: 6 % / Net I/σ(I): 12.6

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.2_1309) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TS4

4ts4


Resolution: 2→29.263 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.02 / Phase error: 23.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2474 1186 5.14 %Random
Rwork0.2011 ---
obs0.2035 23089 95.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→29.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 34 288 2730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082503
X-RAY DIFFRACTIONf_angle_d1.2683387
X-RAY DIFFRACTIONf_dihedral_angle_d16.688926
X-RAY DIFFRACTIONf_chiral_restr0.083357
X-RAY DIFFRACTIONf_plane_restr0.005443
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9967-2.08760.26651580.21092752X-RAY DIFFRACTION98
2.0876-2.19760.26761540.22312668X-RAY DIFFRACTION95
2.1976-2.33530.31641390.25722663X-RAY DIFFRACTION95
2.3353-2.51550.26791630.21492777X-RAY DIFFRACTION99
2.5155-2.76840.25421480.20922830X-RAY DIFFRACTION99
2.7684-3.16860.30571300.20822868X-RAY DIFFRACTION100
3.1686-3.99050.25011310.18022357X-RAY DIFFRACTION82
3.9905-29.26630.17641630.17242988X-RAY DIFFRACTION99

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