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- PDB-4tt8: Crystal structure of the hydrolase domain of 10-formyltetrahydrof... -

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Basic information

Entry
Database: PDB / ID: 4tt8
TitleCrystal structure of the hydrolase domain of 10-formyltetrahydrofolate dehydrogenase (wild-type) 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 / 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 ...neuromast deposition / 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, 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
Chem-6DD / 10-formyltetrahydrofolate dehydrogenase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 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 20, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 2.0Dec 18, 2019Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Source and taxonomy
Category: atom_site / citation ...atom_site / citation / citation_author / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list
Item: _atom_site.occupancy / _citation.pdbx_database_id_PubMed ..._atom_site.occupancy / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
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

Downloads & links

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Assembly

Deposited unit
A: 10-formyltetrahydrofolate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1333
Polymers35,4561
Non-polymers6772
Water2,918162
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint5 kcal/mol
Surface area14520 Å2
Unit cell
Length a, b, c (Å)104.075, 52.694, 60.500
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-538-

HOH

21A-539-

HOH

31A-552-

HOH

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Components

#1: Protein 10-formyltetrahydrofolate dehydrogenase


Mass: 35456.438 Da / Num. of mol.: 1
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: obtained synthetically / Formula: C22H21N5O7
#3: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER / Bis-tris methane


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.34 Å3/Da / Density % sol: 47.42 %
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)
PH range: 5.5 - 6.5

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 15370 / % possible obs: 100 % / Redundancy: 5.6 % / Net I/σ(I): 15.8

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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: 2.301→26.347 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.224 766 4.99 %Random
Rwork0.1794 ---
obs0.1819 15339 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.301→26.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2415 0 48 162 2625
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042523
X-RAY DIFFRACTIONf_angle_d0.9683411
X-RAY DIFFRACTIONf_dihedral_angle_d17.822962
X-RAY DIFFRACTIONf_chiral_restr0.057356
X-RAY DIFFRACTIONf_plane_restr0.003443
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3006-2.47810.28141460.2132846X-RAY DIFFRACTION100
2.4781-2.72730.28671700.20922842X-RAY DIFFRACTION100
2.7273-3.12140.25741550.20622886X-RAY DIFFRACTION100
3.1214-3.93050.2161460.1692915X-RAY DIFFRACTION100
3.9305-26.34870.17741490.1583084X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.03060.01350.02870.02230.02570.01810.01490.0469-0.09240.1358-0.12150.11040.2584-0.19320-0.0852-0.3827-0.2868-0.0605-0.3645-0.3208-16.45916.4682-22.8861
20.00080.00740.00590.01050.00480.00450.017-0.0322-0.00810.0476-0.0648-0.00050.099-0.0887-00.1096-0.01490.01070.01240.01570.0653-9.13519.7768-15.5828
30.0405-0.01010.01760.05980.04610.02920.0592-0.01-0.00760.0516-0.039-0.00250.0589-0.0851-00.00350.02810.01370.0037-0.00380.0445-17.312827.1013-12.1651
40.0083-0.01280.0072-0.0011-0.00250.00610.00310.05270.1195-0.079-0.0041-0.0023-0.0793-0.0589-00.11990.03150.02620.14490.00840.1142-40.567741.8773-10.0671
50.0151-0.02030.01170.00460.00540.01130.05420.0445-0.0276-0.04590.075-0.0620.0186-0.072700.07840.0031-0.02460.1055-0.01290.0882-41.250737.8103-14.126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 76 )
2X-RAY DIFFRACTION2chain 'A' and (resid 77 through 106 )
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 239 )
4X-RAY DIFFRACTION4chain 'A' and (resid 240 through 270 )
5X-RAY DIFFRACTION5chain 'A' and (resid 271 through 308 )

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