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- PDB-4ts4: Crystal structure of the hydrolase domain of 10-formyltetrahydrof... -

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Basic information

Entry
Database: PDB / ID: 4ts4
TitleCrystal structure of the hydrolase domain of 10-formyltetrahydrofolate dehydrogenase (wild-type) from zebrafish
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
10-formyltetrahydrofolate dehydrogenase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 18, 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
Category: atom_site / citation ...atom_site / citation / citation_author / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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


Theoretical massNumber of molelcules
Total (without water)35,4561
Polymers35,4561
Non-polymers00
Water5,981332
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15250 Å2
Unit cell
Length a, b, c (Å)104.665, 53.878, 60.632
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-441-

HOH

21A-482-

HOH

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Components

#1: Protein 10-formyltetrahydrofolate dehydrogenase


Mass: 35456.438 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / 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: 2.41 Å3/Da / Density % sol: 48.98 %
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: SPring-8 / Beamline: BL12B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. obs: 35347 / % possible obs: 99.9 % / Redundancy: 6.9 % / Net I/σ(I): 33.8
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4 / % possible all: 99.9

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.7.3_928) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1s3i

1s3i


Resolution: 1.75→24.025 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 1768 5.01 %Random selection
Rwork0.1803 ---
obs0.1813 35288 99.82 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.776 Å2 / ksol: 0.347 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.1351 Å20 Å2-0 Å2
2--6.7154 Å20 Å2
3----4.5804 Å2
Refinement stepCycle: LAST / Resolution: 1.75→24.025 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2415 0 0 332 2747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072475
X-RAY DIFFRACTIONf_angle_d1.3023348
X-RAY DIFFRACTIONf_dihedral_angle_d14.708923
X-RAY DIFFRACTIONf_chiral_restr0.126356
X-RAY DIFFRACTIONf_plane_restr0.005438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7496-1.79690.31951250.24962535X-RAY DIFFRACTION99
1.7969-1.84970.25511350.22472510X-RAY DIFFRACTION100
1.8497-1.90940.2311200.1972553X-RAY DIFFRACTION100
1.9094-1.97760.21021430.18682561X-RAY DIFFRACTION100
1.9776-2.05680.2461520.1862514X-RAY DIFFRACTION100
2.0568-2.15030.20051420.17922547X-RAY DIFFRACTION100
2.1503-2.26360.21951380.17472559X-RAY DIFFRACTION100
2.2636-2.40530.20991280.16862583X-RAY DIFFRACTION100
2.4053-2.59080.21691200.17182580X-RAY DIFFRACTION100
2.5908-2.85120.20431360.18082585X-RAY DIFFRACTION100
2.8512-3.26290.21691450.19292608X-RAY DIFFRACTION100
3.2629-4.10760.16241410.17562636X-RAY DIFFRACTION100
4.1076-24.02680.17831430.16752749X-RAY DIFFRACTION99
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)
11.2248-0.2604-0.10541.4137-0.20033.6186-0.1371-0.1337-0.2133-0.0417-0.0846-0.27290.92920.58960.18580.33460.11270.04370.23850.04640.186914.37077.589220.7034
21.68130.9817-0.71831.0261-0.58910.77950.0213-0.09890.0348-0.0135-0.0162-0.04710.01420.10420.0010.12580.00030.00770.1413-0.02460.137617.421627.780512.1027
34.75850.4403-0.59460.5611-1.32083.15420.0903-0.46420.34950.2228-0.1672-0.0418-0.50260.40480.10080.2272-0.05920.00270.2213-0.04260.174240.50543.512110.3304
43.33080.46990.54421.7240.02173.63280.0485-0.4374-0.01690.2102-0.0742-0.14340.12870.27890.0150.1794-0.0080.00380.2238-0.00230.168541.166938.880414.1827
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:106)
2X-RAY DIFFRACTION2chain 'A' and (resseq 107:239)
3X-RAY DIFFRACTION3chain 'A' and (resseq 240:270)
4X-RAY DIFFRACTION4chain 'A' and (resseq 271:308)

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