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

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Basic information

Entry
Database: PDB / ID: 4qpd
TitleCrystal structure of the hydrolase domain of 10-formyltetrahydrofolate dehydrogenase (wild-type) complex with tetrahydrofolate
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
DI(HYDROXYETHYL)ETHER / (6S)-5,6,7,8-TETRAHYDROFOLATE / 10-formyltetrahydrofolate dehydrogenase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsLin, C.C. / Chen, C.J. / Fu, T.F. / Chuankhayan, P. / Kao, T.T. / Chang, W.N.
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 1.1Dec 18, 2019Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.country / _citation.journal_id_CSD ..._citation.country / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 10-formyltetrahydrofolate dehydrogenase
B: 10-formyltetrahydrofolate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,4617
Polymers70,9132
Non-polymers1,5495
Water7,782432
1
A: 10-formyltetrahydrofolate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0083
Polymers35,4561
Non-polymers5522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: 10-formyltetrahydrofolate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,4534
Polymers35,4561
Non-polymers9973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.501, 100.415, 122.519
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 10-formyltetrahydrofolate dehydrogenase


Mass: 35456.438 Da / Num. of mol.: 2 / 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-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-THG / (6S)-5,6,7,8-TETRAHYDROFOLATE


Mass: 445.429 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C19H23N7O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 432 / 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: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1~0.2M Bis-Tris, pH 5.5, 25~29%(w/v) PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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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: Jun 24, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 39592 / Num. obs: 39592 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.18 Å / % possible all: 89

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→29.373 Å / SU ML: 0.2 / σ(F): 1.34 / Phase error: 23.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.233 1986 5.03 %
Rwork0.1852 --
obs0.1876 39492 98.69 %
all-39592 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→29.373 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4830 0 110 432 5372
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055064
X-RAY DIFFRACTIONf_angle_d1.056847
X-RAY DIFFRACTIONf_dihedral_angle_d15.7611893
X-RAY DIFFRACTIONf_chiral_restr0.037718
X-RAY DIFFRACTIONf_plane_restr0.004891
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1001-2.15260.27711150.2267229586
2.1526-2.21080.27861310.2152259597
2.2108-2.27590.28931440.22042694100
2.2759-2.34930.23621530.20072641100
2.3493-2.43320.26821460.19232679100
2.4332-2.53060.23151410.18972690100
2.5306-2.64570.26721470.20262684100
2.6457-2.78510.23811310.19412715100
2.7851-2.95940.29111540.20452670100
2.9594-3.18770.26581540.19582711100
3.1877-3.5080.21691400.18962721100
3.508-4.01450.19741380.16422751100
4.0145-5.05360.19061460.14932775100
5.0536-29.37590.21041460.1838288599
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)
11.974-0.01180.22481.8819-0.0231.9695-0.1204-0.13140.42370.1401-0.1297-0.4106-0.23070.40180.18640.1821-0.0178-0.07070.24590.0160.322132.33713.273851.4423
21.4761-1.23730.31383.3577-0.32270.60090.05290.06310.0285-0.2628-0.00310.0328-0.05630.0156-0.04760.1472-0.00370.00520.12590.00070.096912.227814.147843.6906
30.7627-0.91650.11355.93540.66675.5831-0.0763-0.03290.23910.1195-0.10370.2152-0.685-0.31250.11240.28650.0224-0.01910.1760.00760.21920.251838.827143.1933
42.91830.021-0.03592.49130.56142.7956-0.03380.093-0.459-0.2561-0.0617-0.34210.45680.34350.11560.22290.04550.08640.25610.00190.248158.270231.79083.681
51.9982-0.0553-0.07851.03720.25471.07910.0215-0.3276-0.19810.0994-0.1928-0.46090.11080.60240.14160.1423-0.0334-0.01730.38940.0940.298361.813237.915415.319
61.20280.7653-0.26542.3-0.48740.70860.0937-0.0717-0.02270.0472-0.04230.05480.02320.0508-0.04440.1241-0.0224-0.01160.1420.0060.117439.649834.89816.3705
74.70395.72790.25878.82820.49090.8985-0.09550.27570.3043-0.2710.2650.3806-0.0818-0.0567-0.15250.1999-0.01120.00640.14230.02590.136145.72942.19144.8505
81.53191.1011-0.66362.9751-0.59580.85450.0239-0.2463-0.23560.2393-0.1015-0.20050.12920.07850.07770.1716-0.0006-0.02390.17910.04030.14338.578625.288522.265
90.55131.4689-1.03024.6598-1.45114.1494-0.13710.1638-0.2109-0.26390.11630.64380.4597-0.61990.0740.2439-0.0531-0.00480.2695-0.00470.358523.41869.72720.6594
103.4205-0.1921-0.52784.34250.69114.92110.01460.312-0.319-0.5978-0.08840.03530.5082-0.08610.08320.2987-0.02420.02360.19850.01630.244927.00268.411216.8103
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 106 )
2X-RAY DIFFRACTION2chain 'A' and (resid 107 through 227 )
3X-RAY DIFFRACTION3chain 'A' and (resid 228 through 308 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 59 )
5X-RAY DIFFRACTION5chain 'B' and (resid 60 through 106 )
6X-RAY DIFFRACTION6chain 'B' and (resid 107 through 167 )
7X-RAY DIFFRACTION7chain 'B' and (resid 168 through 184 )
8X-RAY DIFFRACTION8chain 'B' and (resid 185 through 239 )
9X-RAY DIFFRACTION9chain 'B' and (resid 240 through 270 )
10X-RAY DIFFRACTION10chain 'B' and (resid 271 through 308 )

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