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

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Basic information

Entry
Database: PDB / ID: 4qpc
TitleCrystal structure of the hydrolase domain of 10-formyltetrahydrofolate dehydrogenase (Y200A) from zebrafish
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
10-formyltetrahydrofolate dehydrogenase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.902 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 1.2Nov 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
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)35,3641
Polymers35,3641
Non-polymers00
Water6,215345
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: 10-formyltetrahydrofolate dehydrogenase

A: 10-formyltetrahydrofolate dehydrogenase


Theoretical massNumber of molelcules
Total (without water)70,7292
Polymers70,7292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area1630 Å2
ΔGint-9 kcal/mol
Surface area28400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.460, 53.959, 60.877
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-690-

HOH

21A-721-

HOH

31A-722-

HOH

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Components

#1: Protein 10-formyltetrahydrofolate dehydrogenase


Mass: 35364.344 Da / Num. of mol.: 1 / Fragment: UNP residues 1-311 / Mutation: Y200A
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 / Water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.43 Å3/Da / Density % sol: 49.29 %
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: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 27430 / Num. obs: 27430 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.97 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TS4

4ts4


Resolution: 1.902→24 Å / SU ML: 0.18 / σ(F): 1.33 / Phase error: 23.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2247 1376 5.04 %RANDOM
Rwork0.2035 ---
obs0.2046 27326 98.57 %-
all-27430 --
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.134 Å2 / ksol: 0.312 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.9419 Å2-0 Å2-0 Å2
2--4.6307 Å2-0 Å2
3----0.6887 Å2
Refinement stepCycle: LAST / Resolution: 1.902→24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 0 345 2753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062467
X-RAY DIFFRACTIONf_angle_d1.0533337
X-RAY DIFFRACTIONf_dihedral_angle_d15.367920
X-RAY DIFFRACTIONf_chiral_restr0.067356
X-RAY DIFFRACTIONf_plane_restr0.005437
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9021-1.970.37371260.3274252098
1.97-2.04890.28091320.22262589100
2.0489-2.14210.21841360.20872596100
2.1421-2.25490.28741250.2501258699
2.2549-2.39610.30361430.2273253699
2.3961-2.58090.22691500.20022615100
2.5809-2.84020.22841350.20062629100
2.8402-3.25040.20841520.20422637100
3.2504-4.09180.19971260.1806245492
4.0918-24.00180.17911510.1753278899
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)
11.83150.8880.31872.932-0.49732.03690.0647-0.2627-0.51710.1458-0.3085-0.78060.41870.42990.10630.26270.0371-0.00320.26310.1290.357414.63337.869521.0329
23.19121.5996-0.62711.7223-0.32510.83870.1192-0.20440.03870.1561-0.0393-0.0133-0.01690.0565-0.07640.11680.0107-0.00490.10770.00810.096912.732127.066715.6642
34.75381.5948-0.45621.1891-0.39910.9982-0.00290.2764-0.3293-0.04950.0212-0.16780.06090.1518-0.01840.15290.03310.00480.0995-0.04320.142224.008929.06467.5944
45.33380.4254-0.79450.1664-0.7834.72310.2287-0.24150.75020.2383-0.1012-0.172-0.63170.3961-0.01850.2425-0.03830.03880.1887-0.0220.25440.280543.16379.7091
56.4081-0.2710.89653.3283-0.71756.06870.0662-0.27250.11960.2672-0.0911-0.24290.20960.61680.00590.1508-0.00430.01750.2079-0.01740.121441.019139.091113.8231
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:106)
2X-RAY DIFFRACTION2chain 'A' and (resseq 107:184)
3X-RAY DIFFRACTION3chain 'A' and (resseq 185:239)
4X-RAY DIFFRACTION4chain 'A' and (resseq 240:270)
5X-RAY DIFFRACTION5chain 'A' and (resseq 271:308)

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