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- PDB-4r8v: Crystal structure of the hydrolase domain of 10-formyltetrahydrof... -

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Basic information

Entry
Database: PDB / ID: 4r8v
TitleCrystal structure of the hydrolase domain of 10-formyltetrahydrofolate dehydrogenase (wild-type) complex with formate
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
FORMIC ACID / DI(HYDROXYETHYL)ETHER / 10-formyltetrahydrofolate dehydrogenase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.197 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
DepositionSep 3, 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8184
Polymers35,4561
Non-polymers3613
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)103.980, 51.977, 59.936
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-501-

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: 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
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.28 Å3/Da / Density % sol: 46.15 %
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: BL13C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 6, 2014
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.197→30 Å / Num. all: 17126 / Num. obs: 17126 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.197→2.28 Å / % possible all: 99.9

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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
Starting model: 4TS4

4ts4


Resolution: 2.197→25.962 Å / SU ML: 0.19 / σ(F): 1.34 / Phase error: 23.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2369 868 5.08 %RANDOM
Rwork0.1927 ---
obs0.1949 17089 99.53 %-
all-17126 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.197→25.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2415 0 24 85 2524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072496
X-RAY DIFFRACTIONf_angle_d1.1143370
X-RAY DIFFRACTIONf_dihedral_angle_d16.517948
X-RAY DIFFRACTIONf_chiral_restr0.071356
X-RAY DIFFRACTIONf_plane_restr0.004438
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.197-2.33450.30071370.21782669100
2.3345-2.51460.25531530.20972643100
2.5146-2.76740.23451250.20912680100
2.7674-3.16720.24711600.2162682100
3.1672-3.9880.241710.1852271199
3.988-25.96370.20671220.1754283699
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)
12.517-0.58790.30523.93071.54734.5667-0.0446-0.2175-0.3083-0.02130.1178-0.25340.3850.1955-0.0740.25750.0340.02960.20220.0740.242216.20785.782722.8835
21.1957-1.00190.25278.17280.07495.0999-0.11240.1627-0.4595-0.26360.1138-0.01870.48160.11010.02720.22510.01130.03360.20860.00260.26748.91859.039815.5797
34.32592.2019-0.69711.7645-0.48221.2855-0.020.0969-0.0833-0.02560.0276-0.0114-0.00480.0728-0.00620.2260.0427-0.00490.1711-0.00150.175117.21226.53612.0274
48.204-0.8105-0.47320.87420.17915.02510.02750.24741.09220.2867-0.2966-0.7363-1.01340.69450.23050.5555-0.0925-0.03510.43940.07530.438338.228441.746812.2885
55.75590.24661.37773.36860.4897.2015-0.01670.0173-0.0060.23470.1314-0.0545-0.00680.5643-0.11340.2213-0.04490.0140.28630.00330.230642.026737.458611.9834
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 259 )
5X-RAY DIFFRACTION5chain 'A' and (resid 260 through 308 )

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