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- PDB-4gnz: Crystal structure of the c707s mutant of c-terminal domain of 10'... -

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Basic information

Entry
Database: PDB / ID: 4gnz
TitleCrystal structure of the c707s mutant of c-terminal domain of 10'formyltetrahydrofolate dehydrogenase in complex with NADP
ComponentsCytosolic 10-formyltetrahydrofolate dehydrogenase
KeywordsOXIDOREDUCTASE / aldehyde dehydrogenase / FDH
Function / homology
Function and homology information


Metabolism of folate and pterines / aldehyde dehydrogenase (NADP+) activity / formyltetrahydrofolate dehydrogenase / formyltetrahydrofolate dehydrogenase activity / 10-formyltetrahydrofolate catabolic process / aldehyde dehydrogenase [NAD(P)+] activity / NADPH regeneration / aldehyde dehydrogenase (NAD+) activity / folic acid metabolic process / tetrahydrofolate biosynthetic process ...Metabolism of folate and pterines / aldehyde dehydrogenase (NADP+) activity / formyltetrahydrofolate dehydrogenase / formyltetrahydrofolate dehydrogenase activity / 10-formyltetrahydrofolate catabolic process / aldehyde dehydrogenase [NAD(P)+] activity / NADPH regeneration / aldehyde dehydrogenase (NAD+) activity / folic acid metabolic process / tetrahydrofolate biosynthetic process / one-carbon metabolic process / protein-containing complex binding / protein-containing complex / cytosol
Similarity search - Function
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 / Phosphoribosylglycinamide formyltransferase, active site / Phosphoribosylglycinamide formyltransferase active site. / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily ...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 / Phosphoribosylglycinamide formyltransferase, active site / Phosphoribosylglycinamide formyltransferase active site. / Formyl transferase, N-terminal / Formyl transferase / Formyl transferase, N-terminal domain superfamily / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Cytosolic 10-formyltetrahydrofolate dehydrogenase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTsybovsky, Y.
CitationJournal: Chem.Biol.Interact / Year: 2013
Title: The mechanism of discrimination between oxidized and reduced coenzyme in the aldehyde dehydrogenase domain of Aldh1l1.
Authors: Tsybovsky, Y. / Malakhau, Y. / Strickland, K.C. / Krupenko, S.A.
History
DepositionAug 17, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Sep 13, 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_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Cytosolic 10-formyltetrahydrofolate dehydrogenase
B: Cytosolic 10-formyltetrahydrofolate dehydrogenase
C: Cytosolic 10-formyltetrahydrofolate dehydrogenase
D: Cytosolic 10-formyltetrahydrofolate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,45440
Polymers226,4224
Non-polymers6,03236
Water19,0241056
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30350 Å2
ΔGint-440 kcal/mol
Surface area59060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)259.092, 194.255, 97.229
Angle α, β, γ (deg.)90.00, 108.74, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Cytosolic 10-formyltetrahydrofolate dehydrogenase / 10-FTHFDH / FDH / Aldehyde dehydrogenase family 1 member L1 / FBP-CI


Mass: 56605.484 Da / Num. of mol.: 4 / Fragment: C-terminal domain, residues 397-902 / Mutation: C707S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Aldh1l1, Fthfd / Production host: Escherichia coli (E. coli)
References: UniProt: P28037, formyltetrahydrofolate dehydrogenase
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1056 / 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: 5.11 Å3/Da / Density % sol: 75.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 1.5 M Ammonium Sulfate, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 6, 2006
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 183270 / Num. obs: 183270 / % possible obs: 95.89 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.096 / Net I/σ(I): 7.7
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 1.7 / % possible all: 94.3

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Processing

Software
NameVersionClassification
d*TREKdata scaling
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2O2P

2o2p


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / SU B: 4.152 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20979 9660 5 %RANDOM
Rwork0.17989 ---
all0.18139 183270 --
obs0.18139 183270 95.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.982 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20.92 Å2
2---0.37 Å20 Å2
3---0.51 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15296 0 356 1056 16708
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.02216229
X-RAY DIFFRACTIONr_angle_refined_deg1.3721.98222004
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.35451999
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.0524.68718
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.131152803
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.121587
X-RAY DIFFRACTIONr_chiral_restr0.0920.22439
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112067
X-RAY DIFFRACTIONr_mcbond_it0.5311.59908
X-RAY DIFFRACTIONr_mcangle_it1.024215990
X-RAY DIFFRACTIONr_scbond_it1.7736321
X-RAY DIFFRACTIONr_scangle_it2.8674.56003
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 724 -
Rwork0.253 13217 -
obs-13217 93.87 %

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