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- PDB-2o2p: Crystal structure of the C-terminal domain of rat 10'formyltetrah... -

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Basic information

Entry
Database: PDB / ID: 2o2p
TitleCrystal structure of the C-terminal domain of rat 10'formyltetrahydrofolate dehydrogenase
ComponentsFormyltetrahydrofolate 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 / bile acid signaling pathway / folic acid metabolic 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 / bile acid signaling pathway / 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, N-terminal / Aldehyde dehydrogenase, C-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
Cytosolic 10-formyltetrahydrofolate dehydrogenase / Cytosolic 10-formyltetrahydrofolate dehydrogenase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsTsybovsky, Y. / Donato, H. / Krupenko, N.I. / Davies, C. / Krupenko, S.A.
CitationJournal: Biochemistry / Year: 2007
Title: Crystal structures of the carboxyl terminal domain of rat 10-formyltetrahydrofolate dehydrogenase: implications for the catalytic mechanism of aldehyde dehydrogenases.
Authors: Tsybovsky, Y. / Donato, H. / Krupenko, N.I. / Davies, C. / Krupenko, S.A.
History
DepositionNov 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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: Formyltetrahydrofolate dehydrogenase
B: Formyltetrahydrofolate dehydrogenase
C: Formyltetrahydrofolate dehydrogenase
D: Formyltetrahydrofolate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,54436
Polymers226,4864
Non-polymers3,05832
Water32,3371795
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25470 Å2
ΔGint-421 kcal/mol
Surface area60100 Å2
MethodPISA
2
A: Formyltetrahydrofolate dehydrogenase
B: Formyltetrahydrofolate dehydrogenase
C: Formyltetrahydrofolate dehydrogenase
D: Formyltetrahydrofolate dehydrogenase
hetero molecules

A: Formyltetrahydrofolate dehydrogenase
B: Formyltetrahydrofolate dehydrogenase
C: Formyltetrahydrofolate dehydrogenase
D: Formyltetrahydrofolate dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)459,08972
Polymers452,9728
Non-polymers6,11664
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area52430 Å2
ΔGint-863 kcal/mol
Surface area118710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)259.500, 194.400, 97.300
Angle α, β, γ (deg.)90.00, 108.90, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological unit is the tetramer

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Components

#1: Protein
Formyltetrahydrofolate dehydrogenase /


Mass: 56621.547 Da / Num. of mol.: 4 / Fragment: C-terminal domain, residues 397-902
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: FTHFD / Plasmid: PRSET-B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: Q5HZB2, UniProt: P28037*PLUS, formyltetrahydrofolate dehydrogenase
#2: Chemical...
ChemComp-SO4 / SULFATE ION / Sulfate


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


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


Mass: 18.015 Da / Num. of mol.: 1795 / 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

Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.4 M AMMONIUM SULPHATE, 0.1M TRIS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 22, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 485421 / Num. obs: 485421 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 10.1
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.558 / Mean I/σ(I) obs: 2.5 / Num. unique all: 47647 / Rsym value: 0.558 / % possible all: 95.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MAR345CCDdata collection
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2O2Q

2o2q


Resolution: 1.7→50 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.236 / SU ML: 0.041 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.064 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.189 24236 5 %RANDOM
Rwork0.174 ---
all0.175 485404 --
obs0.175 485404 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.203 Å2
Baniso -1Baniso -2Baniso -3
1-0.62 Å20 Å20.49 Å2
2---0.01 Å20 Å2
3----0.29 Å2
Refinement stepCycle: LAST / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15296 0 164 1795 17255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02216135
X-RAY DIFFRACTIONr_angle_refined_deg1.2561.96421870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20352030
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.89524.693716
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.256152790
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.7091580
X-RAY DIFFRACTIONr_chiral_restr0.0920.22423
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212124
X-RAY DIFFRACTIONr_nbd_refined0.1920.28016
X-RAY DIFFRACTIONr_nbtor_refined0.3050.211197
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.21625
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0660.213
X-RAY DIFFRACTIONr_mcbond_it0.6941.510307
X-RAY DIFFRACTIONr_mcangle_it1.137216177
X-RAY DIFFRACTIONr_scbond_it1.92636551
X-RAY DIFFRACTIONr_scangle_it2.9864.55683
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 1728 -
Rwork0.259 33456 -
obs-35184 95.4 %

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