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- PDB-3rhj: Crystal structure of the E673A mutant of the C-terminal domain of... -

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Basic information

Entry
Database: PDB / ID: 3rhj
TitleCrystal structure of the E673A mutant of the C-terminal domain of RAT 10'FORMYLTETRAHYDROFOLATE DEHYDROGENASE in complex with co-purified NADP
ComponentsAldehyde dehydrogenase 1 family, member L1
KeywordsOXIDOREDUCTASE / 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 / Cytosolic 10-formyltetrahydrofolate dehydrogenase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsTsybovsky, Y.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Conserved catalytic residues of the ALDH1L1 aldehyde dehydrogenase domain control binding and discharging of the coenzyme.
Authors: Tsybovsky, Y. / Krupenko, S.A.
History
DepositionApr 11, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 31, 2011Group: Database references
Revision 1.3Sep 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_conn / 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_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Dec 25, 2024Group: Advisory / Derived calculations / Structure summary
Category: pdbx_distant_solvent_atoms / pdbx_entry_details / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aldehyde dehydrogenase 1 family, member L1
B: Aldehyde dehydrogenase 1 family, member L1
C: Aldehyde dehydrogenase 1 family, member L1
D: Aldehyde dehydrogenase 1 family, member L1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)231,90236
Polymers226,2544
Non-polymers5,64832
Water26,2121455
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29860 Å2
ΔGint-420 kcal/mol
Surface area59410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)259.391, 194.933, 97.480
Angle α, β, γ (deg.)90.00, 108.94, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Aldehyde dehydrogenase 1 family, member L1


Mass: 56563.508 Da / Num. of mol.: 4 / Fragment: C-TERMINAL DOMAIN, RESIDUES 397-902 / Mutation: E673A
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: Q5HZB2, UniProt: P28037*PLUS
#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.: 24 / 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.: 1455 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1 M Tris, pH 7.8, 1.8 M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Dec 7, 2007
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. all: 355622 / Num. obs: 355622 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 9.8
Reflection shellResolution: 1.89→1.97 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 1.9 / % possible all: 89.2

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
REFMAC5.5.0102refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2O2P

2o2p


Resolution: 1.89→48.91 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.212 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.09 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.203 17875 5 %RANDOM
Rwork0.189 ---
obs0.189 337623 97.8 %-
all-337623 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.33 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å21.75 Å2
2---0.32 Å20 Å2
3---0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.89→48.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15239 0 336 1455 17030
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02216259
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2341.97822070
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.09552022
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.06624.689708
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.38152778
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.6871580
X-RAY DIFFRACTIONr_chiral_restr0.0860.22451
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02112136
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5561.59981
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.073216129
X-RAY DIFFRACTIONr_scbond_it1.72236278
X-RAY DIFFRACTIONr_scangle_it2.8464.55931
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.89→1.94 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 1054 -
Rwork0.29 20109 -
obs--79 %

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