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- PDB-1a4i: HUMAN TETRAHYDROFOLATE DEHYDROGENASE / CYCLOHYDROLASE -

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Basic information

Entry
Database: PDB / ID: 1a4i
TitleHUMAN TETRAHYDROFOLATE DEHYDROGENASE / CYCLOHYDROLASE
ComponentsMETHYLENETETRAHYDROFOLATE DEHYDROGENASE / METHENYLTETRAHYDROFOLATE CYCLOHYDROLASE
KeywordsOXIDOREDUCTASE / THF / BIFUNCTIONAL / DEHYDROGENASE / CYCLOHYDROLASE / FOLATE
Function / homology
Function and homology information


methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity / serine family amino acid biosynthetic process / 10-formyltetrahydrofolate biosynthetic process / purine ribonucleotide biosynthetic process / serine family amino acid metabolic process / methylenetetrahydrofolate dehydrogenase (NAD+) activity / formate-tetrahydrofolate ligase / formate-tetrahydrofolate ligase activity / methylenetetrahydrofolate dehydrogenase (NADP+) / embryonic neurocranium morphogenesis ...methylenetetrahydrofolate dehydrogenase [NAD(P)+] activity / serine family amino acid biosynthetic process / 10-formyltetrahydrofolate biosynthetic process / purine ribonucleotide biosynthetic process / serine family amino acid metabolic process / methylenetetrahydrofolate dehydrogenase (NAD+) activity / formate-tetrahydrofolate ligase / formate-tetrahydrofolate ligase activity / methylenetetrahydrofolate dehydrogenase (NADP+) / embryonic neurocranium morphogenesis / methenyltetrahydrofolate cyclohydrolase / methenyltetrahydrofolate cyclohydrolase activity / embryonic viscerocranium morphogenesis / methylenetetrahydrofolate dehydrogenase (NADP+) activity / methionine metabolic process / somite development / methionine biosynthetic process / Metabolism of folate and pterines / transsulfuration / neutrophil homeostasis / purine nucleotide biosynthetic process / tetrahydrofolate interconversion / neural tube closure / one-carbon metabolic process / heart development / mitochondrion / extracellular exosome / ATP binding / membrane / cytosol
Similarity search - Function
Formate-tetrahydrofolate ligase, FTHFS / Formate-tetrahydrofolate ligase, FTHFS, conserved site / Formate--tetrahydrofolate ligase / Formate--tetrahydrofolate ligase signature 1. / Formate--tetrahydrofolate ligase signature 2. / Tetrahydrofolate dehydrogenase/cyclohydrolase signature 1. / Tetrahydrofolate dehydrogenase/cyclohydrolase signature 2. / Tetrahydrofolate dehydrogenase/cyclohydrolase, conserved site / Tetrahydrofolate dehydrogenase/cyclohydrolase / Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain ...Formate-tetrahydrofolate ligase, FTHFS / Formate-tetrahydrofolate ligase, FTHFS, conserved site / Formate--tetrahydrofolate ligase / Formate--tetrahydrofolate ligase signature 1. / Formate--tetrahydrofolate ligase signature 2. / Tetrahydrofolate dehydrogenase/cyclohydrolase signature 1. / Tetrahydrofolate dehydrogenase/cyclohydrolase signature 2. / Tetrahydrofolate dehydrogenase/cyclohydrolase, conserved site / Tetrahydrofolate dehydrogenase/cyclohydrolase / Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, catalytic domain / Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain / Leucine Dehydrogenase, chain A, domain 1 / Aminoacid dehydrogenase-like, N-terminal domain superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NDP / C-1-tetrahydrofolate synthase, cytoplasmic
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD SELENOMET / Resolution: 1.5 Å
AuthorsAllaire, M. / Li, Y. / Mackenzie, R.E. / Cygler, M.
CitationJournal: Structure / Year: 1998
Title: The 3-D structure of a folate-dependent dehydrogenase/cyclohydrolase bifunctional enzyme at 1.5 A resolution.
Authors: Allaire, M. / Li, Y. / MacKenzie, R.E. / Cygler, M.
History
DepositionJan 30, 1998Processing site: BNL
Revision 1.0Feb 9, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: METHYLENETETRAHYDROFOLATE DEHYDROGENASE / METHENYLTETRAHYDROFOLATE CYCLOHYDROLASE
B: METHYLENETETRAHYDROFOLATE DEHYDROGENASE / METHENYLTETRAHYDROFOLATE CYCLOHYDROLASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7924
Polymers65,3012
Non-polymers1,4912
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint-15 kcal/mol
Surface area24390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.523, 135.843, 61.403
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.993999, -0.109179, 0.006835), (0.10294, -0.912405, 0.396132), (-0.037013, 0.394458, 0.918168)
Vector: 15.13118, 56.48041, -12.3738)

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Components

#1: Protein METHYLENETETRAHYDROFOLATE DEHYDROGENASE / METHENYLTETRAHYDROFOLATE CYCLOHYDROLASE / METHYLENETHF DEHYDROGENASE / METHENYLTHF CYCLOHYDROLASE


Mass: 32650.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cellular location: CYTOPLASM / Production host: Escherichia coli (E. coli)
References: UniProt: P11586, methylenetetrahydrofolate dehydrogenase (NADP+), methenyltetrahydrofolate cyclohydrolase
#2: Chemical ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.1 Å3/Da / Density % sol: 44 %
Crystal growpH: 5.5 / Details: pH 5.5
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
117 mg/mlprotein1drop
20.1 mMsodium citrate1reservoir
30.2 Mammonium acetate1reservoir
421 %PEG33501reservoir
55 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.918
DetectorType: PRINCETON 2K / Detector: CCD / Date: Oct 1, 1996 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionHighest resolution: 1.5 Å / Num. obs: 75578 / % possible obs: 90 % / Redundancy: 10 % / Biso Wilson estimate: 16.3 Å2 / Rmerge(I) obs: 0.068
Reflection
*PLUS
Num. measured all: 753128

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Processing

Software
NameClassification
MLPHAREphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD SELENOMET / Resolution: 1.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: DISORDERED RESIDUES (A241-A250,A297-A301,B297-B301) AND DISORDERED SIDE CHAINS (A83,A251,A292,A296,B296), BAD ELECTRON DENSITY (A142).
RfactorNum. reflection% reflectionSelection details
Rfree0.235 3816 5 %RANDOM
Rwork0.199 ---
obs-71679 90 %-
Displacement parametersBiso mean: 19.5 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4396 0 96 407 4899
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.040.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.62
X-RAY DIFFRACTIONp_mcangle_it2.13
X-RAY DIFFRACTIONp_scbond_it2.52
X-RAY DIFFRACTIONp_scangle_it3.93
X-RAY DIFFRACTIONp_plane_restr0.0260.03
X-RAY DIFFRACTIONp_chiral_restr0.1440.15
X-RAY DIFFRACTIONp_singtor_nbd0.1780.3
X-RAY DIFFRACTIONp_multtor_nbd0.2540.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1620.3
X-RAY DIFFRACTIONp_planar_tor4.47
X-RAY DIFFRACTIONp_staggered_tor15.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor3320
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS

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