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- PDB-1kol: Crystal structure of formaldehyde dehydrogenase -

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Basic information

Entry
Database: PDB / ID: 1kol
TitleCrystal structure of formaldehyde dehydrogenase
Componentsformaldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / dehydrogenase
Function / homology
Function and homology information


formaldehyde dismutase / formaldehyde dismutase activity / formaldehyde dehydrogenase / formaldehyde dehydrogenase (NAD+) activity / acetaldehyde dehydrogenase (NAD+) activity / zinc ion binding
Similarity search - Function
Formaldehyde dehydrogenase, glutathione-independent / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain / Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily ...Formaldehyde dehydrogenase, glutathione-independent / Alanine dehydrogenase/PNT, C-terminal domain / Alanine dehydrogenase/pyridine nucleotide transhydrogenase, NAD(H)-binding domain / Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Glutathione-independent formaldehyde dehydrogenase
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.65 Å
AuthorsTanaka, N. / Kusakabe, Y. / Ito, K. / Yoshimoto, T. / Nakamura, K.T.
CitationJournal: J.mol.biol. / Year: 2002
Title: Crystal Structure of Formaldehyde Dehydrogenase from Pseudomonas putida: the Structural Origin of the Tightly Bound Cofactor in Nicotinoprotein Dehydrogenases
Authors: Tanaka, N. / Kusakabe, Y. / Ito, K. / Yoshimoto, T. / Nakamura, K.T.
History
DepositionDec 21, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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_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: formaldehyde dehydrogenase
B: formaldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,75710
Polymers83,9762
Non-polymers1,7818
Water17,421967
1
A: formaldehyde dehydrogenase
B: formaldehyde dehydrogenase
hetero molecules

A: formaldehyde dehydrogenase
B: formaldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)171,51320
Polymers167,9524
Non-polymers3,56116
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_566x,x-y+1,-z+11
Buried area18140 Å2
ΔGint-279 kcal/mol
Surface area50410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.686, 85.686, 190.752
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number151
Space group name H-MP3112
DetailsThe biological assembly is a tetramer. Two subunits (1/2 tetramer) exist in an asymmetric unit.

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Components

#1: Protein formaldehyde dehydrogenase / Glutathione-independent formaldehyde dehydrogenase


Mass: 41987.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas putida (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: P46154, formaldehyde dehydrogenase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 967 / 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: 2.41 Å3/Da / Density % sol: 48.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Tris, ammonium sulfate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
120 mg/mlPFDH1drop
24 mg/mlNAD+1drop
30.02 MTris1droppH8.0
41.8 Mammonium sulfate1reservoir
510 %(v/v)dioxane1reservoir
60.1 MTris1reservoirpH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→30 Å / Num. all: 94085 / Num. obs: 94085 / % possible obs: 97.4 % / Redundancy: 10 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 8.2
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.273 / Mean I/σ(I) obs: 2.8 / % possible all: 83.9
Reflection
*PLUS
Lowest resolution: 30 Å
Reflection shell
*PLUS
Lowest resolution: 1.74 Å / % possible obs: 83.9 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MLPHAREphasing
REFMACrefinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.65→30 Å
RfactorNum. reflection% reflection
Rfree0.206 4714 5.28 %
Rwork0.171 --
obs-89312 -
Refinement stepCycle: LAST / Resolution: 1.65→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5868 0 102 967 6937
Refine LS restraintsType: p_bond_d / Dev ideal: 0.009
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: p_angle_d / Dev ideal: 0.025

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