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- PDB-1nvm: Crystal structure of a bifunctional aldolase-dehydrogenase : sequ... -

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Basic information

Entry
Database: PDB / ID: 1nvm
TitleCrystal structure of a bifunctional aldolase-dehydrogenase : sequestering a reactive and volatile intermediate
Components
  • 4-hydroxy-2-oxovalerate aldolase
  • acetaldehyde dehydrogenase (acylating)
KeywordsLYASE/OXIDOREDUCTASE / Sequestered tunnel / substrate channeling / Bifunctional enzyme / LYASE-OXIDOREDUCTASE COMPLEX
Function / homology
Function and homology information


phenol-containing compound catabolic process / 4-hydroxy-2-oxovalerate aldolase / 4-hydroxy-2-oxovalerate aldolase activity / acetaldehyde dehydrogenase (acetylating) / acetaldehyde dehydrogenase (acetylating) activity / benzoate catabolic process via hydroxylation / : / NAD binding / NADP binding / manganese ion binding
Similarity search - Function
DmpG-like communication / 4-hydroxy-2-oxovalerate aldolase / 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain / DmpG-like communication domain / Acetaldehyde dehydrogenase / Acetaldehyde dehydrogenase, C-terminal / Prokaryotic acetaldehyde dehydrogenase, dimerisation / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain ...DmpG-like communication / 4-hydroxy-2-oxovalerate aldolase / 4-hydroxy-2-oxovalerate aldolase, N-terminal catalytic TIM barrel domain / DmpG-like communication domain / Acetaldehyde dehydrogenase / Acetaldehyde dehydrogenase, C-terminal / Prokaryotic acetaldehyde dehydrogenase, dimerisation / Semialdehyde dehydrogenase, NAD binding domain / Semialdehyde dehydrogenase, NAD-binding / Semialdehyde dehydrogenase, NAD binding domain / Pyruvate carboxyltransferase / HMGL-like / Pyruvate carboxyltransferase domain. / Helicase, Ruva Protein; domain 3 - #60 / Dihydrodipicolinate Reductase; domain 2 / Dihydrodipicolinate Reductase; domain 2 / Helicase, Ruva Protein; domain 3 / Aldolase class I / Aldolase-type TIM barrel / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / TIM Barrel / Alpha-Beta Barrel / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / OXALATE ION / 4-hydroxy-2-oxovalerate aldolase / Acetaldehyde dehydrogenase
Similarity search - Component
Biological speciesPseudomonas sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsManjasetty, A.B. / Powlowski, J. / Vrielink, A.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Crystal structure of a bifunctional aldolase-dehydrogenase: Sequestering a reactive and volatile intermediate
Authors: Manjasetty, A.B. / Powlowski, J. / Vrielink, A.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and preliminary X-ray analysis of dmpFG-encoded 4-hydroxy-2-ketovalerate aldolase-aldehyde dehydrogenase (acylating) from Pseudomonas sp.strain CF600
History
DepositionFeb 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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_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.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_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_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: 4-hydroxy-2-oxovalerate aldolase
B: acetaldehyde dehydrogenase (acylating)
C: 4-hydroxy-2-oxovalerate aldolase
D: acetaldehyde dehydrogenase (acylating)
E: 4-hydroxy-2-oxovalerate aldolase
F: acetaldehyde dehydrogenase (acylating)
G: 4-hydroxy-2-oxovalerate aldolase
H: acetaldehyde dehydrogenase (acylating)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,36237
Polymers280,9388
Non-polymers4,42429
Water50,6402811
1
A: 4-hydroxy-2-oxovalerate aldolase
B: acetaldehyde dehydrogenase (acylating)
C: 4-hydroxy-2-oxovalerate aldolase
D: acetaldehyde dehydrogenase (acylating)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,03519
Polymers140,4694
Non-polymers2,56615
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13970 Å2
ΔGint-152 kcal/mol
Surface area42210 Å2
MethodPISA
2
E: 4-hydroxy-2-oxovalerate aldolase
F: acetaldehyde dehydrogenase (acylating)
G: 4-hydroxy-2-oxovalerate aldolase
H: acetaldehyde dehydrogenase (acylating)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,32718
Polymers140,4694
Non-polymers1,85814
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13080 Å2
ΔGint-186 kcal/mol
Surface area42660 Å2
MethodPISA
3
E: 4-hydroxy-2-oxovalerate aldolase
F: acetaldehyde dehydrogenase (acylating)
G: 4-hydroxy-2-oxovalerate aldolase
H: acetaldehyde dehydrogenase (acylating)
hetero molecules

A: 4-hydroxy-2-oxovalerate aldolase
B: acetaldehyde dehydrogenase (acylating)
C: 4-hydroxy-2-oxovalerate aldolase
D: acetaldehyde dehydrogenase (acylating)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,36237
Polymers280,9388
Non-polymers4,42429
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+3/2,-y,z+1/21
Buried area28980 Å2
ΔGint-344 kcal/mol
Surface area82950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.200, 140.000, 191.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

#1: Protein
4-hydroxy-2-oxovalerate aldolase / / HOA


Mass: 37520.645 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: CF600 / Gene: DMPG / Plasmid: pT7-5 / Production host: Escherichia coli (E. coli)
References: UniProt: P51016, Lyases; Carbon-carbon lyases; Oxo-acid-lyases
#2: Protein
acetaldehyde dehydrogenase (acylating)


Mass: 32713.812 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas sp. (bacteria) / Strain: CF600 / Gene: DMPF / Plasmid: pT7-5 / Production host: Escherichia coli (E. coli)
References: UniProt: Q52060, acetaldehyde dehydrogenase (acetylating)

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Non-polymers , 6 types, 2840 molecules

#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#4: Chemical
ChemComp-OXL / OXALATE ION / Oxalate


Mass: 88.019 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2O4
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2811 / 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: 2.16 Å3/Da / Density % sol: 42.73 % / Description: 112 SE SUBSTRUCTURE
Crystal growTemperature: 310 K / pH: 7.5
Details: PEG 8000, Ammonium sulfate, PIPES, pH 7.5, Hanging drop and micro seeding, temperature 310.0K, pH 7.50
Crystal grow
*PLUS
Temperature: 290 K / pH: 7.4 / Method: vapor diffusion, hanging drop
Details: Manjasetty, B.A., (2001) Acta Crystallogr.,Sect.D, 57, 582.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
150 mMTris1droppH7.4
21 mMdithiothreitol1drop
39 mg/mlprotein1drop
415 %PEG80001reservoir
5100 mMammonium sulfate1reservoir
6100 mMPIPES1reservoirpH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 14, 2000 / Details: MIRRORS
RadiationMonochromator: CURVED-CRYSTAL SI 111 / Protocol: MULTIPLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. obs: 299052 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 28.3 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 18.7
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 4 % / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2 / Rsym value: 0.565 / % possible all: 99.3
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. measured all: 1829280
Reflection shell
*PLUS
% possible obs: 99.3 % / Mean I/σ(I) obs: 2

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
REFMACrefinement
DENZOdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.7→20 Å / Isotropic thermal model: Isotropic / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: MAXIMUM LIKLIHOOD METHOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23 15063 5 %RANDOM
Rwork0.189 ---
all-298381 --
obs-283318 95 %-
Displacement parametersBiso mean: 28.5 Å2
Refinement stepCycle: LAST / Resolution: 1.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19344 0 268 2811 22423
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0280.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0550.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.1872
X-RAY DIFFRACTIONp_mcangle_it1.6523
X-RAY DIFFRACTIONp_scbond_it1.5142
X-RAY DIFFRACTIONp_scangle_it2.1663
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd0.1720.3
X-RAY DIFFRACTIONp_multtor_nbd0.2570.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1170.3
X-RAY DIFFRACTIONp_planar_tor6.77
X-RAY DIFFRACTIONp_staggered_tor13.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor29.820
X-RAY DIFFRACTIONp_special_tor015
LS refinement shellResolution: 1.7→1.783 Å /
RfactorNum. reflection
Rfree0.302 1963
Rwork0.25 -
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.232
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.012
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg1.5

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