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- PDB-1ez0: CRYSTAL STRUCTURE OF THE NADP+ DEPENDENT ALDEHYDE DEHYDROGENASE F... -

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Basic information

Entry
Database: PDB / ID: 1ez0
TitleCRYSTAL STRUCTURE OF THE NADP+ DEPENDENT ALDEHYDE DEHYDROGENASE FROM VIBRIO HARVEYI.
ComponentsALDEHYDE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / Nucleotide binding domain / NADP+
Function / homology
Function and homology information


aldehyde dehydrogenase (NADP+) / aldehyde dehydrogenase (NADP+) activity
Similarity search - Function
Alpha-ketoglutaric semialdehyde dehydrogenase / : / 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 domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal ...Alpha-ketoglutaric semialdehyde dehydrogenase / : / 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 domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / NADP-dependent fatty aldehyde dehydrogenase
Similarity search - Component
Biological speciesVibrio harveyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 2.1 Å
AuthorsAhvazi, B. / Coulombe, R. / Delarge, M. / Vedadi, M. / Zhang, L. / Meighen, E. / Vrielink, A.
Citation
Journal: Biochem.J. / Year: 2000
Title: Crystal structure of the NADP+-dependent aldehyde dehydrogenase from Vibrio harveyi: structural implications for cofactor specificity and affinity.
Authors: Ahvazi, B. / Coulombe, R. / Delarge, M. / Vedadi, M. / Zhang, L. / Meighen, E. / Vrielink, A.
#1: Journal: Protein Sci. / Year: 1996
Title: Crystallization and Preliminary X-ray Analysis of Aldehyde Dehydrogenase from Vibrio harveyi
Authors: Croteau, N. / Vedadi, M. / Delarge, M. / Meighen, E. / Abu-Abed, M. / Howell, P.L. / Vrielink, A.
History
DepositionMay 9, 2000Deposition site: RCSB / Processing site: RCSB
SupersessionMay 24, 2000ID: 1CO3
Revision 1.0May 24, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Category: struct_conf / struct_conf_type
Revision 1.4Aug 9, 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_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: ALDEHYDE DEHYDROGENASE
B: ALDEHYDE DEHYDROGENASE
C: ALDEHYDE DEHYDROGENASE
D: ALDEHYDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,0118
Polymers218,0374
Non-polymers2,9744
Water11,746652
1
A: ALDEHYDE DEHYDROGENASE
D: ALDEHYDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,5054
Polymers109,0192
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8600 Å2
ΔGint-30 kcal/mol
Surface area34510 Å2
MethodPISA, PQS
2
B: ALDEHYDE DEHYDROGENASE
C: ALDEHYDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,5054
Polymers109,0192
Non-polymers1,4872
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-31 kcal/mol
Surface area34660 Å2
MethodPISA, PQS
3
A: ALDEHYDE DEHYDROGENASE
D: ALDEHYDE DEHYDROGENASE
hetero molecules

B: ALDEHYDE DEHYDROGENASE
C: ALDEHYDE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)221,0118
Polymers218,0374
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_656x+1,y,z+11
Buried area18210 Å2
ΔGint-62 kcal/mol
Surface area68200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.380, 131.180, 92.540
Angle α, β, γ (deg.)90.00, 92.49, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
/ NCS ensembles :
ID
1
2

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Components

#1: Protein
ALDEHYDE DEHYDROGENASE / ALDH


Mass: 54509.277 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio harveyi (bacteria) / Strain: B392 / Gene: ALDH / Plasmid: PT7-3 / Gene (production host): ALDH / Production host: Escherichia coli (E. coli) / Strain (production host): K38
References: UniProt: Q56694, aldehyde dehydrogenase [NAD(P)+]
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 652 / 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: 2.21 Å3/Da / Density % sol: 44.25 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8000, Sodium acetate, Sodium cacodylate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Details: Croteau, N., (1996) Protein Sci., 5, 2130.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118-30 %(w/v)PEG80001reservoir
2200 mMsodium acetate1reservoir
3100 mMsodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.072021
DetectorType: MARRESEARCH / Detector: AREA DETECTOR / Date: Mar 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.072021 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 175195 / Num. obs: 92467 / % possible obs: 83.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.89 % / Biso Wilson estimate: 10.6 Å2 / Rmerge(I) obs: 0.027 / Net I/σ(I): 24.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.93 % / Rmerge(I) obs: 0.051 / Num. unique all: 8082 / % possible all: 73.7
Reflection
*PLUS
Num. measured all: 189982
Reflection shell
*PLUS
% possible obs: 73.7 % / Mean I/σ(I) obs: 17.2

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Processing

Software
NameVersionClassification
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: molecular replacement
Starting model: 1eyy

1eyy


Resolution: 2.1→26.44 Å / Rfactor Rfree error: 0.003 / Data cutoff high rms absF: 2617344.74 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.246 9248 10 %random
Rwork0.215 ---
all-110166 --
obs-92435 83.8 %-
Solvent computationSolvent model: flat model / Bsol: 46.2429 Å2 / ksol: 0.407586 e/Å3
Displacement parametersBiso mean: 19.2 Å2
Baniso -1Baniso -2Baniso -3
1--1.35 Å20 Å2-0.02 Å2
2---2.88 Å20 Å2
3---4.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 2.1→26.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15107 0 192 652 15951
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it0.881.5
X-RAY DIFFRACTIONc_mcangle_it1.332
X-RAY DIFFRACTIONc_scbond_it1.482
X-RAY DIFFRACTIONc_scangle_it2.112.5
Refine LS restraints NCS
Ens-IDDom-IDNCS model detailsRefine-IDWeight Biso Weight position
11CONSTRAINEDX-RAY DIFFRACTION2200
22X-RAY DIFFRACTION2100
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.262 1351 9.8 %
Rwork0.208 12365 -
obs--75 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ndp.parndp.top
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95

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