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- PDB-3ek1: Crystal structure of aldehyde dehydrogenase from brucella meliten... -

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Basic information

Entry
Database: PDB / ID: 3ek1
TitleCrystal structure of aldehyde dehydrogenase from brucella melitensis biovar abortus 2308
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / ALDEHYDE DEHYDROGENASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


succinate-semialdehyde dehydrogenase [NAD(P)+] / succinate-semialdehyde dehydrogenase (NAD+) activity / gamma-aminobutyric acid catabolic process / cytosol
Similarity search - Function
Succinate 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, glutamic acid active site / Aldehyde dehydrogenases glutamic acid active site. / Aldehyde dehydrogenase, cysteine active site / Aldehyde dehydrogenases cysteine active site. ...Succinate 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, 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 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Aldehyde dehydrogenase
Similarity search - Component
Biological speciesBrucella melitensis biovar Abortus 2308 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement, molecular replacement / Resolution: 2.1 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of aldehyde dehydrogenase from brucella melitensis biovar abortus 2308
Authors: Seattle Structural Genomics Center for Infectious Disease (SSGCID)
History
DepositionSep 18, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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
E: Aldehyde dehydrogenase
F: Aldehyde dehydrogenase
G: Aldehyde dehydrogenase
H: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)431,23724
Polymers428,9078
Non-polymers2,33016
Water56,6033142
1
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,61912
Polymers214,4534
Non-polymers1,1658
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19870 Å2
ΔGint-97 kcal/mol
Surface area59290 Å2
MethodPISA
2
E: Aldehyde dehydrogenase
F: Aldehyde dehydrogenase
G: Aldehyde dehydrogenase
H: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)215,61912
Polymers214,4534
Non-polymers1,1658
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19690 Å2
ΔGint-94 kcal/mol
Surface area59380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.870, 93.010, 143.700
Angle α, β, γ (deg.)92.03, 107.58, 109.65
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Aldehyde dehydrogenase


Mass: 53613.355 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella melitensis biovar Abortus 2308 (bacteria)
Strain: BIOVAR ABORTUS 2308 / Gene: gabD, BAB1_1655 / Plasmid: PET28-HISSMT / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q2YRI3, succinate-semialdehyde dehydrogenase [NAD(P)+]
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3142 / 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: 2.54 Å3/Da / Density % sol: 51.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PROPLEX-96 F9: 1.0M AMMONIUM SULPHATE, 100MM MES PH 6.5, VAPOR DIFFUSION, TEMPERATURE 298K, pH 6.50, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9999 / Wavelength: 0.9999 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 20, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 246609 / Num. obs: 231828 / % possible obs: 94 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.81 % / Biso Wilson estimate: 30.6 Å2 / Rmerge(I) obs: 0.061 / Rsym value: 0.061 / Net I/σ(I): 11.02
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 1.71 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 2.3 / Num. unique all: 16866 / Rsym value: 0.354 / % possible all: 92.5

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Processing

Software
NameVersionClassification
BOSdata collection
MOLREPphasing
REFMAC5.5.0046refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: molecular replacement, molecular replacement
Starting model: pdb entry 2opx, modified

2opx


Resolution: 2.1→19.78 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.925 / SU B: 4.67 / SU ML: 0.123 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.208 / ESU R Free: 0.188 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
RfactorNum. reflection% reflectionSelection details
Rfree0.225 11634 5 %RANDOM
Rwork0.161 ---
all0.164 246609 --
obs0.164 231826 94.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20.39 Å2-0.19 Å2
2---0.16 Å2-0.35 Å2
3----0.68 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms28921 0 136 3142 32199
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02229561
X-RAY DIFFRACTIONr_bond_other_d0.0010.0219885
X-RAY DIFFRACTIONr_angle_refined_deg1.6271.98140130
X-RAY DIFFRACTIONr_angle_other_deg0.967348810
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1153905
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.53224.3531098
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.935154977
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6315166
X-RAY DIFFRACTIONr_chiral_restr0.0960.24680
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02133031
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025679
X-RAY DIFFRACTIONr_mcbond_it0.81.519214
X-RAY DIFFRACTIONr_mcbond_other0.2251.57953
X-RAY DIFFRACTIONr_mcangle_it1.432230753
X-RAY DIFFRACTIONr_scbond_it2.613310347
X-RAY DIFFRACTIONr_scangle_it4.1814.59359
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.295 847 -
Rwork0.221 15859 -
obs--92.51 %

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