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- PDB-4qf6: Structure of Aldehyde Dehydrogenase from Bacillus cereus, E194S mutant -

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Basic information

Entry
Database: PDB / ID: 4qf6
TitleStructure of Aldehyde Dehydrogenase from Bacillus cereus, E194S mutant
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Rossmann / Aldehyde Dehydrogenase / E194S
Function / homologyAldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 2 / Aldehyde Dehydrogenase; Chain A, domain 1 / Aldehyde Dehydrogenase; Chain A, domain 1 / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsNgo, H.P.T. / Hong, S.H. / Oh, D.K. / Kang, L.W.
CitationJournal: To be Published
Title: Structural and Kinetic Analysis for Cofactor-binding Residues in Mammalian-like Aldehyde Dehydrogenase from Bacillus cereus Involved in Oxidation and Reduction Activity for All-trans-retinal
Authors: Ngo, H.P.T. / Hong, S.H. / Oh, D.K. / Kang, L.W.
History
DepositionMay 19, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_ref_seq_dif.details / _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
I: Aldehyde dehydrogenase
J: Aldehyde dehydrogenase
K: Aldehyde dehydrogenase
L: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)650,64336
Polymers650,09112
Non-polymers55224
Water31,5081749
1
A: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase
E: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,88112
Polymers216,6974
Non-polymers1848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19260 Å2
ΔGint-182 kcal/mol
Surface area61980 Å2
MethodPISA
2
B: Aldehyde dehydrogenase
G: Aldehyde dehydrogenase
H: Aldehyde dehydrogenase
I: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,88112
Polymers216,6974
Non-polymers1848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19070 Å2
ΔGint-182 kcal/mol
Surface area62310 Å2
MethodPISA
3
F: Aldehyde dehydrogenase
J: Aldehyde dehydrogenase
K: Aldehyde dehydrogenase
L: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)216,88112
Polymers216,6974
Non-polymers1848
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19360 Å2
ΔGint-181 kcal/mol
Surface area61750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.558, 93.655, 247.854
Angle α, β, γ (deg.)90.00, 95.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Aldehyde dehydrogenase


Mass: 54174.242 Da / Num. of mol.: 12 / Mutation: E194S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Strain: ATCC 10876 / Gene: bcere0002_25940 / Production host: Escherichia coli (E. coli) / References: UniProt: C2N217, aldehyde dehydrogenase (NAD+)
#2: Chemical...
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1749 / 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: 2.6 Å3/Da / Density % sol: 52.77 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.15M DL-malic pH 7.0, 20% PEG 3350 , VAPOR DIFFUSION, HANGING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97951 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 24, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 442246 / % possible obs: 84.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 1.9→1.93 Å / % possible all: 81.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASESphasing
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PS9

4ps9
PDB Unreleased entry


Resolution: 1.9→43.56 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.905 / SU B: 3.269 / SU ML: 0.099 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25156 22144 5 %RANDOM
Rwork0.20422 ---
obs0.20658 420074 84.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.678 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å2-0 Å2-0 Å2
2---0.02 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms45381 0 24 1749 47154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.01946516
X-RAY DIFFRACTIONr_bond_other_d0.0020.0244128
X-RAY DIFFRACTIONr_angle_refined_deg2.0591.95162947
X-RAY DIFFRACTIONr_angle_other_deg1.0693101706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.27555887
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.03825.4672065
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.379157800
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.06215144
X-RAY DIFFRACTIONr_chiral_restr0.1770.27036
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02153137
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0210207
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4911.59823534
X-RAY DIFFRACTIONr_mcbond_other1.491.59823533
X-RAY DIFFRACTIONr_mcangle_it2.1012.38829401
X-RAY DIFFRACTIONr_mcangle_other2.0622.39129402
X-RAY DIFFRACTIONr_scbond_it2.3751.88422982
X-RAY DIFFRACTIONr_scbond_other2.3031.88422838
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.5262.71433534
X-RAY DIFFRACTIONr_long_range_B_refined4.47313.21153650
X-RAY DIFFRACTIONr_long_range_B_other4.44113.1653057
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 1559 -
Rwork0.238 29740 -
obs--81.65 %

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