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- PDB-5gt6: Apo structure of Aldehyde Dehydrogenase from Bacillus cereus -

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Basic information

Entry
Database: PDB / ID: 5gt6
TitleApo structure of Aldehyde Dehydrogenase from Bacillus cereus
ComponentsBetaine-aldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Aldehyde Dehydrogenase NAD+ NADP+
Function / homology
Function and homology information


aldehyde dehydrogenase [NAD(P)+] / aldehyde dehydrogenase [NAD(P)+] activity / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor
Similarity search - Function
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 domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal ...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 domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, N-terminal / Aldehyde dehydrogenase, C-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Aldehyde dehydrogenase (NAD) family protein
Similarity search - Component
Biological speciesBacillus cereus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNgo, H.P.T. / Hong, S.H. / Ho, T.H. / Oh, D.K. / Kang, L.W.
CitationJournal: To Be Published
Title: crystal structures of aldehyde dehydrogenase from Bacillus cereus having atypical bidirectional oxidizing and reducing activities for all-trans-retinal
Authors: Ngo, H.P.T. / Hong, S.H. / Ho, T.H. / Oh, D.K. / Kang, L.W.
History
DepositionAug 18, 2016Deposition site: PDBJ / Processing site: PDBJ
SupersessionSep 6, 2017ID: 4PS9
Revision 1.0Sep 6, 2017Provider: 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Betaine-aldehyde dehydrogenase
B: Betaine-aldehyde dehydrogenase
C: Betaine-aldehyde dehydrogenase
D: Betaine-aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,4328
Polymers223,3404
Non-polymers924
Water1,65792
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18760 Å2
ΔGint-131 kcal/mol
Surface area61600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.527, 93.284, 145.472
Angle α, β, γ (deg.)90.00, 98.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Betaine-aldehyde dehydrogenase /


Mass: 55834.969 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus (bacteria) / Gene: AT268_22120 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A150BLG9
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.59 Å3/Da / Density % sol: 52.47 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.15 M DL-malic acid pH 7.0, 18% PEG 3350

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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: Nov 26, 2012
RadiationMonochromator: DCM Si (111) Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97951 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 67464 / % possible obs: 99.2 % / Observed criterion σ(I): 1 / Redundancy: 7.4 % / Rmerge(I) obs: 0.046 / Net I/σ(I): 69.7
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.075 / % possible all: 97.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FR8

4fr8


Resolution: 2.6→49.57 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.867 / SU B: 9.881 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 1.059 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25095 3423 5.1 %RANDOM
Rwork0.18201 ---
obs0.18548 64021 99.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20.01 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.6→49.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15117 0 4 92 15213
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01915457
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214695
X-RAY DIFFRACTIONr_angle_refined_deg1.781.95120943
X-RAY DIFFRACTIONr_angle_other_deg1.096333850
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.09851954
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.02325.472689
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.507152596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6281548
X-RAY DIFFRACTIONr_chiral_restr0.1150.22339
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02117674
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023394
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_it1.2692.0167828
X-RAY DIFFRACTIONr_mcbond_other1.2682.0167827
X-RAY DIFFRACTIONr_mcangle_it2.0763.0219778
X-RAY DIFFRACTIONr_mcangle_other2.0773.0219779
X-RAY DIFFRACTIONr_scbond_it1.8252.2367629
X-RAY DIFFRACTIONr_scbond_other1.8252.2367630
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.0533.25211166
X-RAY DIFFRACTIONr_long_range_B_refined4.04915.78316749
X-RAY DIFFRACTIONr_long_range_B_other4.0515.78616748
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.602→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 248 -
Rwork0.217 4576 -
obs--97.08 %

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