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- PDB-5gtk: NAD+ complex structure of aldehyde dehydrogenase from bacillus cereus -

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Basic information

Entry
Database: PDB / ID: 5gtk
TitleNAD+ complex 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, C-terminal / Aldehyde dehydrogenase, N-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, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / 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 21, 2016Deposition site: PDBJ / Processing site: PDBJ
SupersessionSep 6, 2017ID: 4PT0
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2018Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.2Nov 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)219,58811
Polymers216,8654
Non-polymers2,7237
Water9,584532
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23320 Å2
ΔGint-153 kcal/mol
Surface area60700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.222, 93.253, 145.149
Angle α, β, γ (deg.)90.00, 97.86, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Betaine-aldehyde dehydrogenase


Mass: 54216.277 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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 532 / 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: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.15M DL MALIC ACID PH 7.0, 18% PEG 3350 (W/V)

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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: 67318 / % possible obs: 99.4 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 63.1
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 7 % / Rmerge(I) obs: 0.08 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PS9

4ps9
PDB Unreleased entry


Resolution: 2.6→47.93 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.875 / SU B: 9.163 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 2.462 / ESU R Free: 0.308 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23312 3414 5.1 %RANDOM
Rwork0.16452 ---
obs0.16801 63886 99.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 15.868 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.08 Å2
2--0.13 Å20 Å2
3----0.17 Å2
Refinement stepCycle: 1 / Resolution: 2.6→47.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15126 0 179 532 15837
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01915642
X-RAY DIFFRACTIONr_bond_other_d0.0020.0214783
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.96521261
X-RAY DIFFRACTIONr_angle_other_deg1.071334083
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.05551959
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.75425.478690
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.75152600
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.361548
X-RAY DIFFRACTIONr_chiral_restr0.1110.22374
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02117807
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023453
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_it0.9541.4667836
X-RAY DIFFRACTIONr_mcbond_other0.9531.4667835
X-RAY DIFFRACTIONr_mcangle_it1.612.1969789
X-RAY DIFFRACTIONr_mcangle_other1.612.1969790
X-RAY DIFFRACTIONr_scbond_it1.6111.6977806
X-RAY DIFFRACTIONr_scbond_other1.6111.6977807
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.7032.45811471
X-RAY DIFFRACTIONr_long_range_B_refined3.82511.87417618
X-RAY DIFFRACTIONr_long_range_B_other3.82511.87417619
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.602→2.669 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 231 -
Rwork0.199 4646 -
obs--98.49 %

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