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- PDB-3u4j: Crystal structure of NAD-dependent aldehyde dehydrogenase from Si... -

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Basic information

Entry
Database: PDB / ID: 3u4j
TitleCrystal structure of NAD-dependent aldehyde dehydrogenase from Sinorhizobium meliloti
ComponentsNAD-dependent aldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / PSI-Biology / NYSGRC / Structural Genomics / New York Structural Genomics Research Consortium / tetramer / NAD
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / metal ion binding
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 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
NAD-dependent aldehyde dehydrogenase
Similarity search - Component
Biological speciesSinorhizobium meliloti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsEswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. ...Eswaramoorthy, S. / Chamala, S. / Evans, B. / Foti, R. / Gizzi, A. / Hillerich, B. / Kar, A. / LaFleur, J. / Seidel, R. / Villigas, G. / Zencheck, W. / Almo, S.C. / Swaminathan, S. / New York Structural Genomics Research Consortium (NYSGRC)
CitationJournal: To be Published
Title: Crystal structure of NAD-dependent aldehyde dehydrogenase from Sinorhizobium meliloti
Authors: Eswaramoorthy, S. / Almo, S.C. / Swaminathan, S.
History
DepositionOct 8, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 19, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 13, 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.pdbx_leaving_atom_flag / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)229,1135
Polymers229,0734
Non-polymers401
Water11,133618
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21850 Å2
ΔGint-82 kcal/mol
Surface area60700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.108, 176.660, 83.662
Angle α, β, γ (deg.)90.00, 98.49, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NAD-dependent aldehyde dehydrogenase


Mass: 57268.316 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sinorhizobium meliloti (bacteria) / Gene: RA0117, SMa0220 / Plasmid: PET3A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q930S8
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 618 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PEG400; HEPES pH 7.5; CaCl2; Ethyl Acetate, VAPOR DIFFUSION, SITTING DROP, temperature 272K, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 1, 2011
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 152232 / Num. obs: 152232 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.92 / Net I/σ(I): 7.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.379 / Num. unique all: 15181 / % possible all: 100

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Processing

Software
NameVersionClassification
CBASSdata collection
REFMAC5.5.0110refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1O9J

1o9j


Resolution: 2→47.98 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.918 / SU B: 3.522 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22376 7629 5 %RANDOM
Rwork0.18703 ---
obs0.18885 144436 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.662 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0.01 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→47.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15117 0 1 618 15736
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02215412
X-RAY DIFFRACTIONr_angle_refined_deg1.391.96320912
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08352010
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08523.022642
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.768152462
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.43415138
X-RAY DIFFRACTIONr_chiral_restr0.0980.22349
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02111762
X-RAY DIFFRACTIONr_mcbond_it0.681.59938
X-RAY DIFFRACTIONr_mcangle_it1.28215862
X-RAY DIFFRACTIONr_scbond_it2.57335474
X-RAY DIFFRACTIONr_scangle_it4.0514.55050
LS refinement shellResolution: 2.002→2.053 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 564 -
Rwork0.213 10553 -
obs--99.53 %

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