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- PDB-1wnd: Escherichia coli YdcW gene product is a medium-chain aldehyde deh... -

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Basic information

Entry
Database: PDB / ID: 1wnd
TitleEscherichia coli YdcW gene product is a medium-chain aldehyde dehydrogenase as determined by kinetics and crystal structure
ComponentsPutative betaine aldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / aldehyde dehydrogenase / NADH / fluorescence / kinetics
Function / homology
Function and homology information


: / L-lysine catabolic process / putrescine catabolic process / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / aldehyde dehydrogenase (NAD+) activity / NAD binding / protein homotetramerization / protein-containing complex ...: / L-lysine catabolic process / putrescine catabolic process / aminobutyraldehyde dehydrogenase / aminobutyraldehyde dehydrogenase (NAD+) activity / Oxidoreductases; Acting on the aldehyde or oxo group of donors; With NAD+ or NADP+ as acceptor / aldehyde dehydrogenase (NAD+) activity / NAD binding / protein homotetramerization / protein-containing complex / identical protein binding / cytosol
Similarity search - Function
Gamma-aminobutyraldehyde dehydrogenase / Aminobutyraldehyde 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 domain / Aldehyde dehydrogenase family ...Gamma-aminobutyraldehyde dehydrogenase / Aminobutyraldehyde 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 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
Gamma-aminobutyraldehyde dehydrogenase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGruez, A. / Roig-Zamboni, V. / Tegoni, M. / Cambillau, C.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Crystal Structure and Kinetics Identify Escherichia coli YdcW Gene Product as a Medium-chain Aldehyde Dehydrogenase
Authors: Gruez, A. / Roig-Zamboni, V. / Grisel, S. / Salomoni, A. / Valencia, C. / Campanacci, V. / Tegoni, M. / Cambillau, C.
History
DepositionJul 29, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Dec 28, 2016Group: Structure summary
Revision 1.4Mar 13, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_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.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_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_conn.ptnr2_label_seq_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_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: Putative betaine aldehyde dehydrogenase
B: Putative betaine aldehyde dehydrogenase
C: Putative betaine aldehyde dehydrogenase
D: Putative betaine aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)213,7998
Polymers213,6384
Non-polymers1604
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19170 Å2
ΔGint-169 kcal/mol
Surface area58230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.036, 79.680, 158.669
Angle α, β, γ (deg.)90.00, 95.77, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
12A
22D
32B
42C

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLNGLNHISHIS5AA2 - 47423 - 495
21GLNGLNHISHIS5BB2 - 47423 - 495
31GLNGLNHISHIS5CC2 - 47423 - 495
41GLNGLNHISHIS5DD2 - 47423 - 495
12CACACACA4AE475
22CACACACA4DH475
32CACACACA4BF475
42CACACACA4CG475

NCS ensembles :
ID
1
2

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Components

#1: Protein
Putative betaine aldehyde dehydrogenase / YdcW aldehyde dehydrogenase / BADH


Mass: 53409.586 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Plasmid: pDEST / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P77674, betaine-aldehyde dehydrogenase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.5 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG 4000, Imidazol malate, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 102 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 1, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. all: 797404 / Num. obs: 116969 / % possible obs: 96.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 7.1
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.198 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.1.19refinement
DENZOdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.449 / SU ML: 0.12 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.195 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21309 6119 5 %RANDOM
Rwork0.18445 ---
all0.18588 ---
obs0.18588 115545 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.908 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20 Å20.48 Å2
2--0.08 Å20 Å2
3----0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14300 0 4 270 14574
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02114339
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.491.94919508
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.85331892
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.761152368
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1050.22244
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210821
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.36556
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.51000
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2830.366
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.350.55
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.5881.59380
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.194214933
X-RAY DIFFRACTIONr_scbond_it2.44134959
X-RAY DIFFRACTIONr_scangle_it3.9354.54575
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A3550medium positional0.170.5
12B3550medium positional0.170.5
13C3550medium positional0.160.5
14D3550medium positional0.160.5
21A44medium positional1.040.5
23B44medium positional0.90.5
24C44medium positional1.230.5
22D44medium positional2.190.5
11A3550medium thermal1.072
12B3550medium thermal1.142
13C3550medium thermal1.142
14D3550medium thermal1.12
21A44medium thermal1.532
23B44medium thermal1.292
24C44medium thermal1.632
22D44medium thermal1.732
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.248 425
Rwork0.222 7918
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.84770.06650.07240.2387-0.02910.3135-0.02150.11620.2181-0.06630.02770.0462-0.1279-0.033-0.00620.0493-0.01120.01630.03610.01750.0455-32.89539.166102.549
20.7615-0.0636-0.01150.2811-0.01630.2731-0.001-0.13-0.17420.07130.02320.06860.0927-0.0497-0.02220.0457-0.01140.00630.05540.02780.0384-35.9360.328130.793
30.7416-0.120.11970.21230.01390.4458-0.0174-0.22430.06460.11460.0109-0.0053-0.05080.03340.00640.0467-0.02280.02180.0975-0.02110.0124-13.91726.264141.3
40.92320.1181-0.19460.2261-0.03080.4087-0.04110.1793-0.1026-0.12070.0287-0.02350.06040.02760.01240.0448-0.01860.00730.0489-0.02290.0107-10.84112.13795.294
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 47422 - 495
2X-RAY DIFFRACTION2BB1 - 47422 - 495
3X-RAY DIFFRACTION3CC1 - 47422 - 495
4X-RAY DIFFRACTION4DD1 - 47422 - 495

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