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- PDB-5uju: Crystal structure of NAD-dependent aldehyde dehydrogenase from Bu... -

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Basic information

Entry
Database: PDB / ID: 5uju
TitleCrystal structure of NAD-dependent aldehyde dehydrogenase from Burkholderia multivorans
ComponentsNAD-dependent aldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / Burkholderia multivorans / NAD / aldehyde dehydrogenase / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


glyceraldehyde-3-phosphate dehydrogenase (NAD+) (non-phosphorylating) activity / aldehyde dehydrogenase (NAD+) / aldehyde dehydrogenase (NAD+) activity
Similarity search - Function
Phenylacetic acid degradation protein PaaN2 / : / Aldehyde dehydrogenase domain / Aldehyde dehydrogenase family / Aldehyde dehydrogenase, C-terminal / Aldehyde dehydrogenase, N-terminal / Aldehyde/histidinol dehydrogenase
Similarity search - Domain/homology
IMIDAZOLE / NAD-dependent aldehyde dehydrogenase
Similarity search - Component
Biological speciesBurkholderia multivorans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of NAD-dependent aldehyde dehydrogenase from Burkholderia multivorans
Authors: Abendroth, J. / Mayclin, S.J. / Lorimer, D. / Edwards, T.E.
History
DepositionJan 19, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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_ncs_dom_lim
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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)123,52511
Polymers123,0302
Non-polymers4949
Water12,484693
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6910 Å2
ΔGint-23 kcal/mol
Surface area37870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.430, 114.430, 154.520
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11A-1064-

HOH

21A-1065-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 1 and (name N or name...
21(chain B and (resid 1 through 13 or (resid 14...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETMETMET(chain A and ((resid 1 and (name N or name...AA19
12METMETEDOEDO(chain A and ((resid 1 and (name N or name...AA - D1 - 6029
13METMETEDOEDO(chain A and ((resid 1 and (name N or name...AA - D1 - 6029
14METMETEDOEDO(chain A and ((resid 1 and (name N or name...AA - D1 - 6029
15METMETEDOEDO(chain A and ((resid 1 and (name N or name...AA - D1 - 6029
21METMETLEULEU(chain B and (resid 1 through 13 or (resid 14...BB1 - 139 - 21
22LYSLYSLYSLYS(chain B and (resid 1 through 13 or (resid 14...BB1422
23METMETNANA(chain B and (resid 1 through 13 or (resid 14...BB - H1 - 6029
24METMETNANA(chain B and (resid 1 through 13 or (resid 14...BB - H1 - 6029
25METMETNANA(chain B and (resid 1 through 13 or (resid 14...BB - H1 - 6029
26METMETNANA(chain B and (resid 1 through 13 or (resid 14...BB - H1 - 6029

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Components

#1: Protein NAD-dependent aldehyde dehydrogenase


Mass: 61515.066 Da / Num. of mol.: 2 / Fragment: BumuA.00020.h.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia multivorans (strain ATCC 17616 / 249) (bacteria)
Strain: ATCC 17616 / 249 / Gene: BMULJ_00382 / Plasmid: BumuA.00020.h.B1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: A0A0H3KBY8, aldehyde dehydrogenase (NAD+)
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 693 / 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: 2.38 Å3/Da / Density % sol: 48.3 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: RigakuReagents JCSG+ screen, E1: 100mM Sodium citrate tribasic, 100mM Sodium cocodylate/HCl pH 6.5: BumuA.00020.h.B1.PS37903 at 19.95mg/ml + 2mM NAD: cryo: 20% EG + 2mM NAD: tray 272909e1, ...Details: RigakuReagents JCSG+ screen, E1: 100mM Sodium citrate tribasic, 100mM Sodium cocodylate/HCl pH 6.5: BumuA.00020.h.B1.PS37903 at 19.95mg/ml + 2mM NAD: cryo: 20% EG + 2mM NAD: tray 272909e1, puck LCP4-1. Imidazole tentatively modeled, it was present during purification.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 9, 2016
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 71387 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 8.688 % / Biso Wilson estimate: 31.07 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.089 / Χ2: 0.943 / Net I/σ(I): 15.61
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allNum. unique obsCC1/2Rrim(I) all% possible all
2.05-2.18.6470.5223.37528552850.9430.55399.9
2.1-2.168.6540.4344.1351890.9560.4699.9
2.16-2.228.6890.3614.9149770.9690.38399.9
2.22-2.298.6440.296.0648800.9780.308100
2.29-2.378.7010.2517.1847220.9840.26699.9
2.37-2.458.6710.2228.1645550.9860.23599.8
2.45-2.548.6830.17910.0144180.990.1999.8
2.54-2.658.7110.14912.0542180.9930.15799.8
2.65-2.768.7170.1313.940660.9940.13899.6
2.76-2.98.7140.10916.4738630.9950.11699.4
2.9-3.068.6890.08919.9537030.9970.09499.5
3.06-3.248.6960.07523.1234920.9970.0899.6
3.24-3.478.6720.06427.1132890.9980.06899.5
3.47-3.748.7550.05829.9330440.9980.06199.2
3.74-4.18.7450.05432.4527990.9980.05798.9
4.1-4.588.7310.05333.8725460.9980.05698.9
4.58-5.298.7390.05434.7822130.9980.05798.7
5.29-6.488.7150.05534.3718850.9980.05898.2
6.48-9.178.6530.05235.8314680.9980.05597.5
9.17-508.4130.05336.857750.9980.05692.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å45.98 Å
Translation3.5 Å45.98 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
XDSdata reduction
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
Cootmodel building
BALBESphasing
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3rjl

3rjl


Resolution: 2.05→47.183 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.05
RfactorNum. reflection% reflection
Rfree0.1967 1990 2.79 %
Rwork0.1482 --
obs0.1496 71301 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.62 Å2 / Biso mean: 38.0455 Å2 / Biso min: 17.21 Å2
Refinement stepCycle: final / Resolution: 2.05→47.183 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8314 0 32 705 9051
Biso mean--52.53 42.48 -
Num. residues----1115
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078630
X-RAY DIFFRACTIONf_angle_d0.78811792
X-RAY DIFFRACTIONf_chiral_restr0.0541340
X-RAY DIFFRACTIONf_plane_restr0.0061568
X-RAY DIFFRACTIONf_dihedral_angle_d11.1565128
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A4847X-RAY DIFFRACTION6.629TORSIONAL
12B4847X-RAY DIFFRACTION6.629TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.05-2.10130.25881280.211749505078100
2.1013-2.15810.26241150.191250215136100
2.1581-2.22160.2531340.175249355069100
2.2216-2.29330.2331440.168149705114100
2.2933-2.37530.22251400.163449695109100
2.3753-2.47040.26341430.16849275070100
2.4704-2.58280.22351910.163849185109100
2.5828-2.71890.22581220.169750005122100
2.7189-2.88930.24251630.16864889505299
2.8893-3.11230.22451440.16624968511299
3.1123-3.42540.21821190.157649775096100
3.4254-3.92090.17491580.13014927508599
3.9209-4.93910.15741490.11154950509999
4.9391-47.19560.14061400.1334910505097
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)
10.78940.43090.22913.3032-0.0510.85280.02330.0995-0.2520.1911-0.0009-0.64310.06670.26160.00030.2410.06090.01450.4449-0.00790.42329.820437.563939.3005
23.94560.29553.75741.2269-0.04625.295-0.25320.30190.1712-0.23580.06490.0203-0.44160.22070.19640.2788-0.0327-0.02040.27430.0320.2391-1.73961.766235.2435
30.8385-0.16250.05111.54340.15251.23510.00130.1101-0.0244-0.040.0163-0.1903-0.00730.2484-0.04260.2204-0.01150.02790.28180.00890.23180.522744.577335.5375
41.72581.20191.0622.24210.83791.93190.12220.0641-0.32970.13480.001-0.22410.28760.0439-0.10320.24290.03120.03040.2745-0.00320.258-10.225825.23933.7683
51.95420.1291-0.25532.12320.23491.80570.0039-0.06850.01570.0486-0.06710.1345-0.1312-0.01260.05780.1863-0.0006-0.00390.2173-0.00290.2175-9.627947.782137.5144
60.88260.50950.76460.55320.16181.38980.1169-0.2301-0.19880.1948-0.0475-0.08580.019-0.0217-0.08110.2952-0.0159-0.01070.28170.00170.2559-3.659442.825862.0698
71.72161.1988-0.28741.9944-0.02810.80990.0872-0.1720.1070.3163-0.0810.17570.0378-0.1081-0.02050.3294-0.0292-0.00170.3059-0.03520.2518-2.739451.816569.7077
80.72340.52761.47150.44930.86583.16360.15070.0375-0.12080.1994-0.0354-0.09830.18390.1479-0.13050.309-0.0022-0.02910.28010.00210.2758-7.557931.122454.0719
91.37190.585-0.38680.7623-0.39671.64680.0440.0948-0.38590.00460.1178-0.15270.5547-0.0791-0.15910.46250.0233-0.08420.25790.01070.4471-24.07143.138643.5118
101.54971.09291.04161.54131.23883.72270.2111-0.3805-0.00210.4189-0.1830.25730.4753-0.7898-0.09330.3716-0.06110.03410.50810.07140.3308-46.581413.790154.8801
111.19130.40430.11990.9828-0.06841.36050.1124-0.0941-0.21380.12370.0212-0.19260.18460.0065-0.1430.28540.0364-0.04270.19030.03180.2683-20.609114.963449.9384
123.43981.4399-1.40251.2348-0.35660.7089-0.05690.035-0.2293-0.04690.1046-0.06180.1016-0.1815-0.02930.30740.0155-0.02680.20380.02510.2141-24.184421.325950.9864
131.9370.6540.39152.86360.24712.52980.0544-0.3203-0.26110.2374-0.00950.21910.3081-0.3253-0.11090.3357-0.0260.03340.29920.04920.2648-34.59617.272756.2598
142.5944-0.00011.25013.4009-0.53484.19170.0290.08360.02080.13730.1140.1282-0.16160.14120.00780.27150.00270.02570.26720.00420.27-31.010432.417447.0842
152.10120.33130.35251.7473-0.22341.29790.06070.0734-0.108-0.04620.01780.04680.0773-0.2093-0.07880.23240.0135-0.02280.3094-0.01280.2374-41.945921.225319.9115
161.33210.29131.4420.31440.36973.1380.09740.1752-0.14050.07040-0.11340.16060.1736-0.10880.22050.02820.00040.2344-0.02470.2636-20.269523.45431.6861
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 53 )A1 - 53
2X-RAY DIFFRACTION2chain 'A' and (resid 54 through 88 )A54 - 88
3X-RAY DIFFRACTION3chain 'A' and (resid 89 through 149 )A89 - 149
4X-RAY DIFFRACTION4chain 'A' and (resid 150 through 208 )A150 - 208
5X-RAY DIFFRACTION5chain 'A' and (resid 209 through 300 )A209 - 300
6X-RAY DIFFRACTION6chain 'A' and (resid 301 through 340 )A301 - 340
7X-RAY DIFFRACTION7chain 'A' and (resid 341 through 475 )A341 - 475
8X-RAY DIFFRACTION8chain 'A' and (resid 476 through 558 )A476 - 558
9X-RAY DIFFRACTION9chain 'B' and (resid 1 through 53 )B1 - 53
10X-RAY DIFFRACTION10chain 'B' and (resid 54 through 88 )B54 - 88
11X-RAY DIFFRACTION11chain 'B' and (resid 89 through 185 )B89 - 185
12X-RAY DIFFRACTION12chain 'B' and (resid 186 through 236 )B186 - 236
13X-RAY DIFFRACTION13chain 'B' and (resid 237 through 278 )B237 - 278
14X-RAY DIFFRACTION14chain 'B' and (resid 279 through 309 )B279 - 309
15X-RAY DIFFRACTION15chain 'B' and (resid 310 through 475 )B310 - 475
16X-RAY DIFFRACTION16chain 'B' and (resid 476 through 557 )B476 - 557

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