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- PDB-5kf0: Crystal structure of an Aldedhyde dehydrogenase from Burkholderia... -

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Basic information

Entry
Database: PDB / ID: 5kf0
TitleCrystal structure of an Aldedhyde dehydrogenase from Burkholderia vietnamiensis
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / SSGCID / Aldehyde dehydrogenase / Burkholderia thailandensis / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor / nucleotide 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, 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
ACETATE ION / Chem-NDP / Aldehyde dehydrogenase
Similarity search - Component
Biological speciesBurkholderia vietnamiensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: to be published
Title: Crystal structure of an Aldedhyde dehydrogenase from Burkholderia vietnamiensis
Authors: Abendroth, J. / Fox III, D. / Lorimer, D.D. / Edwards, T.E.
History
DepositionJun 10, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 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_prerelease_seq / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Aldehyde dehydrogenase
B: Aldehyde dehydrogenase
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,65534
Polymers212,1094
Non-polymers5,54630
Water36,8412045
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area30950 Å2
ΔGint-190 kcal/mol
Surface area56820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.640, 145.080, 170.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Aldehyde dehydrogenase / / BuviA.00020.0


Mass: 53027.219 Da / Num. of mol.: 4 / Fragment: BuviA.00020.0.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia vietnamiensis (strain G4 / LMG 22486) (bacteria)
Strain: G4 / LMG 22486 / Gene: Bcep1808_4170 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4JLJ7

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Non-polymers , 6 types, 2075 molecules

#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate


Mass: 745.421 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2045 / 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: 2.43 Å3/Da / Density % sol: 49 % / Mosaicity: 0.15 °
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop
Details: RigakuReagents JCSG+ screen, H5: 45% MPD, 200mM Ammonium acetate, 100mM BisTris/HCl pH 5.5; BuviA.00020.o.B1.PS37818 at 18.55mg/ml + 2mM NADP; cryo: direct; tray 269827h5, puck ehj6-1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 31, 2016
RadiationMonochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 226739 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.3 % / Biso Wilson estimate: 15.96 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Net I/σ(I): 20.3
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.7-1.740.4674.261100
1.74-1.790.3935.061100
1.79-1.840.3256.171100
1.84-1.90.2547.921100
1.9-1.960.2019.951100
1.96-2.030.16412.121100
2.03-2.110.13514.511100
2.11-2.190.11117.371100
2.19-2.290.09619.881100
2.29-2.40.08422.221100
2.4-2.530.07624.521100
2.53-2.690.06528.031100
2.69-2.870.05731.041100
2.87-3.10.0535.061100
3.1-3.40.04439.251100
3.4-3.80.0443.751100
3.8-4.390.03746.31100
4.39-5.380.03547.331100
5.38-7.60.03545.861100
7.6-500.03445.45199.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXdev_2429refinement
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing
ARPmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 3qqa

3qqa


Resolution: 1.7→50 Å / SU ML: 0.1 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 13.96
RfactorNum. reflection% reflection
Rfree0.157 2084 9.2 %
Rwork0.1342 --
obs0.1344 226662 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 71.87 Å2 / Biso mean: 19.5822 Å2 / Biso min: 7.14 Å2
Refinement stepCycle: final / Resolution: 1.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14565 0 365 2083 17013
Biso mean--25.61 31.26 -
Num. residues----1908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00615800
X-RAY DIFFRACTIONf_angle_d0.89221587
X-RAY DIFFRACTIONf_chiral_restr0.0562417
X-RAY DIFFRACTIONf_plane_restr0.0062911
X-RAY DIFFRACTIONf_dihedral_angle_d13.499742
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.73950.1911360.157414823X-RAY DIFFRACTION100
1.7395-1.78310.17111250.15414865X-RAY DIFFRACTION100
1.7831-1.83130.17991330.157414845X-RAY DIFFRACTION100
1.8313-1.88510.1771440.150114830X-RAY DIFFRACTION100
1.8851-1.9460.16581450.140114899X-RAY DIFFRACTION100
1.946-2.01550.15931280.138314869X-RAY DIFFRACTION100
2.0155-2.09620.17731470.13714896X-RAY DIFFRACTION100
2.0962-2.19160.14671350.133114884X-RAY DIFFRACTION100
2.1916-2.30720.14991270.131314951X-RAY DIFFRACTION100
2.3072-2.45170.16021480.136114920X-RAY DIFFRACTION100
2.4517-2.6410.16931370.135514976X-RAY DIFFRACTION100
2.641-2.90670.16611480.136815025X-RAY DIFFRACTION100
2.9067-3.32720.15411360.131915095X-RAY DIFFRACTION100
3.3272-4.19130.13171380.117615174X-RAY DIFFRACTION100
4.1913-410.15171570.132515526X-RAY DIFFRACTION100
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)
10.65610.2557-0.55650.6686-0.31012.6332-0.01120.00770.11970.07690.0112-0.102-0.2468-0.0046-0.01010.1297-0.0186-0.03250.087-0.00880.180845.959234.8954-29.7907
20.52950.3053-0.30520.9593-0.5790.70070.00170.03450.07510.02290.01560.0042-0.0598-0.0329-0.05110.11080.0013-0.00350.0989-0.01060.105829.064422.1945-26.7273
30.31090.09040.08710.53820.07290.4486-0.02670.04410.0616-0.0631-0.0001-0.0292-0.04240.00850.02120.1028-0.01220.00870.08790.00690.098838.298120.5216-42.5729
40.3157-0.0223-0.04020.4025-0.26810.8086-0.01920.073-0.0074-0.1007-0.0017-0.04820.00010.0560.02060.1248-0.00830.01770.1026-0.010.110836.08139.8217-47.8527
51.3653-0.4240.16120.61190.0970.83040.0083-0.0683-0.19110.00610.004-0.0380.1220.0214-0.02590.1205-0.00360.01450.06290.0120.142742.3198-20.0809-22.5643
60.8125-0.47290.13880.6838-0.33540.2653-0.010.0047-0.0089-0.0514-0.0178-0.0518-0.00570.03160.02390.11170.0060.00480.1024-0.01360.101540.1048-7.3928-28.6827
70.4697-0.1306-0.14910.5131-0.13211.0843-0.0609-0.1882-0.05260.15060.0596-0.05310.06590.05890.00160.12170.0254-0.02310.16180.00850.112246.2034-3.9129-0.1877
80.4596-0.1250.1340.3801-0.19810.7671-0.0397-0.1080.01840.08940.021-0.0817-0.03510.13520.0210.09620.0125-0.01390.1208-0.01220.104245.56862.5119-6.3117
90.9663-0.1741-0.0660.55820.12590.93750.01290.01360.1974-0.03290.01130.1488-0.1848-0.0766-0.02050.14450.027400.09240.01120.1956-2.720631.4283-23.7033
100.6903-0.2426-0.22060.95060.2480.29610.0147-0.03560.11240.0123-0.00110.0311-0.0559-0.0123-0.0230.10280.0186-0.0080.1064-0.00770.10156.488818.2536-23.3038
110.42420.07270.40280.43640.00080.8816-0.0258-0.02890.08940.0983-0.00750.0942-0.1087-0.03820.05110.13240.03160.03750.1152-0.02090.1292.41721.7911-3.2475
120.24650.07510.06310.55560.20880.7125-0.0041-0.07560.02760.1551-0.02650.1067-0.0353-0.11190.02990.12270.02470.03650.1116-0.01070.11045.282414.16530.0789
131.21360.41460.34580.46120.0111.20930.0613-0.0899-0.29860.05450.02890.02240.178-0.0995-0.09320.13740.00150.0020.09580.03130.20042.1235-22.9438-13.167
140.88490.39470.11620.86130.11710.27120.0144-0.0039-0.12970.03410.00570.01790.0172-0.051-0.03040.09330.00760.01410.10910.00810.08835.7197-10.05-15.4447
150.56950.1235-0.1790.50410.04931.0543-0.04570.1041-0.1062-0.08710.06120.02180.1328-0.0508-0.00230.1086-0.0165-0.00710.1532-0.0160.1402-1.5854-13.6194-41.6858
160.4440.16660.16330.39620.17310.6136-0.02340.0636-0.0304-0.0530.02180.07440.018-0.14670.00670.0908-0.0024-0.00040.14090.00210.1156-1.7318-5.5096-37.5847
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 61 )A-2 - 61
2X-RAY DIFFRACTION2chain 'A' and (resid 62 through 143 )A62 - 143
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 329 )A144 - 329
4X-RAY DIFFRACTION4chain 'A' and (resid 330 through 477 )A330 - 477
5X-RAY DIFFRACTION5chain 'B' and (resid 2 through 117 )B2 - 117
6X-RAY DIFFRACTION6chain 'B' and (resid 118 through 230 )B118 - 230
7X-RAY DIFFRACTION7chain 'B' and (resid 231 through 329 )B231 - 329
8X-RAY DIFFRACTION8chain 'B' and (resid 330 through 477 )B330 - 477
9X-RAY DIFFRACTION9chain 'C' and (resid 2 through 94 )C2 - 94
10X-RAY DIFFRACTION10chain 'C' and (resid 95 through 195 )C95 - 195
11X-RAY DIFFRACTION11chain 'C' and (resid 196 through 329 )C196 - 329
12X-RAY DIFFRACTION12chain 'C' and (resid 330 through 477 )C330 - 477
13X-RAY DIFFRACTION13chain 'D' and (resid 2 through 94 )D2 - 94
14X-RAY DIFFRACTION14chain 'D' and (resid 95 through 230 )D95 - 230
15X-RAY DIFFRACTION15chain 'D' and (resid 231 through 329 )D231 - 329
16X-RAY DIFFRACTION16chain 'D' and (resid 330 through 477 )D330 - 477

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