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- PDB-6pop: Crystal structure of DauA in complex with NADP+ -

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Basic information

Entry
Database: PDB / ID: 6pop
TitleCrystal structure of DauA in complex with NADP+
ComponentsAldehyde dehydrogenase
KeywordsOXIDOREDUCTASE / Dehydrogenase
Function / homology
Function and homology information


oxidoreductase activity, acting on the aldehyde or oxo group of donors, 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
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Aldehyde dehydrogenase
Similarity search - Component
Biological speciesPseudoalteromonas fuliginea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.147 Å
AuthorsPluvinage, B. / Boraston, A.B.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
CitationJournal: Commun Biol / Year: 2019
Title: Insights into the kappa / iota-carrageenan metabolism pathway of some marinePseudoalteromonasspecies.
Authors: Hettle, A.G. / Hobbs, J.K. / Pluvinage, B. / Vickers, C. / Abe, K.T. / Salama-Alber, O. / McGuire, B.E. / Hehemann, J.H. / Hui, J.P.M. / Berrue, F. / Banskota, A. / Zhang, J. / Bottos, E.M. ...Authors: Hettle, A.G. / Hobbs, J.K. / Pluvinage, B. / Vickers, C. / Abe, K.T. / Salama-Alber, O. / McGuire, B.E. / Hehemann, J.H. / Hui, J.P.M. / Berrue, F. / Banskota, A. / Zhang, J. / Bottos, E.M. / Van Hamme, J. / Boraston, A.B.
History
DepositionJul 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Oct 11, 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
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.ptnr2_auth_seq_id

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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
E: Aldehyde dehydrogenase
F: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)325,64228
Polymers320,2646
Non-polymers5,37822
Water10,160564
1
A: Aldehyde dehydrogenase
E: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,67611
Polymers106,7552
Non-polymers1,9219
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9580 Å2
ΔGint-2 kcal/mol
Surface area31940 Å2
MethodPISA
2
B: Aldehyde dehydrogenase
F: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,4528
Polymers106,7552
Non-polymers1,6976
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-21 kcal/mol
Surface area31830 Å2
MethodPISA
3
C: Aldehyde dehydrogenase
D: Aldehyde dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,5149
Polymers106,7552
Non-polymers1,7597
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-26 kcal/mol
Surface area31940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.687, 232.817, 88.257
Angle α, β, γ (deg.)90.000, 119.180, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Aldehyde dehydrogenase


Mass: 53377.258 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas fuliginea (bacteria) / Gene: DC53_13140 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A063KJS9*PLUS
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 49.92 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.2 M sodium acetate trihydrate, 0.1 M Bis-Tris and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.147→39.853 Å / Num. obs: 167353 / % possible obs: 99.2 % / Redundancy: 5.4 % / CC1/2: 0.989 / Rmerge(I) obs: 0.136 / Rpim(I) all: 0.072 / Net I/σ(I): 9
Reflection shellResolution: 2.15→2.18 Å / Rmerge(I) obs: 0.579 / Num. unique obs: 8002 / CC1/2: 0.671 / Rpim(I) all: 0.328 / % possible all: 98.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.15.2_3472refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6PNU

6pnu


Resolution: 2.147→39.853 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.37
RfactorNum. reflection% reflection
Rfree0.2602 8511 5.09 %
Rwork0.2137 --
obs0.216 167259 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 77.46 Å2 / Biso mean: 36.1514 Å2 / Biso min: 17.57 Å2
Refinement stepCycle: final / Resolution: 2.147→39.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21251 0 346 564 22161
Biso mean--35.57 35.02 -
Num. residues----2850
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.147-2.17140.37522680.3173503296
2.1714-2.1970.33541950.30455381100
2.197-2.22380.3322380.295339100
2.2238-2.25190.31562700.28255299100
2.2519-2.28150.35123380.28995225100
2.2815-2.31280.33683270.27675252100
2.3128-2.34580.29683110.26185280100
2.3458-2.38080.30552920.25145243100
2.3808-2.4180.29762870.25525317100
2.418-2.45770.28933550.24735209100
2.4577-2.50.31863350.2445234100
2.5-2.54550.30082570.2325334100
2.5455-2.59440.29353040.23255287100
2.5944-2.64740.29173010.23035267100
2.6474-2.70490.28783030.22965289100
2.7049-2.76780.29012760.22635310100
2.7678-2.8370.26492390.23055332100
2.837-2.91370.27572570.23175297100
2.9137-2.99940.2972600.23125311100
2.9994-3.09620.31723990.24265209100
3.0962-3.20680.2842920.24575273100
3.2068-3.33520.29932740.23085309100
3.3352-3.48690.26392580.22355338100
3.4869-3.67060.27752630.21785370100
3.6706-3.90040.24752750.20255275100
3.9004-4.20120.2092930.18525324100
4.2012-4.62350.19312230.16955394100
4.6235-5.29120.19322310.16625350100
5.2912-6.66120.21973350.18125272100
6.6612-39.8530.15752550.14385396100

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