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- PDB-7do6: Crystal structure of Azotobacter vinelandii L-rhamnose 1-dehydrog... -

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Basic information

Entry
Database: PDB / ID: 7do6
TitleCrystal structure of Azotobacter vinelandii L-rhamnose 1-dehydrogenase(NADP bound-form)
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / L-Rhamnose metabolism / NADP-dependent dehydrogenase / SDR protein family
Function / homology
Function and homology information


L-rhamnose 1-dehydrogenase [NAD(P)+] / rhamnose metabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / quinone binding / fatty acid biosynthetic process / nucleotide binding
Similarity search - Function
PKS_KR / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / L-rhamnose 1-dehydrogenase (NAD(P)(+))
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.37 Å
AuthorsYoshiwara, K. / Watanabe, Y. / Watanabe, S.
CitationJournal: Febs Lett. / Year: 2021
Title: Crystal structure of l-rhamnose 1-dehydrogenase involved in the nonphosphorylative pathway of l-rhamnose metabolism in bacteria.
Authors: Yoshiwara, K. / Watanabe, S. / Watanabe, Y.
History
DepositionDec 12, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Mar 24, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
C: Short-chain dehydrogenase/reductase SDR
D: Short-chain dehydrogenase/reductase SDR
E: Short-chain dehydrogenase/reductase SDR
F: Short-chain dehydrogenase/reductase SDR
G: Short-chain dehydrogenase/reductase SDR
H: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)227,71216
Polymers221,7658
Non-polymers5,9478
Water6,918384
1
A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
C: Short-chain dehydrogenase/reductase SDR
D: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,8568
Polymers110,8834
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19390 Å2
ΔGint-125 kcal/mol
Surface area31280 Å2
MethodPISA
2
E: Short-chain dehydrogenase/reductase SDR
F: Short-chain dehydrogenase/reductase SDR
G: Short-chain dehydrogenase/reductase SDR
H: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,8568
Polymers110,8834
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19260 Å2
ΔGint-120 kcal/mol
Surface area30990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.633, 81.571, 86.389
Angle α, β, γ (deg.)87.680, 75.530, 89.350
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Short-chain dehydrogenase/reductase SDR / L-Rhamnose 1-dehydrogenase


Mass: 27720.629 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii (strain DJ / ATCC BAA-1303) (bacteria)
Strain: DJ / ATCC BAA-1303 / Gene: Avin_09160 / Production host: Escherichia coli DH5[alpha] (bacteria) / References: UniProt: C1DMX5
#2: Chemical
ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / L-Rhamnose 1-dehydrogenase / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H28N7O17P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / 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: 2.42 Å3/Da / Density % sol: 49.12 %
Description: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 0.1 M Tris-HCl (pH 8.0), 0.2 M NaCl, 24.5% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.37→50.03 Å / Num. obs: 82779 / % possible obs: 96.1 % / Redundancy: 2.185 % / Biso Wilson estimate: 40.602 Å2 / CC1/2: 0.965 / Rmerge(I) obs: 0.205 / Rrim(I) all: 0.268 / Χ2: 0.729 / Net I/σ(I): 3.68 / Num. measured all: 354663
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.37-2.512.1491.0030.925443927248253330.4331.31193
2.51-2.692.10.691.35171525640246240.6060.90596
2.69-2.92.1580.5041.825034823938233300.7390.66197.5
2.9-3.182.2890.3632.74903921926214270.8260.47697.7
3.18-3.552.2390.2274.174324319920193110.9130.29996.9
3.55-4.12.1140.1525.633570017488168840.9540.296.5
4.1-5.012.2430.1037.953187714808142090.9740.13596
5.01-7.052.1970.117.492434211482110790.970.14496.5
7.05-50.032.2830.07111.513960644461160.9820.09294.9

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.37→50.03 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 29.37 / Stereochemistry target values: ML
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.2573 4170 5.04 %
Rwork0.2049 78609 -
obs0.2076 82779 98.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 87.34 Å2 / Biso mean: 33.795 Å2 / Biso min: 13.41 Å2
Refinement stepCycle: final / Resolution: 2.37→50.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13988 0 384 384 14756
Biso mean--48.6 33.66 -
Num. residues----1994
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.37-2.39660.35991280.3142223384
2.3966-2.42480.41541490.3006256998
2.4248-2.45440.35171350.3007266198
2.4544-2.48540.35691310.3027258598
2.4854-2.51810.34711190.2913264398
2.5181-2.55260.3411310.2733266698
2.5526-2.58910.33561290.2719261898
2.5891-2.62780.3581400.2729265498
2.6278-2.66880.32631560.2603257698
2.6688-2.71260.33081270.2586268099
2.7126-2.75930.32481300.2422258698
2.7593-2.80950.32061270.2453270999
2.8095-2.86350.25491310.2278257899
2.8635-2.9220.29941420.2232266499
2.922-2.98550.29521320.2224265199
2.9855-3.05490.27891380.2112262699
3.0549-3.13130.27231390.2104267399
3.1313-3.2160.25961530.208259399
3.216-3.31060.2491630.1944262099
3.3106-3.41740.27541510.1944265899
3.4174-3.53950.23031300.1838264999
3.5395-3.68120.22791460.1811259999
3.6812-3.84870.23561420.1758265099
3.8487-4.05150.20071290.1702267099
4.0515-4.30520.19451540.1576264099
4.3052-4.63740.19771510.146259899
4.6374-5.10370.19391250.1605267699
5.1037-5.84120.24581330.1948265399
5.8412-7.35560.24891500.2018263099
7.3556-50.030.20641590.1783260198

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