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- PDB-7do5: Crystal structure of Azotobacter vinelandii L-rhamnose 1-dehydrog... -

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Basic information

Entry
Database: PDB / ID: 7do5
TitleCrystal structure of Azotobacter vinelandii L-rhamnose 1-dehydrogenase(apo-form)
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / L-Rhamnose metabolism / NADP-dependentdehydrogenase / SDR protein family
Function / homology
Function and homology information


L-rhamnose 1-dehydrogenase [NAD(P)+] / : / 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
L-rhamnose 1-dehydrogenase (NAD(P)(+))
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.836 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 1.3Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)224,07132
Polymers221,7658
Non-polymers2,30624
Water25,9781442
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)112,03516
Polymers110,8834
Non-polymers1,15312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16930 Å2
ΔGint-271 kcal/mol
Surface area33300 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)112,03516
Polymers110,8834
Non-polymers1,15312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17920 Å2
ΔGint-273 kcal/mol
Surface area32070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.371, 81.579, 91.180
Angle α, β, γ (deg.)80.450, 74.550, 75.200
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1442 / 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: 2.34 Å3/Da / Density % sol: 47.5 %
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: 8.5
Details: 100 mM Tris-HCl (pH 8.5), 200 mM lithium sulfate, 25% (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: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 16, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.836→50 Å / Num. obs: 169510 / % possible obs: 92.6 % / Redundancy: 1.842 % / Biso Wilson estimate: 34.747 Å2 / CC1/2: 0.993 / Rmerge(I) obs: 0.075 / Rrim(I) all: 0.106 / Χ2: 1.011 / Net I/σ(I): 6.45
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
1.9-2.011.8070.5441.188574551326474420.4760.76992.4
2.01-2.151.9050.3528581148504450520.7310.49592.9
2.15-2.321.870.213.37893945028422170.8940.29793.8
2.32-2.541.7730.1494.776911241548389740.9410.2193.8
2.54-2.841.8180.1016.866349737444349310.9720.14393.3
2.84-3.281.8920.0710.155767833190304790.9840.191.8
3.28-4.011.870.05314.234658527910249090.9890.07589.2
4.01-5.651.7740.04216.473533821608199220.9920.0692.2
5.65-47.531.8770.03517.942115312064112690.9950.04993.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata scaling
PDB_EXTRACT3.27data extraction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2UVD

2uvd


Resolution: 1.836→47.5872 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 19.69 / Stereochemistry target values: ML
Details: The entry contains friedel pairs in F_plus/minus columns and I_plus/minus columns
RfactorNum. reflection% reflection
Rfree0.1881 8539 5.04 %
Rwork0.1604 160971 -
obs0.1618 169510 96.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 81.95 Å2 / Biso mean: 29.5768 Å2 / Biso min: 14.61 Å2
Refinement stepCycle: final / Resolution: 1.836→47.5872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14466 0 120 1442 16028
Biso mean--52.03 37.42 -
Num. residues----2059
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8362-1.85710.28682680.2555519393
1.8571-1.87890.27972840.2524537596
1.8789-1.90180.26352810.2387531096
1.9018-1.92590.2742700.2297541096
1.9259-1.95120.25712890.223526496
1.9512-1.9780.25382760.2108537096
1.978-2.00620.24642660.1992533496
2.0062-2.03620.24172650.1945547296
2.0362-2.0680.23912670.1841530297
2.068-2.10190.21762700.1817536496
2.1019-2.13810.22183060.1792536497
2.1381-2.1770.21033080.1828538897
2.177-2.21890.21122910.1629539097
2.2189-2.26420.18282950.162530696
2.2642-2.31340.20693030.1654539197
2.3134-2.36720.20362840.1629538097
2.3672-2.42640.1983120.1611537197
2.4264-2.4920.21352850.1651541897
2.492-2.56530.18193060.1592537897
2.5653-2.64810.192970.1612543297
2.6481-2.74280.19132750.1692543597
2.7428-2.85260.20312780.1645541498
2.8526-2.98240.19042790.1604544797
2.9824-3.13960.17242780.158542297
3.1396-3.33630.17842670.1557534897
3.3363-3.59380.16052860.1398537596
3.5938-3.95530.16632740.1343529095
3.9553-4.52720.14582970.1256532096
4.5272-5.70230.17592960.1474533396
5.7023-47.58720.16332860.1581537597

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