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- PDB-7do7: Crystal structure of Azotobacter vinelandii L-rhamnose 1-dehydrog... -

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Basic information

Entry
Database: PDB / ID: 7do7
TitleCrystal structure of Azotobacter vinelandii L-rhamnose 1-dehydrogenase(NAD and L-rhamnose bound-form)
ComponentsShort-chain dehydrogenase/reductase SDR
KeywordsOXIDOREDUCTASE / L-Rhamnose metabolism / NADP-dependentdehydrogenase / SDR protein family
Function / homologyPKS_KR / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / oxidoreductase activity / NAD(P)-binding domain superfamily / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / beta-L-rhamnopyranose / Short-chain dehydrogenase/reductase SDR
Function and homology information
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 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

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Assembly

Deposited unit
A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4258
Polymers55,4412
Non-polymers1,9836
Water5,621312
1
A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
hetero molecules

A: Short-chain dehydrogenase/reductase SDR
B: Short-chain dehydrogenase/reductase SDR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,84916
Polymers110,8834
Non-polymers3,96712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area20860 Å2
ΔGint-139 kcal/mol
Surface area29350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.470, 97.931, 70.302
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-549-

HOH

21B-554-

HOH

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Components

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


Mass: 27720.629 Da / Num. of mol.: 2
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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Sugar
ChemComp-RM4 / beta-L-rhamnopyranose / beta-L-rhamnose / 6-deoxy-beta-L-mannopyranose / L-rhamnose / rhamnose / Rhamnose


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H12O5 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
LRhapbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-rhamnopyranoseCOMMON NAMEGMML 1.0
b-L-RhapIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
RhaSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.13 Å3/Da / Density % sol: 42.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
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: Jul 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→50 Å / Num. obs: 66716 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.991 / Rmerge(I) obs: 0.291 / Rpim(I) all: 0.081 / Rrim(I) all: 0.303 / Net I/σ(I): 8.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.57-1.613.91.0084557632850.8860.2781.0461.9100
8.6-48.9711.60.0755864810.9990.0190.07318.799.2

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.57→48.9893 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2588 3370 5.07 %
Rwork0.2225 63049 -
obs0.2243 66419 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 53.45 Å2 / Biso mean: 19.462 Å2 / Biso min: 6.76 Å2
Refinement stepCycle: final / Resolution: 1.57→48.9893 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3639 0 132 312 4083
Biso mean--20.76 26.05 -
Num. residues----512
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.57-1.59250.30241350.26712629100
1.5925-1.61620.28721480.26222595100
1.6162-1.64150.27391500.25272567100
1.6415-1.66840.26531520.24752591100
1.6684-1.69720.30061380.24742606100
1.6972-1.7280.3171460.2532595100
1.728-1.76130.24571710.23722584100
1.7613-1.79720.2981640.23362579100
1.7972-1.83630.28211330.23182597100
1.8363-1.8790.27021390.23932624100
1.879-1.9260.32481030.3105262698
1.926-1.97810.32511060.2529259598
1.9781-2.03630.2821380.23392612100
2.0363-2.1020.35631170.26352628100
2.102-2.17710.26331390.22442633100
2.1771-2.26430.30211620.2619257398
2.2643-2.36740.24181130.2205263899
2.3674-2.49220.23611230.21472634100
2.4922-2.64830.26011530.21262660100
2.6483-2.85280.23761410.21342648100
2.8528-3.13980.23181550.2012635100
3.1398-3.5940.22011520.20242673100
3.594-4.52760.23431640.18912686100
4.5276-48.98930.24221280.1988284199

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