5T79

X-Ray Crystal Structure of a Novel Aldo-keto Reductases for the Biocatalytic Conversion of 3-hydroxybutanal to 1,3-butanediol

> Summary

Summary for 5T79

Related3ERP
DescriptorAldo-keto Reductase, OXIDOREDUCTASE, SULFATE ION, CHLORIDE ION, ... (5 entities in total)
Functional Keywordscenter for structural genomics of infectious diseases, csgid, niaid, national institute of allergy and infectious diseases, nadp-dependent oxidoreductase, translation
Biological sourceSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Total number of polymer chains1
Total molecular weight38403.54
Authors
Primary citation
Kim, T.,Flick, R.,Brunzelle, J.,Singer, A.,Evdokimova, E.,Brown, G.,Joo, J.C.,Minasov, G.A.,Anderson, W.F.,Mahadevan, R.,Savchenko, A.,Yakunin, A.F.
Structural and biochemical studies of novel aldo-keto reductases for the biocatalytic conversion of 3-hydroxybutanal to 1,3-butanediol.
Appl. Environ. Microbiol., 2017
PubMed: 28130301 (PDB entries with the same primary citation)
DOI: 10.1128/AEM.03172-16
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.86 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.185200.4%3.5%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5t79
no rotation
Molmil generated image of 5t79
rotated about x axis by 90°
Molmil generated image of 5t79
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 5t79
no rotation
Molmil generated image of 5t79
rotated about x axis by 90°
Molmil generated image of 5t79
rotated about y axis by 90°
(*)In the case of coarse surface representation, the asymmetric unit is shown as red ribbon representation.
Coordinate files for Biological unit (5t79.pdb1.gz [118.67 KB])
Coordinate files for Biological unit (5t79.pdb2.gz [930.16 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
AAldo-keto Reductase, OXIDOREDUCTASEpolymer33237430.51
UniProt (Q8ZNA1)
Pfam (PF00248)
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
SULFATE IONnon-polymer96.12
CHLORIDE IONnon-polymer35.51
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATEnon-polymer745.41
waterwater18.0448

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains1
Total molecular weight37430.5
Non-Polymers*Number of molecules4
Total molecular weight973.0
All*Total molecular weight38403.5
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.86 Å)

Cell axes94.38794.38791.677
Cell angles90.0090.0090.00
SpacegroupP 4 2 2
Resolution limits29.85 - 1.86
the highest resolution shell value1.920 - 1.860
R-factor0.166
R-work0.16400
the highest resolution shell value0.257
R-free0.19300
the highest resolution shell value0.256
RMSD bond length0.010
RMSD bond angle0.950

Data Collection Statistics

Resolution limits30.00 - 1.85
the highest resolution shell value -
Number of reflections35207
Rmerge_l_obs0.073
the highest resolution shell value0.563
Completeness99.5
Redundancy7.7
the highest resolution shell value7.4
I/sigma(I)-3

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
1VAPOR DIFFUSION, HANGING DROP7.5295

Crystallization Reagents

IDcrystal IDsolution IDreagent nameconcentrationdetails
Crystallization Reagents in Literatures*
IDcrystal IDsolutionreagent nameconcentration (unit)details
Annotated Information is extracted from Literature Info*

> Functional details

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Functional Information from GO Data

ChainGOidnamespacecontents
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Functional Information from PDB Data

site_idNumber of ResiduesDetails
AC18binding site for residue SO4 A 401
ChainResidue
AARG201
AARG287
AASN288
ACYS321
AHOH504
AHOH516
AHOH671
AHOH733

AC27binding site for residue SO4 A 402
ChainResidue
APRO145
ALEU146
AHOH550
AHOH551
AHOH615
AHOH650
AHOH667

AC33binding site for residue CL A 403
ChainResidue
AARG89
AGLU130
ATYR131

AC431binding site for residue NDP A 404
ChainResidue
AGLY31
ALEU32
ATRP33
AASP61
ATYR66
AHIS138
ASER168
AASN169
AGLN193
APHE221
ASER222
APRO223
ALEU224
AGLY226
AGLY227
ATHR230
AARG232
ASER278
ALEU295
AILE296
AGLY297
ASER299
AGLN303
AASP306
AHOH507
AHOH569
AHOH575
AHOH587
AHOH597
AHOH707
AHOH753

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Functional Information from PDB atom coordinates for the "HETATM" binding sites

site_idNumber of ResiduesDetails
NDP_5t79_A_40436NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE binding site
ChainResidueligand
AGLY31-ASN35NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
AASP61-LEU62NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ATYR66NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ALYS97NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ATYR100NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
AHIS138NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ASER168-ASN169NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
AGLN193NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
AALA220-GLY227NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ATHR230-ARG232NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ALYS276NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ASER278NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
ALEU295-LYS300NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
AGLN303NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
AASP306-ALA307NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

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Functional Information from PROSITE/UniProt

site_idNumber of ResiduesDetails
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Functional Information from SwissProt/UniProt

site_idNumber of ResiduesDetails
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Catalytic Information from CSA

site_idNumber of ResiduesDetails

> Sequence Neighbor

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