5G30

Crystallographic structure of mutant D60S of thioredoxin from Litopenaeus vannamei

> Summary

Summary for 5G30

Related5G2Z 5G31
DescriptorTHIOREDOXIN (E.C.1.8.1.9)
Functional Keywordsoxidoreductase, thioredoxin, shrimp, litopenaeus vannamei, mutant, disulfide bond
Biological sourceLITOPENAEUS VANNAMEI (WHITELEG SHRIMP)
Total number of polymer chains4
Total molecular weight48112.17
Authors
Campos-Acevedo, A.A.,Rudino-Pinera, E. (deposition date: 2016-04-18, release date: 2017-03-15, Last modification date: 2017-04-19)
Primary citation
Campos-Acevedo, A.A.,Sotelo-Mundo, R.R.,Perez, J.,Rudino-Pinera, E.
Is dimerization a common feature in thioredoxins? The case of thioredoxin from Litopenaeus vannamei.
Acta Crystallogr D Struct Biol, 73:326-339, 2017
PubMed: 28375144
DOI: 10.1107/S2059798317002066
MImport into Mendeley
Experimental method
X-RAY DIFFRACTION (1.65 Å)
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Structure validation

RfreeClashscoreRamachandran outliersSidechain outliersRSRZ outliers0.2011201.3%1.4%MetricValuePercentile RanksWorseBetterPercentile relative to all X-ray structuresPercentile relative to X-ray structures of similar resolution

More Asymmetric unit images

Molmil generated image of 5g30
no rotation
Molmil generated image of 5g30
rotated about x axis by 90°
Molmil generated image of 5g30
rotated about y axis by 90°

More Biological unit images

Molmil generated image of 5g30
no rotation
Molmil generated image of 5g30
rotated about x axis by 90°
Molmil generated image of 5g30
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 (5g30.pdb1.gz [42.52 KB])
Coordinate files for Biological unit (5g30.pdb2.gz [39.41 KB])

> Structural details

Entity

Chain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
A, B, C, DTHIOREDOXINpolymer10511930.74
UniProt (B1PWB9)
Pfam (PF00085)
LITOPENAEUS VANNAMEI (WHITELEG SHRIMP)
ACETATE IONnon-polymer59.03
DI(HYDROXYETHYL)ETHERnon-polymer106.12
waterwater18.0391

Sequence viewer

Contents of the asymmetric unit

PolymersNumber of chains4
Total molecular weight47722.8
Non-Polymers*Number of molecules5
Total molecular weight389.4
All*Total molecular weight48112.2
*Water molecules are not included.

> Experimental details

Refinement Statistics

Experimental method:X-RAY DIFFRACTION (1.65 Å)

Cell axes58.49182.71282.206
Cell angles90.00102.5890.00
SpacegroupC 1 2 1
Resolution limits19.47 - 1.65
the highest resolution shell value1.686 - 1.650
R-factor0.1671
R-work0.16530
the highest resolution shell value0.209
R-free0.20080
the highest resolution shell value0.276
RMSD bond length0.006
RMSD bond angle0.855

Data Collection Statistics

Resolution limits19.46 - 1.65
the highest resolution shell value -
Number of reflections45126
Rmerge_l_obs0.040
the highest resolution shell value0.250
Completeness98.4
Redundancy2.6
the highest resolution shell value2.7
I/sigma(I)0

Crystallization Conditions

crystal IDmethodpHpH rangetemperatureunit
16

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
AC12BINDING SITE FOR RESIDUE ACT D 1106
ChainResidue
AGLN67
DLYS36

AC24BINDING SITE FOR RESIDUE ACT C 1106
ChainResidue
BMET1
BGLN47
CLYS41
CGLU44

AC36BINDING SITE FOR RESIDUE ACT C 1107
ChainResidue
CLEU15
CMET80
CLYS81
CASN82
CGLY83
CHOH2037

AC47BINDING SITE FOR RESIDUE PEG C 1108
ChainResidue
CGLU61
CCYS62
CGLU63
CASP64
CILE65
CHOH2011
CHOH2017

AC58BINDING SITE FOR RESIDUE PEG C 1109
ChainResidue
CLYS41
CALA92
CASN93
CTYR94
CASP95
CHOH2059
DGLN8
DASP68

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

site_idNumber of ResiduesDetails
ACT_5g30_D_11062ACETATE ION binding site
ChainResidueligand
AGLN67ACT: ACETATE ION
DLYS36ACT: ACETATE ION

PEG_5g30_C_110810DI(HYDROXYETHYL)ETHER binding site
ChainResidueligand
CLYS6-GLN8PEG: DI(HYDROXYETHYL)ETHER
CVAL59-ILE65PEG: DI(HYDROXYETHYL)ETHER

ACT_5g30_C_110711ACETATE ION binding site
ChainResidueligand
CLEU15-ASN16ACT: ACETATE ION
CALA18-GLY19ACT: ACETATE ION
CLYS21ACT: ACETATE ION
CVAL23ACT: ACETATE ION
CMET80-GLN84ACT: ACETATE ION

PEG_5g30_C_110912DI(HYDROXYETHYL)ETHER binding site
ChainResidueligand
CPRO34PEG: DI(HYDROXYETHYL)ETHER
CMET37-ILE38PEG: DI(HYDROXYETHYL)ETHER
CLYS41PEG: DI(HYDROXYETHYL)ETHER
CALA92-LYS96PEG: DI(HYDROXYETHYL)ETHER
DGLN8PEG: DI(HYDROXYETHYL)ETHER
DTHR12PEG: DI(HYDROXYETHYL)ETHER
DASP68PEG: DI(HYDROXYETHYL)ETHER

ACT_5g30_C_11063ACETATE ION binding site
ChainResidueligand
CPRO40-LYS41ACT: ACETATE ION
CGLU44ACT: ACETATE ION

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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

> Downloads

Resources

File formatFile name (file size)
PDBallpdb5g30.ent.gz (84.27 KB)
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all (no-compress)pdb5g30.ent (347.33 KB)
header onlypdb5g30.ent.gz (6.41 KB)
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PDBx/mmCIF5g30.cif.gz (102.65 KB)
PDBMLall5g30.xml.gz (138.63 KB)
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no-atom5g30-noatom.xml.gz (22.54 KB)
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ext-atom5g30-extatom.xml.gz (87 KB)
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PDBMLplusall5g30-plus.xml.gz (140.23 KB)
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no-atom5g30-plus-noatom.xml.gz (24.14 KB)
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add only5g30-add.xml.gz (1.6 KB)
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RDF5g30.rdf.gz (45.17 KB)
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Structure factorsr5g30sf.ent.gz (780.96 KB)
Biological unit (PDB format)5g30.pdb1.gz (42.52 KB) (B,C)
*author and software defined assembly, 2 molecule(s) (dimeric)
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5g30.pdb2.gz (39.41 KB) (A,D)
*author and software defined assembly, 2 molecule(s) (dimeric)
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Validation reportsPDF5g30​_validation.pdf.gz (302.53 KB)
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PDF-full5g30​_full​_validation.pdf.gz (308.99 KB)
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XML5g30​_validation.xml.gz (22.33 KB)
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PNG5g30​_multipercentile​_validation.png.gz (156.5 KB)
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SVG5g30​_multipercentile​_validation.svg.gz (923 B)
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Sequence (fasta)5g30​_seq.txt
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