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- PDB-5u63: Crystal structure of putative thioredoxin reductase from Haemophi... -

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Basic information

Entry
Database: PDB / ID: 5u63
TitleCrystal structure of putative thioredoxin reductase from Haemophilus influenzae
ComponentsThioredoxin reductase
KeywordsLYASE / cofactor / nucleotide / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / cell redox homeostasis / cytoplasm
Similarity search - Function
Thioredoxin reductase / Pyridine nucleotide-disulphide oxidoreductase, class-II, active site / Pyridine nucleotide-disulphide oxidoreductases class-II active site. / : / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Thioredoxin reductase
Similarity search - Component
Biological speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsMichalska, K. / Maltseva, N. / Mulligan, R. / Grimshaw, S. / Joachimiak, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: To Be Published
Title: Crystal structure of putative thioredoxin reductase from Haemophilus influenzae
Authors: Michalska, K. / Maltseva, N. / Mulligan, R. / Grimshaw, S. / Joachimiak, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionDec 7, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin reductase
B: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,22116
Polymers69,4102
Non-polymers3,81114
Water6,449358
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11930 Å2
ΔGint-35 kcal/mol
Surface area24460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.313, 153.974, 58.193
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsTHE AUTHOR STATES THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Thioredoxin reductase / TRXR


Mass: 34705.066 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) (bacteria)
Strain: ATCC 51907 / DSM 11121 / KW20 / Rd / Gene: trxB, HI_1158 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Magic
References: UniProt: P43788, thioredoxin-disulfide reductase

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Non-polymers , 6 types, 372 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.56 Å3/Da / Density % sol: 51.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.16 M Mg acetate, 0.08 M Na cacodylate, pH 6.5, 16% PEG 8K, 20% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2016 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.99→30 Å / Num. obs: 49269 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 25 % / Rmerge(I) obs: 0.148 / Net I/σ(I): 25.52
Reflection shellResolution: 2→2.03 Å / Redundancy: 20.2 % / Rmerge(I) obs: 1.117 / Mean I/σ(I) obs: 2.46 / CC1/2: 0.754 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1TDE

1tde


Resolution: 1.99→29.759 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.55 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1819 1475 3 %random
Rwork0.1474 ---
obs0.1484 49207 98.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.99→29.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4818 0 217 358 5393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095151
X-RAY DIFFRACTIONf_angle_d1.0376991
X-RAY DIFFRACTIONf_dihedral_angle_d17.642981
X-RAY DIFFRACTIONf_chiral_restr0.062777
X-RAY DIFFRACTIONf_plane_restr0.006888
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9896-2.05380.26231010.21613805X-RAY DIFFRACTION88
2.0538-2.12720.24141370.18734310X-RAY DIFFRACTION100
2.1272-2.21230.17411190.1744330X-RAY DIFFRACTION100
2.2123-2.31290.21561350.16794350X-RAY DIFFRACTION100
2.3129-2.43480.22041200.16684360X-RAY DIFFRACTION100
2.4348-2.58730.24211580.16444325X-RAY DIFFRACTION100
2.5873-2.78690.19651320.15974381X-RAY DIFFRACTION100
2.7869-3.06710.18841370.15784392X-RAY DIFFRACTION100
3.0671-3.51040.17161600.1414379X-RAY DIFFRACTION100
3.5104-4.42040.14651420.11954443X-RAY DIFFRACTION100
4.4204-29.76280.16591340.1374657X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.43860.02030.00953.98651.6872.3480.0049-0.2250.17880.43350.0783-0.267-0.03630.1557-0.090.27090.0041-0.060.2747-0.00820.239459.619362.578341.2334
21.41010.0896-0.49360.7234-0.22270.30610.1146-0.33010.11780.40860.0224-0.0909-0.01030.1028-0.14310.48240.0095-0.03230.3054-0.02890.261539.584560.424747.8103
33.1307-0.7768-0.41324.94921.82173.86050.0319-0.0836-0.00710.2085-0.11540.3032-0.0431-0.22710.06310.1984-0.05280.01270.17120.02010.194227.762251.823440.1074
41.19760.6343-0.28452.01290.25540.15650.1933-0.14510.20990.324-0.08320.0708-0.07670.0501-0.15360.34050.0426-0.02420.2491-0.00720.275342.014268.309238.7264
51.7770.23140.82564.59031.2343.52960.06420.09050.3269-0.10340.0365-0.3098-0.41040.1843-0.08430.25780.01060.02370.1970.01470.255457.857969.518328.736
62.0068-0.3931-0.05561.6006-0.08522.460.12170.4346-0.0531-0.2752-0.1218-0.09020.1646-0.0732-0.00690.23170.04310.01880.2355-0.02270.177455.978448.161312.3553
73.49890.3631-0.32932.9523-0.29425.11570.2528-0.05890.5425-0.1695-0.1366-0.6617-0.41490.6362-0.09770.3122-0.03220.10670.4685-0.08290.758384.982555.836614.7787
82.4088-0.3637-0.15251.58230.08011.87850.07180.44490.2175-0.2906-0.071-0.1713-0.245-0.1013-0.02090.28520.03030.04140.27510.04210.230356.005260.502313.0506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 106 )
2X-RAY DIFFRACTION2chain 'A' and (resid 107 through 144 )
3X-RAY DIFFRACTION3chain 'A' and (resid 145 through 233 )
4X-RAY DIFFRACTION4chain 'A' and (resid 234 through 267 )
5X-RAY DIFFRACTION5chain 'A' and (resid 268 through 317 )
6X-RAY DIFFRACTION6chain 'B' and (resid -2 through 128 )
7X-RAY DIFFRACTION7chain 'B' and (resid 129 through 233 )
8X-RAY DIFFRACTION8chain 'B' and (resid 234 through 316 )

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