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- PDB-7tkv: Crystal Structure of the Thioredox_DsbH Domain-Containing Unchara... -

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Basic information

Entry
Database: PDB / ID: 7tkv
TitleCrystal Structure of the Thioredox_DsbH Domain-Containing Uncharacterized Protein Bab1_2064 from Brucella abortus
ComponentsThioredox_DsbH domain-containing protein
KeywordsUNKNOWN FUNCTION / TRX domain / protein of unkown function / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID
Function / homology
Function and homology information


carbohydrate metabolic process
Similarity search - Function
Domain of unknown function DUF255 / Spermatogenesis-associated protein 20 / Protein of unknown function, DUF255 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / DUF255 domain-containing protein
Similarity search - Component
Biological speciesBrucella abortus 2308 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsKim, Y. / Crawford, M. / Endres, M. / Babnigg, G. / Crosson, S. / Joachimiak, A. / 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) United States
CitationJournal: To Be Published
Title: Crystal Structure of the Thioredox_DsbH Domain-Containing Uncharacterized Protein Bab1_2064 from Brucella abortus
Authors: Kim, Y. / Crawford, M. / Endres, M. / Babnigg, G. / Crosson, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 17, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredox_DsbH domain-containing protein
B: Thioredox_DsbH domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)151,56012
Polymers150,6792
Non-polymers88210
Water55831
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-70 kcal/mol
Surface area47010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.201, 94.201, 327.726
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein Thioredox_DsbH domain-containing protein


Mass: 75339.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Brucella abortus 2308 (bacteria) / Strain: 2308 / Gene: BAB1_2064 / Plasmid: pMCSG68 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Gold / References: UniProt: Q2YR10
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.43 Å3/Da / Density % sol: 49.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: 1.0 M sodium-potassium phosphate pH 5.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 35972 / % possible obs: 95.5 % / Redundancy: 5.5 % / Biso Wilson estimate: 62.43 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.17 / Net I/σ(I): 10.3
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 5.4 % / Rmerge(I) obs: 1.181 / Mean I/σ(I) obs: 1.22 / Num. unique obs: 1622 / CC1/2: 0.402 / % possible all: 87.8

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDEphasing
MLPHAREphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.8→47.25 Å / SU ML: 0.3541 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.3655
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2622 1753 4.9 %
Rwork0.2248 34038 -
obs0.2266 35791 94.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 70.14 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9921 0 49 31 10001
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001910264
X-RAY DIFFRACTIONf_angle_d0.45313946
X-RAY DIFFRACTIONf_chiral_restr0.03611462
X-RAY DIFFRACTIONf_plane_restr0.00411849
X-RAY DIFFRACTIONf_dihedral_angle_d13.30153708
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-2.870.37321160.33382247X-RAY DIFFRACTION83.47
2.87-2.960.30621360.31292443X-RAY DIFFRACTION90.24
2.96-3.050.29471300.30022565X-RAY DIFFRACTION95.36
3.05-3.160.33761400.29912637X-RAY DIFFRACTION97.34
3.16-3.290.3641350.29472617X-RAY DIFFRACTION97.62
3.29-3.440.2921320.25352669X-RAY DIFFRACTION97.49
3.44-3.620.27251380.2322646X-RAY DIFFRACTION97.34
3.62-3.840.25711320.22162655X-RAY DIFFRACTION97.11
3.84-4.140.27711430.21552664X-RAY DIFFRACTION96.83
4.14-4.560.22131280.18292667X-RAY DIFFRACTION96.51
4.56-5.210.22041450.18892682X-RAY DIFFRACTION96.19
5.21-6.570.24921530.22432686X-RAY DIFFRACTION95.43
6.57-47.250.22121250.192860X-RAY DIFFRACTION93.78
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)
13.69837471114-1.1428029098-0.6983950197865.132940274191.494971664162.675906355240.3050874793590.4226586331470.309539448702-0.7818977717590.0151442522911-0.660108064227-0.4803708846070.234313876121-0.2962978537150.55682504986-0.04326949773390.1351878830310.807462201423-0.09391632029780.51262543355953.331195676921.1900994325123.702977556
22.032413602070.097454159643-0.2587186746421.876456957361.179608460412.110436071030.1125388291220.1121579116150.231884127371-0.204849509615-0.2227922943050.359946331505-0.313829857911-0.1960971187150.1716043350970.4105899910280.0371359988892-0.09713259561230.359936051563-0.03140443844250.36204272882522.844702739820.3346423408123.788537764
31.36751508019-0.243928053334-0.7715655231531.665807330891.356016303443.31619929585-0.02452443259360.250264833254-0.271787049204-0.089334577543-0.09939573085560.2137361804690.2570388240220.007072243269120.04046403365180.3137622194580.0644419799156-0.06334847869410.356777052082-0.06398703113130.38230649675528.23522131237.11304604023126.512424058
43.150221172690.362312157535-1.132984377661.55352008392-0.1012854382182.68867645656-0.2140208701990.0865195452656-0.5073096968420.136111380222-0.0453302670010.2532714872550.458380534913-0.2399214654010.2182535612690.4056810093010.006482026217790.04135847507530.383899209325-0.1317987999290.584877089879.2512207890711.9569902902143.996430658
53.81087657097-2.007201049930.104847471934.31974809893-1.122514815035.432197553270.10659755345-0.06584498903730.8338089000020.160308572741-0.08783690084091.82403400138-1.34059303348-0.6095651914-0.05202654073160.8866628966410.1385329669410.005060641997460.647437538296-0.1510709664111.28961218865-9.0532154077158.3834129333158.123277463
62.518270289090.0462168669702-0.03261551395531.586847256720.5104354691441.28241613216-0.00709042509410.1659933046180.1825630830210.0166893605866-0.2783980496380.751376733521-0.0279126219813-0.3997441706450.2428044950140.3792923060830.0274324479929-0.002723329940260.5583252836-0.2490944678190.735410841565-15.017943624332.4687898763155.627477318
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 3 through 151 )AA3 - 1511 - 142
22chain 'A' and (resid 152 through 307 )AA152 - 307143 - 298
33chain 'A' and (resid 308 through 551 )AA308 - 551299 - 542
44chain 'A' and (resid 552 through 665 )AA552 - 665543 - 642
55chain 'B' and (resid 3 through 118 )BD3 - 1181 - 116
66chain 'B' and (resid 119 through 622 )BD119 - 622117 - 612

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