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- PDB-6bkv: Crystal structure of Thioredoxin from Helicobacter pylori (strain G27) -

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Basic information

Entry
Database: PDB / ID: 6bkv
TitleCrystal structure of Thioredoxin from Helicobacter pylori (strain G27)
ComponentsThioredoxin
KeywordsELECTRON TRANSPORT / SSGCID / Helicobacter pylori / thioredoxin / trxA / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


glycerol ether metabolic process / protein-disulfide reductase activity / cell redox homeostasis
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin / Thioredoxin
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of Thioredoxin from Helicobacter pylori (strain G27)
Authors: Abendroth, J. / Dranow, D.M. / Lorimer, D.D. / Edwards, T.E.
History
DepositionNov 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin
B: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)25,7982
Polymers25,7982
Non-polymers00
Water90150
1
A: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)12,8991
Polymers12,8991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin


Theoretical massNumber of molelcules
Total (without water)12,8991
Polymers12,8991
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.160, 93.160, 78.050
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid -2 through 8 or (resid 9...
21(chain B and (resid -2 through 61 or (resid 62...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11HISHISTHRTHR(chain A and (resid -2 through 8 or (resid 9...AA-2 - 86 - 16
12GLUGLUGLUGLU(chain A and (resid -2 through 8 or (resid 9...AA917
13HISHISLEULEU(chain A and (resid -2 through 8 or (resid 9...AA-2 - 1056 - 113
14HISHISLEULEU(chain A and (resid -2 through 8 or (resid 9...AA-2 - 1056 - 113
15HISHISLEULEU(chain A and (resid -2 through 8 or (resid 9...AA-2 - 1056 - 113
16HISHISLEULEU(chain A and (resid -2 through 8 or (resid 9...AA-2 - 1056 - 113
21HISHISGLNGLN(chain B and (resid -2 through 61 or (resid 62...BB-2 - 616 - 69
22GLUGLUGLUGLU(chain B and (resid -2 through 61 or (resid 62...BB62 - 6370 - 71
23HISHISLEULEU(chain B and (resid -2 through 61 or (resid 62...BB-4 - 1054 - 113
24HISHISLEULEU(chain B and (resid -2 through 61 or (resid 62...BB-4 - 1054 - 113
25HISHISLEULEU(chain B and (resid -2 through 61 or (resid 62...BB-4 - 1054 - 113
26HISHISLEULEU(chain B and (resid -2 through 61 or (resid 62...BB-4 - 1054 - 113

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Components

#1: Protein Thioredoxin


Mass: 12898.868 Da / Num. of mol.: 2 / Fragment: HepyC.00029.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Gene: BV499_05595, BZK25_01255, BZK28_00485, HPY207_04265 / Plasmid: HepyC.00029.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0B2EU35, UniProt: P66928*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 50 / Source method: isolated from a natural source / Formula: H2O

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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: 3.8 Å3/Da / Density % sol: 67.6 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Microlytic MCSG1 screen, E12: 2.4 mM sodium malonate, 24.59 mg/mL HepyC.00029.a.B1.PS38229, cryoprotectant: direct, tray 290729 E12, puck BYM2-1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 2, 2017
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.35→40.339 Å / Num. obs: 16569 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 5.563 % / Biso Wilson estimate: 60.02 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.046 / Rrim(I) all: 0.05 / Χ2: 1.007 / Net I/σ(I): 20.13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.35-2.415.7130.5572.711970.8860.61398.8
2.41-2.485.670.4733.1711700.9190.5299.2
2.48-2.555.6880.3444.411370.9470.37899.1
2.55-2.635.6680.2845.2811190.9660.31299.3
2.63-2.715.6540.2186.7510940.9790.2499.5
2.71-2.815.6440.1758.5910480.9850.19399.4
2.81-2.915.6650.12611.8910040.9930.13899.4
2.91-3.035.6060.08916.019880.9950.09999.5
3.03-3.175.6270.07120.269200.9960.07899.7
3.17-3.325.5880.0625.029130.9970.06699.7
3.32-3.55.5570.04930.738530.9980.05399.6
3.5-3.725.5310.04334.338120.9980.04799.4
3.72-3.975.5160.03838.887640.9980.04299.5
3.97-4.295.4370.03639.197120.9980.03999.4
4.29-4.75.4550.03441.956680.9980.03899.3
4.7-5.255.3890.03442.046060.9990.03799.7
5.25-6.075.3190.03241.155420.9980.03599.6
6.07-7.435.2760.03341.54490.9980.03698.9
7.43-10.515.090.03242.663670.9960.03798.1
10.51-40.3394.5390.03440.492060.9970.03890.7

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
MoRDaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2ynxA

Resolution: 2.35→40.339 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.34
RfactorNum. reflection% reflectionSelection details
Rfree0.2024 1670 10.08 %0, RANDOM
Rwork0.1751 ---
obs0.1779 16566 99.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 164.2 Å2 / Biso mean: 76.3428 Å2 / Biso min: 40.79 Å2
Refinement stepCycle: final / Resolution: 2.35→40.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1649 0 0 50 1699
Biso mean---66.38 -
Num. residues----218
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A986X-RAY DIFFRACTION3.191TORSIONAL
12B986X-RAY DIFFRACTION3.191TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3501-2.41920.31621230.26971225134899
2.4192-2.49730.27421320.24771233136599
2.4973-2.58660.28831400.24161239137999
2.5866-2.69010.31331400.25331196133699
2.6901-2.81250.30831520.264612161368100
2.8125-2.96070.29241480.247312171365100
2.9607-3.14620.25171160.225612571373100
3.1462-3.3890.28751530.212212371390100
3.389-3.72980.19181480.18041233138199
3.7298-4.2690.16911640.138412321396100
4.269-5.37650.1461230.124812831406100
5.3765-40.34540.15971310.15781328145998
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)
17.7522-0.23822.90378.9558-0.1337.7987-0.0240.28740.49480.09560.22040.83480.6427-0.6025-0.21160.6755-0.2326-0.08510.57540.02370.834937.1304-24.65421.9734
27.96792.8151-0.94315.43710.70894.84350.21230.1990.07960.7463-0.3019-0.05190.3222-0.2370.09890.5983-0.16370.0210.4257-0.07210.510631.4124-32.27691.6395
35.51341.78113.24626.51170.32656.33890.683-1.1921-0.01481.2222-0.79170.42250.5459-0.71260.13030.9403-0.33430.17060.6767-0.08890.629225.2137-34.55210.7999
47.36881.4632-2.68824.3564.31857.6767-0.11140.17660.62342.0143-0.22370.57251.5362-1.57410.17611.2331-0.23210.27660.65520.02150.709542.15333.12235.7938
54.09520.64392.60366.06487.31139.6336-0.41210.0867-0.0036-1.8404-0.0889-0.1647-0.1802-0.9615-0.29961.3976-0.35610.03430.6575-0.02490.673245.1372-3.2252-10.6236
67.28290.2169-2.8593.7222-0.85347.437-0.06750.92150.5424-1.71080.63670.5802-0.1086-0.6482-0.51180.8523-0.1744-0.09660.49150.01610.842743.9726-9.8561-5.9937
78.064-3.81490.65464.2587-0.3037.6888-0.2185-0.05740.7070.25310.59770.09-0.0945-0.1599-0.33530.6464-0.0566-0.12610.36980.02310.749843.4927-10.34645.7097
85.02511.12-1.08669.5227-0.1825.2847-0.19650.6485-0.4581-1.71070.49160.1380.247-0.1024-0.25650.7908-0.1626-0.080.4221-0.10480.59344.3365-15.8517-4.1638
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 19 )A-2 - 19
2X-RAY DIFFRACTION2chain 'A' and (resid 20 through 82 )A20 - 82
3X-RAY DIFFRACTION3chain 'A' and (resid 83 through 105 )A83 - 105
4X-RAY DIFFRACTION4chain 'B' and (resid -4 through 5 )B-4 - 5
5X-RAY DIFFRACTION5chain 'B' and (resid 6 through 10 )B6 - 10
6X-RAY DIFFRACTION6chain 'B' and (resid 11 through 30 )B11 - 30
7X-RAY DIFFRACTION7chain 'B' and (resid 31 through 51 )B31 - 51
8X-RAY DIFFRACTION8chain 'B' and (resid 52 through 105 )B52 - 105

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