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- PDB-6udg: Crystal structure of a Probable thiol peroxidase from Elizabethki... -

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Basic information

Entry
Database: PDB / ID: 6udg
TitleCrystal structure of a Probable thiol peroxidase from Elizabethkingia anophelis NUHP1
ComponentsThiol peroxidase
KeywordsOXIDOREDUCTASE / SSGCID / Structural Genomics / Elizabethkingia anophelis / tpx / Thiol peroxidase / Seattle Structural Genomics Center for Infectious Disease
Function / homology
Function and homology information


thioredoxin-dependent peroxiredoxin / thioredoxin peroxidase activity
Similarity search - Function
Thiol peroxidase Tpx / Thiol peroxidase conserved site / Tpx family signature. / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily ...Thiol peroxidase Tpx / Thiol peroxidase conserved site / Tpx family signature. / Redoxin / Redoxin / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesElizabethkingia anophelis NUHP1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: TO BE PUBLISHED
Title: Crystal structure of a Probable thiol peroxidase from Elizabethkingia anophelis NUHP1
Authors: Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.
History
DepositionSep 19, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 16, 2019Provider: 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: Thiol peroxidase
B: Thiol peroxidase
C: Thiol peroxidase
D: Thiol peroxidase


Theoretical massNumber of molelcules
Total (without water)74,3714
Polymers74,3714
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-31 kcal/mol
Surface area25570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.590, 107.800, 113.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 or (resid 6 through 7...
21(chain B and (resid 5 through 13 or (resid 14...
31(chain C and (resid 5 through 13 or (resid 14...
41(chain D and (resid 5 through 8 or (resid 9...

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
11THRTHRTHRTHR(chain A and (resid 5 or (resid 6 through 7...AA513
12LEULEULYSLYS(chain A and (resid 5 or (resid 6 through 7...AA6 - 714 - 15
13ASNASNLYSLYS(chain A and (resid 5 or (resid 6 through 7...AA3 - 16511 - 173
14ASNASNLYSLYS(chain A and (resid 5 or (resid 6 through 7...AA3 - 16511 - 173
15ASNASNLYSLYS(chain A and (resid 5 or (resid 6 through 7...AA3 - 16511 - 173
21THRTHRTHRTHR(chain B and (resid 5 through 13 or (resid 14...BB5 - 1313 - 21
22VALVALVALVAL(chain B and (resid 5 through 13 or (resid 14...BB1422
23THRTHRLYSLYS(chain B and (resid 5 through 13 or (resid 14...BB5 - 16513 - 173
31THRTHRTHRTHR(chain C and (resid 5 through 13 or (resid 14...CC5 - 1313 - 21
32VALVALVALVAL(chain C and (resid 5 through 13 or (resid 14...CC1422
33ILEILELYSLYS(chain C and (resid 5 through 13 or (resid 14...CC4 - 16512 - 173
34ILEILELYSLYS(chain C and (resid 5 through 13 or (resid 14...CC4 - 16512 - 173
35ILEILELYSLYS(chain C and (resid 5 through 13 or (resid 14...CC4 - 16512 - 173
36ILEILELYSLYS(chain C and (resid 5 through 13 or (resid 14...CC4 - 16512 - 173
41THRTHRGLYGLY(chain D and (resid 5 through 8 or (resid 9...DD5 - 813 - 16
42ASNASNILEILE(chain D and (resid 5 through 8 or (resid 9...DD9 - 1117 - 19
43ILEILELYSLYS(chain D and (resid 5 through 8 or (resid 9...DD4 - 16512 - 173
44ILEILELYSLYS(chain D and (resid 5 through 8 or (resid 9...DD4 - 16512 - 173
45ILEILELYSLYS(chain D and (resid 5 through 8 or (resid 9...DD4 - 16512 - 173
46ILEILELYSLYS(chain D and (resid 5 through 8 or (resid 9...DD4 - 16512 - 173

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Components

#1: Protein
Thiol peroxidase / Tpx / Peroxiredoxin tpx / Prx / Thioredoxin peroxidase


Mass: 18592.791 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Elizabethkingia anophelis NUHP1 (bacteria)
Gene: tpx, BD94_2659 / Plasmid: ElanA.00055.a.B1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21(DE3) / References: UniProt: A0A077EJK0, peroxiredoxin
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.21 Å3/Da / Density % sol: 44.39 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Anatrace Morpheus screen, well g8: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD: 20mM of each sodium formate, ammonium acetate, trisodium citrate, sodium potassium Ltartrate, sodium ...Details: Anatrace Morpheus screen, well g8: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD: 20mM of each sodium formate, ammonium acetate, trisodium citrate, sodium potassium Ltartrate, sodium oxamate: 100mM MOPS/HEPES-Na pH 7.5: ElanA.00055.a.B1, PW38308, at 23mg/ml: cryo: direct: tray 294018 g8: puck xoe2-6.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Nov 24, 2017
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.65→48.7 Å / Num. obs: 19753 / % possible obs: 99.7 % / Redundancy: 4.84 % / Biso Wilson estimate: 64.797 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.07 / Rrim(I) all: 0.078 / Χ2: 0.991 / Net I/σ(I): 14.18 / Num. measured all: 95601 / Scaling rejects: 4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.65-2.724.9830.6182.847131143414310.8820.69399.8
2.72-2.794.9830.5013.397056141714160.9080.56299.9
2.79-2.874.9790.4523.746682134313420.9180.50799.9
2.87-2.964.9680.3364.966632133713350.9620.37799.9
2.96-3.064.9380.2576.026330128512820.9740.28999.8
3.06-3.174.9540.1987.486262126712640.9830.22299.8
3.17-3.294.910.1668.435809118311830.9860.187100
3.29-3.424.9130.12810.755674115611550.9920.14399.9
3.42-3.574.9130.09213.75596114011390.9960.10399.9
3.57-3.754.8680.07316.75121105510520.9970.08299.7
3.75-3.954.820.06518.564940102510250.9970.073100
3.95-4.194.7910.05620.7946289689660.9970.06399.8
4.19-4.484.7260.04723.7443869349280.9980.05299.4
4.48-4.844.7560.04427.1840098478430.9980.04999.5
4.84-5.34.7080.04127.9336637817780.9970.04699.6
5.3-5.934.6920.04427.4934257327300.9980.04999.7
5.93-6.844.5660.04129.2929046396360.9980.04699.5
6.84-8.384.4850.03532.2824715545510.9980.0499.5
8.38-11.854.2890.03536.0118834434390.9980.03999.1
11.85-48.73.8720.03433.989992702580.9990.03895.6

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement
PDB_EXTRACT3.25data extraction
MoRDaphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4je1A

Resolution: 2.65→48.7 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.8
RfactorNum. reflection% reflection
Rfree0.2805 2096 10.63 %
Rwork0.2095 --
obs0.2171 19723 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 206.73 Å2 / Biso mean: 80.7365 Å2 / Biso min: 38.83 Å2
Refinement stepCycle: final / Resolution: 2.65→48.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4546 0 0 11 4557
Biso mean---56.5 -
Num. residues----648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0044612
X-RAY DIFFRACTIONf_angle_d0.7336327
X-RAY DIFFRACTIONf_dihedral_angle_d13.4492738
X-RAY DIFFRACTIONf_chiral_restr0.048775
X-RAY DIFFRACTIONf_plane_restr0.006859
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2619X-RAY DIFFRACTION12.011TORSIONAL
12B2619X-RAY DIFFRACTION12.011TORSIONAL
13C2619X-RAY DIFFRACTION12.011TORSIONAL
14D2619X-RAY DIFFRACTION12.011TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.65-2.710.40761510.35411511302100
2.71-2.780.43651460.326211201266100
2.78-2.850.42751500.314211651315100
2.85-2.940.38311180.291411611279100
2.94-3.030.41151400.28551151129199
3.03-3.140.41831350.270311671302100
3.14-3.270.31991390.265111541293100
3.27-3.420.33191020.24212031305100
3.42-3.60.30631320.208311931325100
3.6-3.820.25681550.20111531308100
3.82-4.120.32761160.195612001316100
4.12-4.530.22531700.1681142131299
4.53-5.190.23661380.160811971335100
5.19-6.530.22851560.209411971353100
6.53-48.70.22531480.16861273142198
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)
14.5441-1.58210.14033.06870.99354.0256-0.1512-0.16690.44890.06860.11450.2444-0.1719-0.23160.0720.38850.01410.05150.43630.02980.7449-15.23669.1545-27.6511
22.77930.41510.35995.9109-0.86585.657-0.1348-0.3619-0.62310.39290.2524-0.02080.18780.0999-0.17080.45820.08850.08260.45490.05240.65559.812428.2507-16.4513
33.47650.4837-0.52063.475-1.83766.263-0.27620.52610.3-0.84530.45180.79970.0387-0.3571-0.17480.6632-0.143-0.11830.54990.13120.76095.989936.3675-45.6495
45.3304-1.8524-0.79331.92270.6431.43320.10260.3425-0.0864-0.38080.0801-0.69690.00630.2465-0.2080.5277-0.0780.15260.5174-0.16320.957310.06760.448-42.8723
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 3 through 165)A3 - 165
2X-RAY DIFFRACTION2(chain 'B' and resid 5 through 165)B5 - 165
3X-RAY DIFFRACTION3(chain 'C' and resid 4 through 165)C4 - 165
4X-RAY DIFFRACTION4(chain 'D' and resid 4 through 165)D4 - 165

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