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- PDB-4je1: Crystal structure of thiol peroxidase from BURKHOLDERIA CENOCEPAC... -

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Basic information

Entry
Database: PDB / ID: 4je1
TitleCrystal structure of thiol peroxidase from BURKHOLDERIA CENOCEPACIA J2315
ComponentsProbable thiol peroxidase
KeywordsOXIDOREDUCTASE / SSGCID / THIOL PEROXIDASE / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / 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 speciesBurkholderia cenocepacia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: To be Published
Title: Crystal structure of thiol peroxidase from BURKHOLDERIA CENOCEPACIA J2315
Authors: SSGCID / Davies, D.R. / Abendroth, J.A. / Clifton, M.C. / Edwards, T. / Lorimer, D.
History
DepositionFeb 26, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1May 25, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable thiol peroxidase
B: Probable thiol peroxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,6123
Polymers36,5492
Non-polymers621
Water8,575476
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-9 kcal/mol
Surface area14520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.910, 44.290, 53.080
Angle α, β, γ (deg.)88.13, 101.34, 115.10
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Probable thiol peroxidase


Mass: 18274.725 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia cenocepacia (bacteria) / Strain: J2315 / Gene: tpx, BceJ2315_33620, BCAL3424 / Plasmid: BG1861 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: B4E5V4, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 476 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.56 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: EBS INTERNAL TRACKING NUMBER HEPES (PH 7.0), 500 MM NACL, 2 MM DTT, 0.025% SODIUM AZIDE, 5% GLYCEROL, 0.4 UL X 0.4 UL DROP WITH 200 MM AMMONIUM NITRATE, 20% (W/V) PEG 3350. 20% ETHYLENE ...Details: EBS INTERNAL TRACKING NUMBER HEPES (PH 7.0), 500 MM NACL, 2 MM DTT, 0.025% SODIUM AZIDE, 5% GLYCEROL, 0.4 UL X 0.4 UL DROP WITH 200 MM AMMONIUM NITRATE, 20% (W/V) PEG 3350. 20% ETHYLENE GLYCOL CRYOPROTECTANT, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.283619 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 16, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.283619 Å / Relative weight: 1
ReflectionResolution: 1.4→30 Å / Num. obs: 61735

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Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.7.0032refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→19.67 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.496 / SU ML: 0.032 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.054 / ESU R Free: 0.055 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.171 3127 5.1 %RANDOM
Rwork0.151 ---
obs0.152 61735 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 11.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20.06 Å2-0.35 Å2
2---0.15 Å2-0.04 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.4→19.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2441 0 4 476 2921
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0192569
X-RAY DIFFRACTIONr_bond_other_d0.0010.022478
X-RAY DIFFRACTIONr_angle_refined_deg1.3371.9643537
X-RAY DIFFRACTIONr_angle_other_deg0.7253.0025684
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9845364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.69524.63295
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.11815378
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9711512
X-RAY DIFFRACTIONr_chiral_restr0.0750.2443
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213003
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02553
X-RAY DIFFRACTIONr_mcbond_it0.5380.5461389
X-RAY DIFFRACTIONr_mcbond_other0.5310.5451388
X-RAY DIFFRACTIONr_mcangle_it0.9580.8171740
LS refinement shellResolution: 1.4→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.219 205 -
Rwork0.187 4327 -
obs--98.27 %
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)
13.14761.4546-1.969714.9323-1.35831.25640.3810.0692-0.01010.5368-0.3871-0.2838-0.26860.00690.00610.0868-0.06840.00360.1554-0.01730.0111.5447-39.1283-38.2072
23.64890.56291.10821.0408-0.80942.3170.05430.0199-0.06860.0462-0.0590.06830.03090.04120.00470.06930.0225-0.00340.02860.00250.040920.5032-24.4014-26.5481
30.0538-0.0770.0220.21740.18570.48190.0014-0.0031-0.0044-0.0164-0.0010.0209-0.01810.0093-0.00050.0459-0.0017-0.00220.04180.00220.048812.6919-8.769-35.7533
41.5974-0.59711.48031.1646-0.57144.57990.03880.0745-0.0197-0.0286-0.0651-0.0107-0.19320.08770.02630.0612-0.0041-0.00690.0355-0.00180.033415.5341-15.7155-47.5741
51.16120.21561.65383.2165-0.42052.52260.008-0.04110.02390.0837-0.01650.1193-0.0136-0.05770.00860.05550.0198-0.01690.03390.00370.0536.3615.8242-15.5648
60.10370.14310.1580.2850.18550.25460.01150.0035-0.00530.017-0.0029-0.02460.0170.0121-0.00860.04980.00560.00640.05010.00630.039519.75231.6665-9.8683
70.09540.01260.07870.19820.07030.2414-0.00080.0045-0.01640.00770.00140.0047-0.01690.0215-0.00050.04690.00230.00120.04910.00510.047820.78993.3695-11.2441
83.3328-0.27392.81420.553-0.22322.37860.02020.2001-0.02820.0399-0.0005-0.03370.00380.1665-0.01970.05280.0069-0.00020.0512-0.0060.038322.190114.4081-6.9257
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-6 - 1
2X-RAY DIFFRACTION2A2 - 11
3X-RAY DIFFRACTION3A12 - 155
4X-RAY DIFFRACTION4A156 - 167
5X-RAY DIFFRACTION5B2 - 9
6X-RAY DIFFRACTION6B10 - 64
7X-RAY DIFFRACTION7B65 - 152
8X-RAY DIFFRACTION8B153 - 167

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