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- PDB-1q98: Structure of a Thiol Peroxidase from Haemophilus influenzae Rd -

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Basic information

Entry
Database: PDB / ID: 1q98
TitleStructure of a Thiol Peroxidase from Haemophilus influenzae Rd
ComponentsThiol Peroxidase
KeywordsOXIDOREDUCTASE / structural genomics / tpx / peroxidase / NYSGXRC / T1429 / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
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 speciesHaemophilus influenzae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS ON HG / Resolution: 1.9 Å
AuthorsKniewel, R. / Buglino, J. / Solorzano, V. / Wu, J. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Structure of a Thiol Peroxidase from Haemophilus influenzae Rd
Authors: Kniewel, R. / Buglino, J. / Solorzano, V. / Wu, J. / Lima, C.D.
History
DepositionAug 22, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiol Peroxidase
B: Thiol Peroxidase


Theoretical massNumber of molelcules
Total (without water)35,2822
Polymers35,2822
Non-polymers00
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-10 kcal/mol
Surface area13850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.033, 43.667, 104.587
Angle α, β, γ (deg.)90.00, 97.34, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#1: Protein Thiol Peroxidase / E.C.1.11.1.- / Tpx


Mass: 17640.990 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Haemophilus influenzae (bacteria) / Gene: tpx, HI0751 / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3
References: UniProt: Q57549, Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.07 Å3/Da / Density % sol: 40.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 19-24% PEGv 4000, 0.1M Ammonium Acetate, 0.1M Sodium Acetate pH 4.5, 5%Ethylene Glycol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9798 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 27, 2003
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. all: 24969 / Num. obs: 24220 / % possible obs: 97 % / Observed criterion σ(I): -3 / Redundancy: 4 % / Biso Wilson estimate: 26.6 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 7.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4 % / Rmerge(I) obs: 0.162 / Num. unique all: 2399 / % possible all: 96.4

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNS1.1refinement
RefinementMethod to determine structure: SIRAS ON HG / Resolution: 1.9→18.91 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.267 1203 5 %RANDOM
Rwork0.225 ---
obs0.2251 23960 95.7 %-
all-24969 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.7964 Å2 / ksol: 0.372079 e/Å3
Displacement parametersBiso mean: 37.6 Å2
Baniso -1Baniso -2Baniso -3
1-5.91 Å20 Å2-9.31 Å2
2---0.3 Å20 Å2
3----5.6 Å2
Refine analyzeLuzzati coordinate error free: 0.3 Å / Luzzati sigma a free: 0.2 Å
Refinement stepCycle: LAST / Resolution: 1.9→18.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2464 0 0 275 2739
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.42
X-RAY DIFFRACTIONc_scbond_it2.052
X-RAY DIFFRACTIONc_scangle_it3.012.5
LS refinement shellResolution: 1.9→2.02 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 194 5 %
Rwork0.274 3654 -
obs--93.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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