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- PDB-3bey: Crystal structure of the protein O27018 from Methanobacterium the... -

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Basic information

Entry
Database: PDB / ID: 3bey
TitleCrystal structure of the protein O27018 from Methanobacterium thermoautotrophicum. Northeast Structural Genomics Consortium target TT217
ComponentsConserved protein O27018
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / O27018 / TT217 / MT935 / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


peroxiredoxin activity
Similarity search - Function
Alkylhydroperoxidase AhpD core / AhpD-like / Carboxymuconolactone decarboxylase-like / AhpD-like / Carboxymuconolactone decarboxylase family / AhpD-like / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMethanothermobacter thermautotrophicus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsKuzin, A.P. / Gu, J. / Xu, X. / Neely, H. / Forouhar, F. / Owens, L. / Mao, L. / Xiao, R. / Liu, J. / Baran, M.C. ...Kuzin, A.P. / Gu, J. / Xu, X. / Neely, H. / Forouhar, F. / Owens, L. / Mao, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the protein O27018 from Methanobacterium thermoautotrophicum.
Authors: Kuzin, A.P. / Gu, J. / Xu, X. / Neely, H. / Forouhar, F. / Owens, L. / Mao, L. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L.
History
DepositionNov 20, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Conserved protein O27018
B: Conserved protein O27018
C: Conserved protein O27018
D: Conserved protein O27018
E: Conserved protein O27018
F: Conserved protein O27018


Theoretical massNumber of molelcules
Total (without water)62,6196
Polymers62,6196
Non-polymers00
Water25214
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.528, 71.985, 61.418
Angle α, β, γ (deg.)90.00, 99.08, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Conserved protein O27018


Mass: 10436.505 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanothermobacter thermautotrophicus (archaea)
Strain: Delta H / Gene: MTH935 / Production host: Escherichia coli (E. coli) / References: UniProt: O27018
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 2.08 Å3/Da / Density % sol: 40.73 %
Crystal growTemperature: 293 K
Details: 0.2M CaCl2, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 23, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 20125 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 23 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 18.9
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.304 / Mean I/σ(I) obs: 3.6 / % possible all: 88.2

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Processing

Software
NameVersionClassification
CNS1.2refinement
DENZOdata reduction
SCALAdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→19.61 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 976748.25 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: ENGH & HUBER / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.258 851 4.2 %RANDOM
Rwork0.206 ---
obs0.206 17466 86.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.5919 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 40.4 Å2
Baniso -1Baniso -2Baniso -3
1-5.503 Å20 Å29.072 Å2
2---12.856 Å20 Å2
3---7.353 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 2.4→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4068 0 0 14 4082
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.09
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.3571.5
X-RAY DIFFRACTIONc_mcangle_it2.2432
X-RAY DIFFRACTIONc_scbond_it2.6322
X-RAY DIFFRACTIONc_scangle_it3.9032.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.281 134 5.4 %
Rwork0.227 2346 -
obs--74 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER.PARAMWATER.TOP

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