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- PDB-1lql: Crystal structure of OsmC like protein from Mycoplasma pneumoniae -

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Basic information

Entry
Database: PDB / ID: 1lql
TitleCrystal structure of OsmC like protein from Mycoplasma pneumoniae
Componentsosmotical inducible protein C like family
KeywordsUNKNOWN FUNCTION / OsmC / New Fold / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / peroxidase activity / cytoplasm
Similarity search - Function
OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / K homology (KH) domain / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / GMP Synthetase; Chain A, domain 3 / Single Sheet / K homology domain-like, alpha/beta / 2-Layer Sandwich ...OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / K homology (KH) domain / N-terminal domain of TfIIb - #10 / N-terminal domain of TfIIb / GMP Synthetase; Chain A, domain 3 / Single Sheet / K homology domain-like, alpha/beta / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Hydroperoxide reductase
Similarity search - Component
Biological speciesMycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.85 Å
AuthorsChoi, I.-G. / Shin, D.H. / Brandsen, J. / Jancarik, J. / Kim, R. / Yokota, H. / Kim, S.-H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2003
Title: Crystal structure of a stress inducible protein from Mycoplasma pneumoniae at 2.85 A resolution
Authors: Choi, I.-G. / Shin, D.H. / Brandsen, J. / Jancarik, J. / Busso, D. / Yokota, H. / Kim, R. / Kim, S.-H.
History
DepositionMay 10, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: osmotical inducible protein C like family
B: osmotical inducible protein C like family
C: osmotical inducible protein C like family
D: osmotical inducible protein C like family
E: osmotical inducible protein C like family
F: osmotical inducible protein C like family
G: osmotical inducible protein C like family
H: osmotical inducible protein C like family
I: osmotical inducible protein C like family
J: osmotical inducible protein C like family


Theoretical massNumber of molelcules
Total (without water)184,73910
Polymers184,73910
Non-polymers00
Water3,945219
1
A: osmotical inducible protein C like family
B: osmotical inducible protein C like family


Theoretical massNumber of molelcules
Total (without water)36,9482
Polymers36,9482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-54 kcal/mol
Surface area13170 Å2
MethodPISA
2
C: osmotical inducible protein C like family
D: osmotical inducible protein C like family


Theoretical massNumber of molelcules
Total (without water)36,9482
Polymers36,9482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-54 kcal/mol
Surface area14430 Å2
MethodPISA
3
E: osmotical inducible protein C like family
F: osmotical inducible protein C like family


Theoretical massNumber of molelcules
Total (without water)36,9482
Polymers36,9482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-54 kcal/mol
Surface area13830 Å2
MethodPISA
4
G: osmotical inducible protein C like family
H: osmotical inducible protein C like family


Theoretical massNumber of molelcules
Total (without water)36,9482
Polymers36,9482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6080 Å2
ΔGint-55 kcal/mol
Surface area13180 Å2
MethodPISA
5
I: osmotical inducible protein C like family
J: osmotical inducible protein C like family


Theoretical massNumber of molelcules
Total (without water)36,9482
Polymers36,9482
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6310 Å2
ΔGint-55 kcal/mol
Surface area13870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.360, 95.600, 308.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
osmotical inducible protein C like family / OsmC


Mass: 18473.908 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
Production host: Escherichia coli (E. coli) / References: UniProt: P75170
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.7 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, sodium iodide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112.9 mg/mlprotein1drop
220 mMTris1droppH7.5
31 mMEDTA1drop
41 mMdithiothreitol1drop
5300 mM1dropNaCl
60.2 Msodium iodide1reservoirpH6.9
720 %PEG33501reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 2.85→20 Å / Num. obs: 90144 / % possible obs: 99.9 % / Redundancy: 5 % / Biso Wilson estimate: 62.4 Å2 / Rsym value: 0.091 / Net I/σ(I): 23.7
Reflection shellResolution: 2.85→2.92 Å / Redundancy: 5.1 % / Mean I/σ(I) obs: 4.1 / Rsym value: 0.391 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 20 Å / Redundancy: 5 % / Rmerge(I) obs: 0.091
Reflection shell
*PLUS
% possible obs: 99.9 % / Num. unique obs: 6014 / Rmerge(I) obs: 0.391

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 2.85→19.91 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 75248.24 / Data cutoff high rms absF: 75248.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.276 4433 10.1 %RANDOM
Rwork0.217 ---
all0.2252 45795 --
obs0.219 44034 94.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.6029 Å2 / ksol: 0.2893301 e/Å3
Displacement parametersBiso mean: 50.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2--10.87 Å20 Å2
3----11.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.4 Å
Refinement stepCycle: LAST / Resolution: 2.85→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11038 0 0 219 11257
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_mcbond_it5.761.5
X-RAY DIFFRACTIONc_mcangle_it9.132
X-RAY DIFFRACTIONc_scbond_it8.962
X-RAY DIFFRACTIONc_scangle_it13.212.5
LS refinement shellResolution: 2.85→3.03 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.352 656 10 %
Rwork0.298 5930 -
obs--85.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Refinement
*PLUS
Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.87

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