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- PDB-3lmb: The crystal structure of the protein OLEI01261 with unknown funct... -

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Basic information

Entry
Database: PDB / ID: 3lmb
TitleThe crystal structure of the protein OLEI01261 with unknown function from Chlorobaculum tepidum TLS
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown function / protein OLEI01261 / Chlorobaculum tepidum TLS / PSI2 / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics
Function / homologyHotdog Thioesterase / Thiol Ester Dehydrase; Chain A / Roll / Alpha Beta
Function and homology information
Biological speciesOleispira antarctica RB-8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsZhang, R. / Evdokimova, E. / Egorova, O. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: Nat Commun / Year: 2013
Title: Genome sequence and functional genomic analysis of the oil-degrading bacterium Oleispira antarctica.
Authors: Kube, M. / Chernikova, T.N. / Al-Ramahi, Y. / Beloqui, A. / Lopez-Cortez, N. / Guazzaroni, M.E. / Heipieper, H.J. / Klages, S. / Kotsyurbenko, O.R. / Langer, I. / Nechitaylo, T.Y. / ...Authors: Kube, M. / Chernikova, T.N. / Al-Ramahi, Y. / Beloqui, A. / Lopez-Cortez, N. / Guazzaroni, M.E. / Heipieper, H.J. / Klages, S. / Kotsyurbenko, O.R. / Langer, I. / Nechitaylo, T.Y. / Lunsdorf, H. / Fernandez, M. / Juarez, S. / Ciordia, S. / Singer, A. / Kagan, O. / Egorova, O. / Alain Petit, P. / Stogios, P. / Kim, Y. / Tchigvintsev, A. / Flick, R. / Denaro, R. / Genovese, M. / Albar, J.P. / Reva, O.N. / Martinez-Gomariz, M. / Tran, H. / Ferrer, M. / Savchenko, A. / Yakunin, A.F. / Yakimov, M.M. / Golyshina, O.V. / Reinhardt, R. / Golyshin, P.N.
History
DepositionJan 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 29, 2012Group: Database references / Source and taxonomy
Revision 1.3Jul 24, 2013Group: Database references
Revision 1.4Aug 7, 2013Group: Database references
Revision 1.5Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)37,6372
Polymers37,6372
Non-polymers00
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-17 kcal/mol
Surface area14880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.090, 72.962, 79.755
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 Uncharacterized protein


Mass: 18818.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Oleispira antarctica RB-8 (bacteria) / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.25 Å3/Da / Density % sol: 45.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Mg Formate, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 11, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.1→53.83 Å / Num. all: 19342 / Num. obs: 19329 / % possible obs: 99.93 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 26.43
Reflection shellResolution: 2.1→2.154 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.416 / Mean I/σ(I) obs: 2.73 / Num. unique all: 1487 / % possible all: 99.8

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
HKL-3000phasing
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→53.83 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.936 / SU B: 9.102 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.203 / ESU R Free: 0.178
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22193 1043 5.1 %RANDOM
Rwork0.16644 ---
obs0.16924 19329 99.93 %-
all-19342 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.599 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å20 Å20 Å2
2---0.34 Å20 Å2
3---0.94 Å2
Refinement stepCycle: LAST / Resolution: 2.1→53.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2555 0 0 134 2689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0250.0222631
X-RAY DIFFRACTIONr_angle_refined_deg2.0041.9583561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2715329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.48525.528123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.88815455
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.151158
X-RAY DIFFRACTIONr_chiral_restr0.1810.2388
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212008
X-RAY DIFFRACTIONr_mcbond_it1.1991.51641
X-RAY DIFFRACTIONr_mcangle_it2.26122639
X-RAY DIFFRACTIONr_scbond_it4.1163990
X-RAY DIFFRACTIONr_scangle_it6.0614.5922
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 89 -
Rwork0.18 1395 -
obs-1484 99.8 %
Refinement TLS params.Method: refined / Origin x: 10.714 Å / Origin y: 34.586 Å / Origin z: 0.184 Å
111213212223313233
T0.0708 Å2-0.0039 Å20.0063 Å2-0.0395 Å2-0.0065 Å2--0.0288 Å2
L1.481 °2-0.7631 °20.1535 °2-1.8082 °2-0.1993 °2--0.823 °2
S0.0062 Å °0.0707 Å °0.0386 Å °0.0705 Å °0.0032 Å °0.0883 Å °-0.0814 Å °-0.0443 Å °-0.0094 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 50
2X-RAY DIFFRACTION1A51 - 100
3X-RAY DIFFRACTION1A101 - 164
4X-RAY DIFFRACTION1B2 - 50
5X-RAY DIFFRACTION1B51 - 100
6X-RAY DIFFRACTION1B101 - 164

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