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- PDB-3t8k: The crystal structure of a functionally unknown protein Lebu_0176... -

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Basic information

Entry
Database: PDB / ID: 3t8k
TitleThe crystal structure of a functionally unknown protein Lebu_0176 from Leptotrichia buccalis C-1013-b
Componentsuncharacterized protein
KeywordsStructural Genomics / Unknown Function / PSI-Biology / protein structure initiative / midwest center f or structural genomics / MCSG / Midwest Center for Structural Genomics / alpha-hairpin repeat (Ankyrin repeat) fold
Function / homologyAnkyrin repeat-containing domain / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha / Uncharacterized protein
Function and homology information
Biological speciesLeptotrichia buccalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.769 Å
AuthorsTan, K. / Bigelow, L. / Bearden, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a functionally unknown protein Lebu_0176 from Leptotrichia buccalis C-1013-b
Authors: Tan, K. / Bigelow, L. / Bearden, J. / Joachimiak, A.
History
DepositionAug 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 27, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: uncharacterized protein
B: uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)43,5422
Polymers43,5422
Non-polymers00
Water5,855325
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-8 kcal/mol
Surface area17130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.193, 101.019, 108.184
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsExperimentally unknown. It is predicted that the A and B chains form a dimer.

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Components

#1: Protein uncharacterized protein


Mass: 21771.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leptotrichia buccalis (bacteria) / Strain: C-1013-b / Gene: Lebu_0176 / Plasmid: pMCSG48 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: C7NDE2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 0.2M Ammonium Chloride, 20% (w/v) PEG 3350, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 31, 2011 / Details: Mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.769→34 Å / Num. all: 38999 / Num. obs: 38999 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.104 / Net I/σ(I): 39.6
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 1939 / % possible all: 98.7

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.769→33.962 Å / SU ML: 0.38 / σ(F): 1.37 / Phase error: 21.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2152 1951 5.01 %random
Rwork0.1787 ---
all0.1805 38932 --
obs0.1805 38932 98.01 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.463 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.0267 Å2-0 Å20 Å2
2---8.3136 Å2-0 Å2
3---6.2869 Å2
Refinement stepCycle: LAST / Resolution: 1.769→33.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2986 0 0 325 3311
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073061
X-RAY DIFFRACTIONf_angle_d1.0274114
X-RAY DIFFRACTIONf_dihedral_angle_d14.3541166
X-RAY DIFFRACTIONf_chiral_restr0.068455
X-RAY DIFFRACTIONf_plane_restr0.004514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7687-1.8130.29111250.25682413X-RAY DIFFRACTION90
1.813-1.8620.28181520.22682529X-RAY DIFFRACTION98
1.862-1.91680.28031460.21072641X-RAY DIFFRACTION98
1.9168-1.97860.25141390.18772567X-RAY DIFFRACTION98
1.9786-2.04940.21611420.17592592X-RAY DIFFRACTION98
2.0494-2.13140.21851330.17112649X-RAY DIFFRACTION98
2.1314-2.22840.20771300.16672602X-RAY DIFFRACTION98
2.2284-2.34580.20331420.16942643X-RAY DIFFRACTION99
2.3458-2.49280.2431550.17662638X-RAY DIFFRACTION99
2.4928-2.68520.23381430.1932666X-RAY DIFFRACTION99
2.6852-2.95520.23031360.18632721X-RAY DIFFRACTION100
2.9552-3.38250.21551300.18922736X-RAY DIFFRACTION100
3.3825-4.26030.17841470.16122743X-RAY DIFFRACTION100
4.2603-33.96850.19451310.16832841X-RAY DIFFRACTION97
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)
10.48550.5534-0.13792.2351-0.98151.19370.02050.0155-0.1132-0.10220.0222-0.2938-0.150.0898-0.00590.229-0.07570.08170.1649-0.03270.16589.7401-10.554767.463
21.440.5247-0.14681.70420.19431.31840.02880.0405-0.02690.1378-0.0349-0.070.15910.01760.00910.0297-0.0012-0.00730.07480.00370.0632.9956-7.742890.1767
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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