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- PDB-3edp: The crystal structure of the protein lin2111 (functionally unknow... -

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Basic information

Entry
Database: PDB / ID: 3edp
TitleThe crystal structure of the protein lin2111 (functionally unknown) from Listeria innocua Clip11262
ComponentsLin2111 protein
Keywordsstructural genomics / unknown function / APC88337 / lin2111 / Listeria innocua Clip11262 / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG / DNA-binding / Transcription / Transcription regulation
Function / homology
Function and homology information


DNA-binding transcription factor activity / DNA binding
Similarity search - Function
UbiC transcription regulator-associated / UTRA domain / : / Chorismate lyase / Chorismate lyase-like / Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor ...UbiC transcription regulator-associated / UTRA domain / : / Chorismate lyase / Chorismate lyase-like / Chorismate pyruvate-lyase/UbiC transcription regulator-associated domain superfamily / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.092 Å
AuthorsTan, K. / Gu, M. / Jaurequi, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the protein lin2111 (functionally unknown) from Listeria innocua Clip11262
Authors: Tan, K. / Gu, M. / Jaurequi, L. / Joachimiak, A.
History
DepositionSep 3, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 20, 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_site
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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lin2111 protein
B: Lin2111 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,5499
Polymers54,9042
Non-polymers6457
Water2,684149
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-14 kcal/mol
Surface area23640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.345, 66.620, 100.751
Angle α, β, γ (deg.)90.00, 95.03, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAuthors state that the biological unit is experimentally unknown. The chains A and B are predicted to form a dimer.

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Components

#1: Protein Lin2111 protein


Mass: 27452.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Strain: Clip11262 / Gene: lin2111 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q92A11
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 3.07 Å3/Da / Density % sol: 59.88 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1M Tri-sodium citrate 0.1M Sodium cacodylate, pH 6.5, 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 315 / Detector: CCD / Date: Aug 4, 2008 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.092→43.4 Å / Num. obs: 75991 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 34.67 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 20.6
Reflection shellResolution: 2.1→2.14 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.825 / Mean I/σ(I) obs: 1.6 / Num. unique all: 1888 / % possible all: 99.3

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
RESOLVEmodel building
HKL-3000phasing
PHENIX(phenix.refine)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.092→43.367 Å / SU ML: 0.31 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2424 3838 5.05 %random
Rwork0.1999 ---
all0.2021 75991 --
obs0.2021 75991 98.74 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.922 Å2 / ksol: 0.395 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.6919 Å20 Å20.0706 Å2
2--10.6469 Å20 Å2
3----9.955 Å2
Refinement stepCycle: LAST / Resolution: 2.092→43.367 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3594 0 42 149 3785
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_refined_d0.005
X-RAY DIFFRACTIONf_angle_refined_deg0.879
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.092-2.11850.29561120.30692192X-RAY DIFFRACTION81
2.1185-2.14640.34691500.29562600X-RAY DIFFRACTION97
2.1464-2.17580.30721100.28232651X-RAY DIFFRACTION98
2.1758-2.20680.32721640.27412677X-RAY DIFFRACTION99
2.2068-2.23980.34061290.27042720X-RAY DIFFRACTION99
2.2398-2.27480.29441510.26092717X-RAY DIFFRACTION99
2.2748-2.31210.26751500.26072635X-RAY DIFFRACTION99
2.3121-2.35190.28721450.23022703X-RAY DIFFRACTION100
2.3519-2.39470.31981200.24072783X-RAY DIFFRACTION100
2.3947-2.44080.27351550.2212603X-RAY DIFFRACTION100
2.4408-2.49060.33721290.23672734X-RAY DIFFRACTION100
2.4906-2.54470.28111210.2192736X-RAY DIFFRACTION100
2.5447-2.60390.25381640.20682686X-RAY DIFFRACTION100
2.6039-2.6690.21141180.19142716X-RAY DIFFRACTION100
2.669-2.74120.23121750.19592689X-RAY DIFFRACTION100
2.7412-2.82180.25191560.20042685X-RAY DIFFRACTION100
2.8218-2.91290.26381430.19912710X-RAY DIFFRACTION100
2.9129-3.0170.29821090.2112748X-RAY DIFFRACTION100
3.017-3.13770.24461280.2052689X-RAY DIFFRACTION100
3.1377-3.28050.22111110.20212748X-RAY DIFFRACTION100
3.2805-3.45340.27331600.19432709X-RAY DIFFRACTION100
3.4534-3.66960.23381440.17492693X-RAY DIFFRACTION99
3.6696-3.95280.20051590.16542650X-RAY DIFFRACTION99
3.9528-4.35030.17671600.14962657X-RAY DIFFRACTION99
4.3503-4.9790.24531510.1462689X-RAY DIFFRACTION99
4.979-6.26990.18441530.17822693X-RAY DIFFRACTION100
6.2699-43.37660.22531710.21812640X-RAY DIFFRACTION98
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)
1-0.05711.2682-0.63040.943-1.25161.3344-0.0855-0.0818-0.0693-0.0221-0.0731-0.3490.1625-0.10370.12580.26160.01580.02460.27110.05710.304847.082724.7363-9.2201
21.7970.0756-0.93620.814-0.10711.7089-0.16270.31140.0312-0.18130.0265-0.0555-0.1771-0.14570.12160.2259-0.0355-0.04130.18360.01170.16232.461118.814812.9904
30.524-1.36690.70250.7198-0.86331.4302-0.0801-0.0454-0.0290.05760.0339-0.2058-0.1847-0.15710.04280.28440.0091-0.04280.31520.04650.259740.91624.870458.4549
42.021-0.03460.23261.27890.31472.3736-0.212-0.2342-0.08510.20450.03710.03660.0716-0.26690.15340.21940.02340.02880.22930.00810.193330.394111.591434.3594
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 4:87
2X-RAY DIFFRACTION2chain A and resid 93:233
3X-RAY DIFFRACTION3chain B and resid 5:86
4X-RAY DIFFRACTION4chain B and resid 94:233

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