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- PDB-3neu: The crystal structure of a functionally-unknown protein lin1836 f... -

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Basic information

Entry
Database: PDB / ID: 3neu
TitleThe crystal structure of a functionally-unknown protein lin1836 from Listeria innocua Clip11262
ComponentsLin1836 protein
KeywordsStructural Genomics / Unknown function / PSI-2 / protein structure initiative / midwest center for structural genomics / MCSG
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
Helix Hairpins - #2110 / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helix Hairpins / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...Helix Hairpins - #2110 / GntR-type HTH domain profile. / helix_turn_helix gluconate operon transcriptional repressor / Transcription regulator HTH, GntR / Bacterial regulatory proteins, gntR family / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Helix Hairpins / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.58 Å
AuthorsTan, K. / Li, H. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a functionally-unknown protein lin1836 from Listeria innocua Clip11262
Authors: Tan, K. / Li, H. / Gu, M. / Joachimiak, A.
History
DepositionJun 9, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lin1836 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5862
Polymers14,4941
Non-polymers921
Water1,76598
1
A: Lin1836 protein
hetero molecules

A: Lin1836 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1724
Polymers28,9872
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3150 Å2
ΔGint-23 kcal/mol
Surface area14690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.828, 88.051, 38.341
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Lin1836 protein


Mass: 14493.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Strain: Clip11262 / Gene: lin1836 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q92AT3
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 2.44 Å3/Da / Density % sol: 49.5 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 10%(w/v)PEG1000, 10%(w/v)PEG8000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 4, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.58→28.5 Å / Num. all: 19919 / Num. obs: 19919 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 38
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 2.1 / Num. unique all: 986 / % possible all: 100

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Processing

Software
NameVersionClassification
SBC-Collectdata collection
SHELXDphasing
MLPHAREphasing
DMmodel building
ARPmodel building
WARPmodel building
HKL-3000phasing
PHENIX(phenix.refine: 1.5_2)refinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 1.58→28.264 Å / SU ML: 0.16 / σ(F): 0.1 / σ(I): 0 / Phase error: 21.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2219 973 5.09 %random
Rwork0.1936 ---
obs0.1951 19100 95.03 %-
all-19100 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 66.427 Å2 / ksol: 0.44 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.512 Å20 Å2-0 Å2
2--4.8111 Å20 Å2
3----0.299 Å2
Refinement stepCycle: LAST / Resolution: 1.58→28.264 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms953 0 6 98 1057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061043
X-RAY DIFFRACTIONf_angle_d0.9661415
X-RAY DIFFRACTIONf_dihedral_angle_d17.082423
X-RAY DIFFRACTIONf_chiral_restr0.066154
X-RAY DIFFRACTIONf_plane_restr0.004183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5796-1.66290.30521010.26292329X-RAY DIFFRACTION86
1.6629-1.7670.27141450.21272435X-RAY DIFFRACTION92
1.767-1.90340.22371430.18542577X-RAY DIFFRACTION96
1.9034-2.09490.22731450.18662653X-RAY DIFFRACTION99
2.0949-2.39790.2051400.17822699X-RAY DIFFRACTION99
2.3979-3.02060.21511560.18812730X-RAY DIFFRACTION100
3.0206-28.26820.21681430.19422704X-RAY DIFFRACTION94
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)
11.91940.0862-0.9840.5986-0.23831.7771-0.01750.1470.0651-0.0350.0562-0.01070.0151-0.0758-0.06430.2012-0.018-0.0060.2028-0.01860.21887.172919.3027-0.9768
20.5797-0.0776-0.45730.2638-0.36491.07030.13780.09290.13880.411-0.04510.25410.0312-0.0733-0.02530.258-0.0269-0.00110.2743-0.0310.2318-3.02369.181914.1217
31.15040.3586-0.46360.4184-0.31471.09080.3214-0.09750.11140.2753-0.3382-0.03120.82580.13090.08830.36950.0068-0.01450.29440.02610.24271.1328-6.016823.1376
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A resid 2:76
2X-RAY DIFFRACTION2chain A resid 77:102
3X-RAY DIFFRACTION3chain A resid 103:120

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