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- PDB-3oop: The structure of a protein with unknown function from Listeria in... -

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Basic information

Entry
Database: PDB / ID: 3oop
TitleThe structure of a protein with unknown function from Listeria innocua Clip11262
ComponentsLin2960 protein
Keywordsstructural genomics / unknown function / Protein Structure Initiative / PSI-2 / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


DNA-binding transcription factor activity
Similarity search - Function
Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / 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 ...Transcriptional regulator MarR-type, conserved site / MarR-type HTH domain signature. / MarR family / MarR-type HTH domain profile. / helix_turn_helix multiple antibiotic resistance protein / MarR-type HTH domain / 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 / Mainly Alpha
Similarity search - Domain/homology
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å
AuthorsFan, Y. / Li, H. / Zhou, Y. / Gu, M. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The structure of a protein with unknown function from Listeria innocua Clip11262
Authors: Fan, Y. / Li, H. / Zhou, Y. / Gu, M. / Joachimiak, A.
History
DepositionAug 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lin2960 protein


Theoretical massNumber of molelcules
Total (without water)16,6231
Polymers16,6231
Non-polymers00
Water1,78399
1
A: Lin2960 protein

A: Lin2960 protein


Theoretical massNumber of molelcules
Total (without water)33,2472
Polymers33,2472
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area4050 Å2
ΔGint-37 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.687, 77.834, 33.065
Angle α, β, γ (deg.)90.00, 113.36, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-159-

HOH

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Components

#1: Protein Lin2960 protein


Mass: 16623.309 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Strain: Clip11262 / Gene: lin2960 / Production host: Escherichia coli (E. coli) / References: UniProt: Q926T1
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M calcium acetate, 0.1M tris pH7.0, 20%w/v PEG3000, 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: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2010 / Details: mirror
RadiationMonochromator: Si 111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.78→50 Å / Num. all: 13923 / Num. obs: 13923 / % possible obs: 96.2 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 49.37
Reflection shellResolution: 1.78→1.81 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.271 / Mean I/σ(I) obs: 6.56 / Num. unique all: 599 / % possible all: 81.3

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Processing

Software
NameVersionClassification
SBC-Collectcollectdata collection
SHELXDphasing
MLPHAREphasing
ARPmodel building
WARPmodel building
HKL-3000phasing
REFMAC5.5.0109refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.78→47.21 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.534 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R Free: 0.137
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23638 694 5 %RANDOM
Rwork0.21022 ---
all0.21156 13225 --
obs0.21156 13225 96.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.168 Å2
Baniso -1Baniso -2Baniso -3
1-0.47 Å20 Å22.02 Å2
2--0.5 Å20 Å2
3---0.63 Å2
Refinement stepCycle: LAST / Resolution: 1.78→47.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1121 0 0 99 1220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221250
X-RAY DIFFRACTIONr_angle_refined_deg1.0261.9721713
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1715170
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.91924.42661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.06315255
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0971512
X-RAY DIFFRACTIONr_chiral_restr0.0720.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02938
X-RAY DIFFRACTIONr_mcbond_it0.8961.5753
X-RAY DIFFRACTIONr_mcangle_it1.69221253
X-RAY DIFFRACTIONr_scbond_it2.473497
X-RAY DIFFRACTIONr_scangle_it4.1614.5446
X-RAY DIFFRACTIONr_rigid_bond_restr1.15931250
LS refinement shellResolution: 1.781→1.827 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 40 -
Rwork0.222 921 -
obs--88.33 %
Refinement TLS params.Method: refined / Origin x: 47.6901 Å / Origin y: 60.5962 Å / Origin z: -7.4651 Å
111213212223313233
T0.0358 Å20.0053 Å2-0.0027 Å2-0.0083 Å2-0.0141 Å2--0.0303 Å2
L0.7663 °20.2064 °2-0.1106 °2-0.1647 °2-0.1026 °2--0.1373 °2
S-0.0086 Å °-0.0191 Å °0.0077 Å °-0.0122 Å °-0.0093 Å °-0.0039 Å °-0.0109 Å °0.0027 Å °0.0179 Å °

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