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- PDB-3ld7: Crystal structure of the Lin0431 protein from Listeria innocua, N... -

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Basic information

Entry
Database: PDB / ID: 3ld7
TitleCrystal structure of the Lin0431 protein from Listeria innocua, Northeast Structural Genomics Consortium Target LkR112
ComponentsLin0431 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Lin0431 / DUF1312 / PF07009 / LkR112 / NESG / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyN-utilization substance G protein NusG, insert domain / NusG, domain 2 / NusG, domain 2 superfamily / NusG domain II / mini-chromosome maintenance (MCM) complex, domain 2 / Sandwich / Mainly Beta / Lin0431 protein
Function and homology information
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.547 Å
AuthorsVorobiev, S. / Chen, Y. / Lee, D. / Patel, D.J. / Ciccosanti, C. / Sahdev, S. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. ...Vorobiev, S. / Chen, Y. / Lee, D. / Patel, D.J. / Ciccosanti, C. / Sahdev, S. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the Lin0431 protein from Listeria innocua
Authors: Vorobiev, S. / Chen, Y. / Lee, D. / Patel, D.J. / Ciccosanti, C. / Sahdev, S. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJan 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lin0431 protein
B: Lin0431 protein
C: Lin0431 protein


Theoretical massNumber of molelcules
Total (without water)34,6133
Polymers34,6133
Non-polymers00
Water5,549308
1
A: Lin0431 protein


Theoretical massNumber of molelcules
Total (without water)11,5381
Polymers11,5381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lin0431 protein


Theoretical massNumber of molelcules
Total (without water)11,5381
Polymers11,5381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Lin0431 protein


Theoretical massNumber of molelcules
Total (without water)11,5381
Polymers11,5381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.360, 54.782, 71.733
Angle α, β, γ (deg.)90.00, 111.60, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-201-

HOH

Detailsmonomer according to gel filtration

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Components

#1: Protein Lin0431 protein


Mass: 11537.740 Da / Num. of mol.: 3 / Fragment: sequence database residues 36-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Strain: CLIP 11262/Serovar 6a / Gene: lin0431 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) +Magic / References: UniProt: Q92EM7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 308 / 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: 2.17 Å3/Da / Density % sol: 43.41 %
Crystal growTemperature: 291 K / Method: microbatch under paraffin oil / pH: 8.2
Details: 0.072M sodium phosphate monobasic, 1.728M potassium phosphate dibasic, pH 8.2, microbatch under paraffin oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97814 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 7, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97814 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. all: 84850 / Num. obs: 84087 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 19.53 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 34.3
Reflection shellHighest resolution: 1.55 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.399 / Mean I/σ(I) obs: 3.4 / Num. unique all: 8496 / % possible all: 98.3

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.5_2)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.547→31.547 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.95 / Phase error: 17.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.194 4234 5.04 %RANDOM
Rwork0.1654 ---
obs0.1669 84064 98.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.156 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.2611 Å2-0 Å2-0.8854 Å2
2---0.2922 Å20 Å2
3---1.5533 Å2
Refinement stepCycle: LAST / Resolution: 1.547→31.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2022 0 0 308 2330
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012055
X-RAY DIFFRACTIONf_angle_d1.2452767
X-RAY DIFFRACTIONf_dihedral_angle_d16.442791
X-RAY DIFFRACTIONf_chiral_restr0.078313
X-RAY DIFFRACTIONf_plane_restr0.005360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5467-1.56430.21871150.16892344X-RAY DIFFRACTION87
1.5643-1.58270.20021350.15572680X-RAY DIFFRACTION99
1.5827-1.6020.20281340.14662679X-RAY DIFFRACTION99
1.602-1.62230.1871430.13832598X-RAY DIFFRACTION99
1.6223-1.64360.20621660.13762733X-RAY DIFFRACTION99
1.6436-1.66620.20771400.14052666X-RAY DIFFRACTION99
1.6662-1.690.17491350.14012632X-RAY DIFFRACTION99
1.69-1.71520.22261090.13392759X-RAY DIFFRACTION99
1.7152-1.7420.19371220.13162655X-RAY DIFFRACTION99
1.742-1.77050.16231450.12952765X-RAY DIFFRACTION99
1.7705-1.80110.16851370.13792601X-RAY DIFFRACTION100
1.8011-1.83380.19951300.13812743X-RAY DIFFRACTION100
1.8338-1.86910.17731430.13782659X-RAY DIFFRACTION100
1.8691-1.90720.20291650.12732667X-RAY DIFFRACTION100
1.9072-1.94870.13871460.13822675X-RAY DIFFRACTION100
1.9487-1.9940.15681450.13232704X-RAY DIFFRACTION100
1.994-2.04390.19011600.14422689X-RAY DIFFRACTION100
2.0439-2.09910.19211310.14672703X-RAY DIFFRACTION100
2.0991-2.16090.19341480.14542685X-RAY DIFFRACTION100
2.1609-2.23060.16281460.14852668X-RAY DIFFRACTION100
2.2306-2.31030.17651300.15392687X-RAY DIFFRACTION100
2.3103-2.40280.17961480.15842678X-RAY DIFFRACTION100
2.4028-2.51210.19261280.17592724X-RAY DIFFRACTION100
2.5121-2.64450.23571440.18472676X-RAY DIFFRACTION100
2.6445-2.81010.24431570.18972701X-RAY DIFFRACTION100
2.8101-3.02690.18181440.19032670X-RAY DIFFRACTION100
3.0269-3.33120.19021430.1732729X-RAY DIFFRACTION100
3.3312-3.81250.15391600.15472642X-RAY DIFFRACTION99
3.8125-4.80060.17651320.15982595X-RAY DIFFRACTION97
4.8006-31.55390.24041530.19212423X-RAY DIFFRACTION90

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