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- PDB-3lml: Crystal Structure of the sheath tail protein Lin1278 from Listeri... -

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Basic information

Entry
Database: PDB / ID: 3lml
TitleCrystal Structure of the sheath tail protein Lin1278 from Listeria innocua, Northeast Structural Genomics Consortium Target LkR115
ComponentsLin1278 protein
KeywordsStructural Genomics / Unknown function / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / LkR115
Function / homology
Function and homology information


Nuclear Transport Factor 2; Chain: A, - #690 / Dna Ligase; domain 1 - #450 / Immunoglobulin-like - #4290 / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Tail sheath protein Gp18 domain III N-terminal region / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain ...Nuclear Transport Factor 2; Chain: A, - #690 / Dna Ligase; domain 1 - #450 / Immunoglobulin-like - #4290 / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Tail sheath protein Gp18 domain III N-terminal region / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain / Nuclear Transport Factor 2; Chain: A, / Dna Ligase; domain 1 / Roll / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.3 Å
AuthorsForouhar, F. / Neely, H. / Seetharaman, J. / Mao, M. / Xiao, R. / Patel, D.J. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. ...Forouhar, F. / Neely, H. / Seetharaman, J. / Mao, M. / Xiao, R. / Patel, D.J. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target LkR115
Authors: Forouhar, F. / Neely, H. / Seetharaman, J. / Mao, M. / Xiao, R. / Patel, D.J. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJan 31, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Lin1278 protein
B: Lin1278 protein
C: Lin1278 protein
D: Lin1278 protein
E: Lin1278 protein
F: Lin1278 protein


Theoretical massNumber of molelcules
Total (without water)302,7036
Polymers302,7036
Non-polymers00
Water00
1
A: Lin1278 protein


Theoretical massNumber of molelcules
Total (without water)50,4501
Polymers50,4501
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lin1278 protein


Theoretical massNumber of molelcules
Total (without water)50,4501
Polymers50,4501
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Lin1278 protein


Theoretical massNumber of molelcules
Total (without water)50,4501
Polymers50,4501
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Lin1278 protein


Theoretical massNumber of molelcules
Total (without water)50,4501
Polymers50,4501
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Lin1278 protein


Theoretical massNumber of molelcules
Total (without water)50,4501
Polymers50,4501
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Lin1278 protein


Theoretical massNumber of molelcules
Total (without water)50,4501
Polymers50,4501
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.314, 153.718, 217.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Lin1278 protein


Mass: 50450.418 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Strain: Clip11262 / Gene: lin1278 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q92CB1
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: 2.52 Å3/Da / Density % sol: 51.2 %
Crystal growTemperature: 291 K / Method: microbatch, under oil / pH: 8.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: 0.1M Tris pH 8.5, 25% PEG 3350, and 0.2M NaCl, Microbatch, under oil, temperature 291K

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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 315 / Detector: CCD / Date: Dec 9, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. all: 88789 / Num. obs: 88701 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.133 / Rsym value: 0.111 / Net I/σ(I): 16.71
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 4.7 / Rsym value: 0.473 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 3.3→19.96 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 126650.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.26 3997 5 %RANDOM
Rwork0.23 ---
obs0.23 79945 90.3 %-
all-88532 --
Solvent computationSolvent model: FLAT MODEL / Bsol: -1.30115 Å2 / ksol: 0.25 e/Å3
Displacement parametersBiso mean: 57 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20 Å20 Å2
2---6.69 Å20 Å2
3---4.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.47 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.65 Å0.56 Å
Refinement stepCycle: LAST / Resolution: 3.3→19.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20036 0 0 0 20036
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 3.3→3.42 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.354 380 5.5 %
Rwork0.307 6498 -
obs--77.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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