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- PDB-3nro: Crystal Structure of putative transcriptional factor Lmo1026 from... -

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Basic information

Entry
Database: PDB / ID: 3nro
TitleCrystal Structure of putative transcriptional factor Lmo1026 from Listeria monocytogenes (FRAGMENT 52-321), Northeast Structural Genomics Consortium Target LmR194
ComponentsLmo1026 protein
Keywordsstructural genomics / unknown function / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homologyLCP protein / Cell envelope-related transcriptional attenuator domain / LytR_cpsA_psr family / Aminopeptidase / membrane => GO:0016020 / 3-Layer(aba) Sandwich / Alpha Beta / Lmo1026 protein
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 Å
AuthorsKuzin, A. / Su, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Su, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Lee, D. / 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 LmR194
Authors: Kuzin, A. / Su, M. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJun 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lmo1026 protein
B: Lmo1026 protein


Theoretical massNumber of molelcules
Total (without water)62,5752
Polymers62,5752
Non-polymers00
Water00
1
A: Lmo1026 protein


Theoretical massNumber of molelcules
Total (without water)31,2881
Polymers31,2881
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lmo1026 protein


Theoretical massNumber of molelcules
Total (without water)31,2881
Polymers31,2881
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Lmo1026 protein

B: Lmo1026 protein


Theoretical massNumber of molelcules
Total (without water)62,5752
Polymers62,5752
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_645-x+1,y-1/2,-z+1/21
Buried area1580 Å2
ΔGint-10 kcal/mol
Surface area23240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.236, 90.301, 118.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsmonomer,33.02 kD,91.5%

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Components

#1: Protein Lmo1026 protein


Mass: 31287.561 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: lmo1026 / Plasmid: pET 21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q8Y889

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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: 1.88 Å3/Da / Density % sol: 34.71 %
Crystal growTemperature: 293 K / pH: 8.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: LI2SO4 0.2M, Peg-4K 30%, 0.1M Tris, pH 8.5, macrobatch under oil, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 3, 2010 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 19967 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rsym value: 0.074 / Net I/σ(I): 19

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: SAD / Resolution: 2.9→29.66 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.39 / σ(F): 1.35 / Phase error: 25.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.264 526 4.8 %
Rwork0.234 --
obs0.235 10958 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.59 Å2 / ksol: 0.32 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.2591 Å20 Å2-0 Å2
2--20.5087 Å20 Å2
3----19.2496 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3647 0 0 0 3647
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093695
X-RAY DIFFRACTIONf_angle_d1.2954979
X-RAY DIFFRACTIONf_dihedral_angle_d17.0931387
X-RAY DIFFRACTIONf_chiral_restr0.091573
X-RAY DIFFRACTIONf_plane_restr0.007646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.902-3.19380.30841280.27342526X-RAY DIFFRACTION98
3.1938-3.65520.30631340.25012560X-RAY DIFFRACTION100
3.6552-4.60240.22291310.21632611X-RAY DIFFRACTION100
4.6024-29.6650.26171330.22452735X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 20.3386 Å / Origin y: 35.6744 Å / Origin z: 45.1144 Å
111213212223313233
T0.1885 Å2-0.0096 Å20.0059 Å2-0.1929 Å20.0073 Å2--0.1998 Å2
L0.2397 °2-0.3653 °2-0.3411 °2-0.3439 °20.2695 °2--0.2319 °2
S-0.0047 Å °0.0085 Å °0.0217 Å °0.0174 Å °-0.0159 Å °0.012 Å °0.051 Å °-0.0458 Å °-0 Å °
Refinement TLS groupSelection details: ALL

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