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- PDB-3owq: X-Ray Structure of Lin1025 protein from Listeria innocua, Northea... -

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Basic information

Entry
Database: PDB / ID: 3owq
TitleX-Ray Structure of Lin1025 protein from Listeria innocua, Northeast Structural Genomics Consortium Target LkR164
ComponentsLin1025 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


LCP protein / : / Cell envelope-related transcriptional attenuator domain / LytR_cpsA_psr family / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Lin1025 protein
Similarity search - Component
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.606 Å
AuthorsKuzin, A. / Su, M. / Lew, S. / Seetharaman, J. / Patel, P. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. ...Kuzin, A. / Su, M. / Lew, S. / Seetharaman, J. / Patel, P. / 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 LkR164
Authors: Kuzin, A. / Su, M. / Lew, S. / Seetharaman, J. / Patel, P. / 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
DepositionSep 20, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lin1025 protein
B: Lin1025 protein
C: Lin1025 protein
D: Lin1025 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)143,8617
Polymers143,5434
Non-polymers3183
Water86548
1
A: Lin1025 protein


Theoretical massNumber of molelcules
Total (without water)35,8861
Polymers35,8861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lin1025 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9922
Polymers35,8861
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Lin1025 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9922
Polymers35,8861
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Lin1025 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9922
Polymers35,8861
Non-polymers1061
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.510, 157.041, 57.277
Angle α, β, γ (deg.)90.00, 98.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Lin1025 protein


Mass: 35885.699 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Gene: lin1025 / References: UniProt: Q92CZ6
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / Source method: isolated from a natural source / Formula: H2O
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

Crystal growMethod: vapor diffusion, hanging drop / pH: 6
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: LiCl 0.1M, PEG1K 22%, MES 0.1M, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 26, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 58846 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 46.72 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 19.6

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.606→28.332 Å / SU ML: 0.33 / σ(F): 1.36 / Phase error: 30.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2598 1513 5.07 %
Rwork0.2253 --
obs0.2271 29868 99.29 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.613 Å2 / ksol: 0.335 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-16.3281 Å2-0 Å2-8.2429 Å2
2---21.3723 Å2-0 Å2
3---5.0442 Å2
Refinement stepCycle: LAST / Resolution: 2.606→28.332 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7292 0 21 48 7361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087403
X-RAY DIFFRACTIONf_angle_d1.3419968
X-RAY DIFFRACTIONf_dihedral_angle_d15.7622769
X-RAY DIFFRACTIONf_chiral_restr0.0961138
X-RAY DIFFRACTIONf_plane_restr0.0061299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6064-2.69040.35791400.32012526X-RAY DIFFRACTION98
2.6904-2.78650.29851290.31432571X-RAY DIFFRACTION100
2.7865-2.8980.34961480.29682564X-RAY DIFFRACTION100
2.898-3.02970.29631420.25342595X-RAY DIFFRACTION100
3.0297-3.18930.29261340.25522602X-RAY DIFFRACTION100
3.1893-3.38880.27451380.25142579X-RAY DIFFRACTION100
3.3888-3.64990.29221320.25052581X-RAY DIFFRACTION100
3.6499-4.01630.27131330.21712605X-RAY DIFFRACTION100
4.0163-4.59530.20691380.17092600X-RAY DIFFRACTION100
4.5953-5.78160.21291370.19112620X-RAY DIFFRACTION100
5.7816-28.33410.23231420.20622512X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 8.3844 Å / Origin y: -0.0362 Å / Origin z: 26.5264 Å
111213212223313233
T0.0482 Å20.0223 Å2-0.0053 Å2-0.0499 Å20.0069 Å2--0.0482 Å2
L0.2183 °2-0.0221 °20.0417 °2-0.1611 °20.0025 °2--0.1766 °2
S0.0339 Å °-0.0208 Å °-0.0796 Å °-0.0115 Å °-0.033 Å °0.0235 Å °-0.0451 Å °-0.0053 Å °-0.0002 Å °
Refinement TLS groupSelection details: all

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