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- PDB-5hqh: 1.32 Angstrom Crystal Structure of Ybbr like Domain of lmo2119 Pr... -

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Basic information

Entry
Database: PDB / ID: 5hqh
Title1.32 Angstrom Crystal Structure of Ybbr like Domain of lmo2119 Protein from Listeria monocytogenes.
ComponentsLmo2119 protein
KeywordsUNKNOWN FUNCTION / Ybbr like domain / CSGID / Structural genomics / Center for Structural Genomics of Infectious Diseases
Function / homologyRNA Polymerase Alpha Subunit; Chain A, domain 2 - #30 / YbbR-like / : / YbbR-like protein / RNA Polymerase Alpha Subunit; Chain A, domain 2 / Beta Complex / Mainly Beta / Lmo2119 protein
Function and homology information
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: To Be Published
Title: 1.32 Angstrom Crystal Structure of Ybbr like Domain of lmo2119 Protein from Listeria monocytogenes.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionJan 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 2, 2016Group: Structure summary
Revision 1.2Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_keywords
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_keywords.pdbx_keywords

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lmo2119 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0373
Polymers11,9051
Non-polymers1322
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-14 kcal/mol
Surface area6370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)22.577, 28.819, 59.733
Angle α, β, γ (deg.)90.00, 95.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Lmo2119 protein


Mass: 11905.333 Da / Num. of mol.: 1 / Fragment: UNP residues 38-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (bacteria)
Strain: ATCC BAA-679 / EGD-e / Gene: lmo2119 / Plasmid: pMCSG7 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE) / References: UniProt: Q8Y5E5
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 1.62 Å3/Da / Density % sol: 24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 7.2 mg/ml, 0.25M Sodium chloride, 0.1M Tris HCl (pH 8.3); Screen: Trap96 (D4), 0.2M NAD, 0.1M HEPES (pH 7.5), 25% (w/v) PEG 3350.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 25, 2013 / Details: C(111)
RadiationMonochromator: Beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.32→30 Å / Num. obs: 18244 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.05 / Rsym value: 0.05 / Net I/σ(I): 22.9
Reflection shellResolution: 1.32→1.34 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.512 / Mean I/σ(I) obs: 2.4 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-3000data reduction
HKL-3000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QDY

4qdy


Resolution: 1.32→29.72 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.96 / SU B: 2.104 / SU ML: 0.045 / Cross valid method: THROUGHOUT / ESU R: 0.062 / ESU R Free: 0.064 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1923 926 5.1 %RANDOM
Rwork0.16198 ---
obs0.16351 17262 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.053 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20.4 Å2
2---0.58 Å20 Å2
3---0.18 Å2
Refinement stepCycle: 1 / Resolution: 1.32→29.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms743 0 6 164 913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.019896
X-RAY DIFFRACTIONr_bond_other_d0.0010.02894
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.9681237
X-RAY DIFFRACTIONr_angle_other_deg0.82932076
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1145124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.30526.85735
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.39115170
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.235153
X-RAY DIFFRACTIONr_chiral_restr0.0860.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0240.021063
X-RAY DIFFRACTIONr_gen_planes_other0.020.02184
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7420.921460
X-RAY DIFFRACTIONr_mcbond_other0.7430.919459
X-RAY DIFFRACTIONr_mcangle_it1.1881.377596
X-RAY DIFFRACTIONr_mcangle_other1.1871.38597
X-RAY DIFFRACTIONr_scbond_it1.2041.084436
X-RAY DIFFRACTIONr_scbond_other1.2061.078433
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.8921.545636
X-RAY DIFFRACTIONr_long_range_B_refined6.67610.2281134
X-RAY DIFFRACTIONr_long_range_B_other5.688.3431023
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.32→1.354 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 58 -
Rwork0.271 1276 -
obs--99.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.53790.31071.22482.6108-1.14697.1055-0.05470.0926-0.0498-0.15010.05850.1558-0.0403-0.0344-0.00380.01650.00050.00120.0563-0.01720.04713.2184-4.3859.3371
20.2070.19490.09320.1940.09081.5607-0.00370.02930.0374-0.01610.01720.0209-0.04810.0045-0.01350.01750.0160.01160.02730.00550.0464.9269-2.180525.5938
30.7309-0.2344-0.22381.12691.32333.4723-0.00710.07560.0091-0.08350.02610.0488-0.02750.1053-0.0190.01710.00050.00140.01370.00390.0168.0121.115715.0415
40.74830.2169-0.82150.31810.13381.5517-0.02670.08950.0291-0.04260.02010.0793-0.0628-0.08470.00660.02340.00160.01270.0470.0070.06791.14673.432319.2773
54.5967-0.39684.02873.7404-1.99715.9338-0.0838-0.5524-0.03940.35330.20450.1309-0.1663-0.5303-0.12080.05550.03340.0320.09150.00470.04352.641-3.547245.6742
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 53
2X-RAY DIFFRACTION2A54 - 77
3X-RAY DIFFRACTION3A78 - 102
4X-RAY DIFFRACTION4A103 - 131
5X-RAY DIFFRACTION5A132 - 138

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