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Basic information

Entry
Database: PDB / ID: 4rfa
TitleCrystal structure of cyclic nucleotide-binding domain containing protein from Listeria monocytogenes EGD-e
ComponentsLmo0740 protein
KeywordsTRANSCRIPTION REGULATOR / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / Crp
Function / homologyCyclic nucleotide-binding domain superfamily / RmlC-like jelly roll fold / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Lmo0740 protein
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.21 Å
AuthorsFilippova, E.V. / Minasov, G. / Kiryukhina, O. / Jedrzejczak, R. / Joachimiak, A. / Anderson, W.F. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of cyclic nucleotide-binding domain containing protein from Listeria monocytogenes EGD-e
Authors: Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Jedrzejczak, R. / Joachimiak, A. / Anderson, W.F.
History
DepositionSep 25, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 15, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lmo0740 protein


Theoretical massNumber of molelcules
Total (without water)26,7161
Polymers26,7161
Non-polymers00
Water81145
1
A: Lmo0740 protein

A: Lmo0740 protein


Theoretical massNumber of molelcules
Total (without water)53,4312
Polymers53,4312
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area3850 Å2
ΔGint-33 kcal/mol
Surface area20990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.987, 91.987, 144.079
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-319-

HOH

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Components

#1: Protein Lmo0740 protein


Mass: 26715.662 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: lmo0740 / Plasmid: pMCSG87 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) magic / References: UniProt: Q8Y902
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / 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: 3.29 Å3/Da / Density % sol: 62.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 1.0 M tri-Sodium Citrate, 0.1 M Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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 21, 2014 / Details: beryllium lenses
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.21→50 Å / Num. all: 18733 / Num. obs: 18733 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 21.3 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 34.9
Reflection shellResolution: 2.21→2.25 Å / Redundancy: 21.8 % / Rmerge(I) obs: 0.68 / Mean I/σ(I) obs: 4.9 / % possible all: 100

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
HKL-3000phasing
REFMAC5.8.0069refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.21→50 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / SU B: 10.823 / SU ML: 0.132 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24253 920 4.9 %RANDOM
Rwork0.20607 ---
obs0.20792 17762 99.71 %-
all-17762 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 67.671 Å2
Baniso -1Baniso -2Baniso -3
1-0.73 Å20.36 Å20 Å2
2--0.73 Å2-0 Å2
3----2.35 Å2
Refinement stepCycle: LAST / Resolution: 2.21→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 0 45 1781
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.021790
X-RAY DIFFRACTIONr_bond_other_d0.0010.021728
X-RAY DIFFRACTIONr_angle_refined_deg1.7221.9972425
X-RAY DIFFRACTIONr_angle_other_deg0.83233989
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7335216
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.3892582
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.97315313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.645157
X-RAY DIFFRACTIONr_chiral_restr0.0950.2280
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021978
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02385
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_it3.224.438864
X-RAY DIFFRACTIONr_mcbond_other3.2214.434863
X-RAY DIFFRACTIONr_mcangle_it4.7046.6281080
X-RAY DIFFRACTIONr_mcangle_other4.7026.6341081
X-RAY DIFFRACTIONr_scbond_it3.9684.978924
X-RAY DIFFRACTIONr_scbond_other3.9684.969922
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.0417.2891345
X-RAY DIFFRACTIONr_long_range_B_refined8.9836.7152050
X-RAY DIFFRACTIONr_long_range_B_other8.97136.6492044
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.209→2.266 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 77 -
Rwork0.282 1245 -
obs--98.95 %
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)
16.4581-2.75550.45372.8568-1.67641.47950.0813-0.26710.0869-0.41010.04040.09510.2914-0.1601-0.12170.17220.0648-0.07650.30930.00860.046319.470735.3752-4.031
26.1047-0.11592.16172.3639-0.85831.71670.00520.1030.3594-0.4591-0.0964-0.0872-0.0349-0.07460.09120.16850.05260.03740.06090.0110.035835.616931.6781-1.4753
31.6206-1.11171.34182.7523-2.58273.96020.0847-0.28250.3048-0.4119-0.1380.0538-0.1812-0.40290.05330.28880.1623-0.05810.3803-0.07320.209825.378236.9171.5297
411.3825-3.62481.36622.45990.38921.1042-0.2277-0.01180.2060.12870.05980.0830.0134-0.16690.16790.1268-0.0072-0.02780.14650.01580.095630.102430.047712.4413
52.1873-1.02830.57265.513-0.95283.67650.0364-0.1855-0.4442-0.4220.22060.35310.441-0.1946-0.2570.1975-0.0116-0.08060.0310.03250.128139.18611.61764.4268
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 37
2X-RAY DIFFRACTION2A38 - 71
3X-RAY DIFFRACTION3A72 - 116
4X-RAY DIFFRACTION4A117 - 140
5X-RAY DIFFRACTION5A141 - 218

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