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- PDB-4zhb: N-terminal structure of ankyrin repeat-containing protein legA11 ... -

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Basic information

Entry
Database: PDB / ID: 4zhb
TitleN-terminal structure of ankyrin repeat-containing protein legA11 from Legionella pneumophila
Components
  • 5-mer peptide
  • Ankyrin repeat-containing protein
KeywordsStructural Genomics / Unknown Function / PSI-Biology / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Domain of unknown function DUF3447 / Ankyrin repeat-containing domain / Ankyrin repeats (3 copies) / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Ankyrin repeat-containing protein
Similarity search - Component
Biological speciesLegionella pneumophila subsp. pneumophila (bacteria)
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsChang, C. / Endres, M. / Mack, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: to be published
Title: N-terminal structure of ankyrin repeat-containing protein legA11 from Legionella pneumophila
Authors: Chang, C. / Endres, M. / Mack, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
History
DepositionApr 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ankyrin repeat-containing protein
B: 5-mer peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1133
Polymers14,0542
Non-polymers591
Water3,981221
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area670 Å2
ΔGint-2 kcal/mol
Surface area6680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.708, 42.708, 145.715
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-418-

HOH

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Components

#1: Protein Ankyrin repeat-containing protein


Mass: 13537.802 Da / Num. of mol.: 1 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) (bacteria)
Strain: Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: legA11, lpg0436 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) pGrow7-K / References: UniProt: Q5ZYD6
#2: Protein/peptide 5-mer peptide


Mass: 516.545 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: unknown poly peptide fragment taken with molecule 1 in the expression/purification step
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21 (DE3) pGrow7-K
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M MES pH 6.5, 12% PEG 20000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97926 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 10, 2012
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. all: 34433 / Num. obs: 31841 / % possible obs: 92.5 % / Observed criterion σ(I): -3 / Redundancy: 12.7 % / Rmerge(I) obs: 0.074 / Χ2: 2.685 / Net I/av σ(I): 53.105 / Net I/σ(I): 12.9 / Num. measured all: 405549
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.3-1.327.50.8829511.14157.5
1.32-1.358.20.71110931.17664.6
1.35-1.378.80.67912281.17272.7
1.37-1.49.20.55614381.22387.3
1.4-1.4310.50.48116061.24994.6
1.43-1.4611.20.39816271.2996.7
1.46-1.5120.33616241.40496.7
1.5-1.5412.90.28116611.41697.1
1.54-1.5914.40.24916651.53797.3
1.59-1.6414.50.21116371.61197.3
1.64-1.714.40.18716601.80897.8
1.7-1.7614.40.15716701.92297.9
1.76-1.8414.40.13916752.24698.1
1.84-1.9414.30.11617002.64298.2
1.94-2.0614.30.08916873.23398.6
2.06-2.2214.20.07817263.69798.7
2.22-2.4514.10.06917224.08998.9
2.45-2.8140.06217584.82299.2
2.8-3.5313.70.04917985.11699.4
3.53-5012.20.04719156.00397.5

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0103refinement
PDB_EXTRACT3.15data extraction
HKL-3000data reduction
HKL-3000phasing
SBC-Collectdata collection
RefinementMethod to determine structure: SAD / Resolution: 1.3→42.71 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.174 / SU ML: 0.022 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.043
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1588 1619 5.1 %RANDOM
Rwork0.1261 ---
obs0.1277 30199 92.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 57.94 Å2 / Biso mean: 16.797 Å2 / Biso min: 8.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20 Å2
2---0.28 Å20 Å2
3---0.56 Å2
Refinement stepCycle: final / Resolution: 1.3→42.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms888 0 4 221 1113
Biso mean--29.22 33.02 -
Num. residues----109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.019990
X-RAY DIFFRACTIONr_bond_other_d0.0020.02946
X-RAY DIFFRACTIONr_angle_refined_deg1.3951.9761349
X-RAY DIFFRACTIONr_angle_other_deg0.9532194
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4795120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.2112650
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.91515172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.972152
X-RAY DIFFRACTIONr_chiral_restr0.0870.2148
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211132
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02214
X-RAY DIFFRACTIONr_mcbond_it0.9251.238472
X-RAY DIFFRACTIONr_mcbond_other0.9271.232471
X-RAY DIFFRACTIONr_mcangle_it1.2081.842594
X-RAY DIFFRACTIONr_rigid_bond_restr0.98831936
X-RAY DIFFRACTIONr_sphericity_free34.579539
X-RAY DIFFRACTIONr_sphericity_bonded8.9452093
LS refinement shellResolution: 1.299→1.333 Å
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)
10.1682-0.0139-0.13170.2461-0.19510.52630.0013-0.01350.01720.01990.0022-0.0044-0.01530.0188-0.00350.0099-0.0002-0.00120.0111-0.0020.002322.14472.349120.7868
20.14790.0293-0.06550.2127-0.15330.18190.0037-0.0029-0.00370.0039-0.0093-0.00860.00110.01710.00560.0064-0.0012-0.00010.00950.0010.00225.7583-4.83712.9899
30.3643-0.1828-0.08130.5412-0.12920.08260.0015-0.018-00.02940.00010.0047-0.01090.0084-0.00160.0112-0.0005-0.00070.0104-00.000213.3329-2.222120.4925
40.0691-0.0136-0.05880.03950.06040.21380.00090.00350.0026-0.0031-0.00010.0017-0.0130.0036-0.00090.009-0.0004-0.00010.00950.00050.001515.92633.81548.4852
50.74060.091-0.02510.54220.23220.6837-0.00170.0145-0.0233-0.00280.0118-0.00070.0120.0132-0.01010.00720.0005-00.0082-0.00010.00116.0151-8.08599.7881
60.13060.02410.05110.23220.01480.0662-0.0011-0.00460.00140.0052-0.00030.007-0.0033-0.00640.00140.00850.00050.00060.01-0.00020.0015.18314.615112.4588
70.1669-0.1311-0.050.33970.04110.018-0.00160.0090.0014-0.00120.00130.0062-0.00340.00220.00030.01-0.0019-0.00160.01220.00080.00065.83075.11160.2957
80.3927-0.00460.00091.14740.36421.46620.00370.0083-0.01570.0060.0016-0.01260.0222-0.008-0.00530.0067-0.001-0.00170.00790.00050.00125.4297-4.82322.8188
91.2766-0.6491-0.60340.33010.30680.2852-0.0139-0.0124-0.01780.00740.00570.00880.00680.00490.00820.00850.0001-0.0010.01240.00350.0017-3.6221-0.21618.3487
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A11 - 24
2X-RAY DIFFRACTION2A25 - 38
3X-RAY DIFFRACTION3A39 - 48
4X-RAY DIFFRACTION4A49 - 70
5X-RAY DIFFRACTION5A71 - 76
6X-RAY DIFFRACTION6A77 - 92
7X-RAY DIFFRACTION7A93 - 104
8X-RAY DIFFRACTION8A105 - 110
9X-RAY DIFFRACTION9A111 - 114

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