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- PDB-4gla: OBody NL8 bound to hen egg-white lysozyme -

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Basic information

Entry
Database: PDB / ID: 4gla
TitleOBody NL8 bound to hen egg-white lysozyme
Components
  • Lysozyme C
  • OBody NL8
KeywordsHYDROLASE/DE NOVO PROTEIN / beta barrel / OB-fold / protein-protein complex / novel scaffold / muraminidase / enzyme inhibition / engineered binding protein / HYDROLASE-DE NOVO PROTEIN complex
Function / homology
Function and homology information


aspartate-tRNA ligase / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / aminoacyl-tRNA synthetase multienzyme complex / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity ...aspartate-tRNA ligase / aspartyl-tRNA aminoacylation / aspartate-tRNA ligase activity / aminoacyl-tRNA synthetase multienzyme complex / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / magnesium ion binding / endoplasmic reticulum / extracellular space / RNA binding / ATP binding / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Aspartate-tRNA synthetase, type 2 / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Nucleic acid-binding proteins / Lysozyme - #10 ...Aspartate-tRNA synthetase, type 2 / Aspartyl/Asparaginyl-tRNA synthetase, class IIb / Aminoacyl-tRNA synthetase, class II (D/K/N) / tRNA synthetases class II (D, K and N) / OB-fold nucleic acid binding domain, AA-tRNA synthetase-type / OB-fold nucleic acid binding domain / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / Nucleic acid-binding proteins / Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Lysozyme-like domain superfamily / Nucleic acid-binding, OB-fold / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Lysozyme C / Aspartate--tRNA(Asp) ligase
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.75 Å
AuthorsSteemson, J.D.
CitationJournal: Plos One / Year: 2014
Title: Tracking Molecular Recognition at the Atomic Level with a New Protein Scaffold Based on the OB-Fold.
Authors: Steemson, J.D. / Baake, M. / Rakonjac, J. / Arcus, V.L. / Liddament, M.T.
History
DepositionAug 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
B: Lysozyme C
C: OBody NL8
D: OBody NL8


Theoretical massNumber of molelcules
Total (without water)52,1794
Polymers52,1794
Non-polymers00
Water81145
1
A: Lysozyme C
D: OBody NL8


Theoretical massNumber of molelcules
Total (without water)26,0902
Polymers26,0902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme C
C: OBody NL8


Theoretical massNumber of molelcules
Total (without water)26,0902
Polymers26,0902
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.759, 76.759, 166.344
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12D
22C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113B1 - 129
2113A1 - 129
1122D20 - 45
2122C20 - 45
1222D54 - 88
2222C54 - 88
1322D97 - 111
2322C97 - 111

NCS ensembles :
ID
1
2

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 2 / Fragment: UNP residues 19-147 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: egg white / References: UniProt: P00698, lysozyme
#2: Protein OBody NL8


Mass: 11758.518 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrobaculum aerophilum (archaea) / Gene: aspS / Plasmid: pProEx Htb / Production host: Escherichia coli (E. coli) / Strain (production host): DH5[alpha] / References: UniProt: Q8ZYM8*PLUS
#3: 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: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 0.2 M HEPES, 7% MPEG5000, pH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Type: SSRL / Wavelength: 0.95666 Å
DetectorType: MAR / Detector: CCD / Date: Nov 16, 2008
Details: flat collimating Rh coated mirror, toroidal focusing mirror
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95666 Å / Relative weight: 1
ReflectionRedundancy: 9 % / Av σ(I) over netI: 32.5 / Number: 144772 / Rmerge(I) obs: 0.073 / Χ2: 1.26 / D res high: 2.6 Å / D res low: 50 Å / Num. obs: 16010 / % possible obs: 99.8
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.6509810.0361.1978.5
4.455.610010.0461.1449.3
3.884.4599.910.0611.1139.1
3.533.8810010.0871.338.9
3.283.5310010.121.3728.9
3.083.2810010.1471.1369.3
2.933.0810010.2261.0029.3
2.82.9310010.3491.0439.3
2.692.810010.5431.1969.2
2.62.6910010.7882.1728.7
ReflectionResolution: 2.6→50 Å / Num. obs: 16010 / % possible obs: 99.8 % / Redundancy: 9 % / Rmerge(I) obs: 0.073 / Χ2: 1.262 / Net I/σ(I): 12.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.6-2.698.70.78815522.1721100
2.69-2.89.20.54315671.1961100
2.8-2.939.30.34915671.0431100
2.93-3.089.30.22615641.0021100
3.08-3.289.30.14715771.1361100
3.28-3.538.90.1215831.3721100
3.53-3.888.90.08716101.331100
3.88-4.459.10.06115971.113199.9
4.45-5.69.30.04616441.1441100
5.6-508.50.03617491.197198

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.69 Å33.62 Å
Translation2.69 Å33.62 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→27.5 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.878 / WRfactor Rfree: 0.3293 / WRfactor Rwork: 0.2584 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7798 / SU B: 32.116 / SU ML: 0.321 / SU R Cruickshank DPI: 0.3743 / SU Rfree: 0.47 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.428 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2964 667 5 %RANDOM
Rwork0.2256 ---
obs0.229 13456 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 68.61 Å2 / Biso mean: 62.746 Å2 / Biso min: 30.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.75→27.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3334 0 0 45 3379
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223399
X-RAY DIFFRACTIONr_angle_refined_deg1.4521.9264600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7485431
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34323.154149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.57615558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3891530
X-RAY DIFFRACTIONr_chiral_restr0.1080.2502
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022578
X-RAY DIFFRACTIONr_nbd_refined0.2410.21494
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22283
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2140
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1750.24
X-RAY DIFFRACTIONr_mcbond_it0.511.52185
X-RAY DIFFRACTIONr_mcangle_it0.87923412
X-RAY DIFFRACTIONr_scbond_it1.43831419
X-RAY DIFFRACTIONr_scangle_it2.3734.51188
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B516TIGHT POSITIONAL0.060.05
1B485LOOSE POSITIONAL0.585
1B516TIGHT THERMAL0.110.5
1B485LOOSE THERMAL1.3910
2D284TIGHT POSITIONAL0.050.05
2D271MEDIUM POSITIONAL0.440.5
2D284TIGHT THERMAL0.130.5
2D271MEDIUM THERMAL0.732
LS refinement shellResolution: 2.75→2.821 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 55 -
Rwork0.264 908 -
all-963 -
obs--99.59 %
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)
16.3577-1.03510.39852.8069-1.32343.34550.0991-0.0696-0.26450.28710.03210.2993-0.00880.0496-0.1312-0.10850.09770.0413-0.06080.0267-0.1488-3.4387-18.831533.7942
26.5796-1.74661.87523.6591-0.6237.4093-0.3895-0.4852-0.57510.12310.2238-0.5051-0.12811.31440.1657-0.0592-0.04920.1520.245-0.07030.201237.377-13.15125.5895
37.9393-1.5249-1.04596.729-0.30341.8162-0.2939-0.0374-0.42280.13640.23340.2985-0.076-0.08840.0605-0.0304-0.10070.0905-0.1012-0.0228-0.155416.8605-2.32821.1773
46.64260.55860.32933.0558-2.90538.57270.04730.07630.0021-0.20580.12040.1009-0.096-0.05-0.1677-0.16180.0020.0242-0.06070.0371-0.1031-3.173-8.043112.8408
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 128
2X-RAY DIFFRACTION2B1 - 128
3X-RAY DIFFRACTION3C22 - 104
4X-RAY DIFFRACTION4D22 - 107

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