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- PDB-4gn4: OBody AM2EP06 bound to hen egg-white lysozyme -

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Basic information

Entry
Database: PDB / ID: 4gn4
TitleOBody AM2EP06 bound to hen egg-white lysozyme
Components
  • Lysozyme C
  • OBody AM2EP06
KeywordsDE NOVO PROTEIN/HYDROLASE / beta barrel / OB-fold / protein-protein complex / novel scaffold / muraminidase / enzyme inhibition / engineered binding protein / inhibitor / DE NOVO PROTEIN-HYDROLASE complex
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
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 ...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 / Beta Barrel / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesPyrobaculum aerophilum (archaea)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.861 Å
AuthorsSteemson, J.D. / Liddament, M.T.
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 16, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2014Group: Database references
Revision 1.2Oct 16, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: OBody AM2EP06
A: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6377
Polymers26,1772
Non-polymers4605
Water4,360242
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.430, 58.330, 81.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein OBody AM2EP06


Mass: 11845.485 Da / Num. of mol.: 1
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]
#2: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 1 / Fragment: UNP residues 19-147 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: egg white / References: UniProt: P00698, lysozyme
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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

CrystalDensity Matthews: 2.3 Å3/Da / Density % sol: 46.49 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M HEPES, 13% MPEG5000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54179 Å
DetectorType: MAR 2300 / Detector: IMAGE PLATE / Date: Sep 2, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionRedundancy: 6.9 % / Av σ(I) over netI: 11.9 / Number: 143392 / Rsym value: 0.039 / D res high: 1.861 Å / D res low: 81.82 Å / Num. obs: 20797 / % possible obs: 99.1
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
5.8834.5899.410.0270.0275.4
4.165.8810010.0260.0266.9
3.394.1610010.030.037.1
2.943.3910010.0270.0277.1
2.632.9410010.0370.0377.1
2.42.6310010.0520.0527.1
2.222.410010.0730.0737
2.082.2210010.0980.0987
1.962.0810010.1510.1516.9
1.861.9694.110.2260.2266.5
ReflectionResolution: 1.861→81.82 Å / Num. all: 20797 / Num. obs: 20797 / % possible obs: 99.1 % / Redundancy: 6.9 % / Rsym value: 0.039 / Net I/σ(I): 29.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.861-1.966.50.2263.41827528190.22694.1
1.96-2.086.90.15151972128580.151100
2.08-2.2270.0987.61866626740.098100
2.22-2.470.0739.71777125230.073100
2.4-2.637.10.05213.61637623050.052100
2.63-2.947.10.037181500021100.037100
2.94-3.397.10.02722.21338718790.027100
3.39-4.167.10.0319.31137316050.03100
4.16-5.886.90.02621.6875012760.026100
5.88-34.5755.40.02715.740737480.02799.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 30.54 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å34.58 Å
Translation2.5 Å34.58 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.861→81.82 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / WRfactor Rfree: 0.1943 / WRfactor Rwork: 0.1484 / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8874 / SU B: 5.944 / SU ML: 0.082 / SU R Cruickshank DPI: 0.126 / SU Rfree: 0.1215 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.1944 1064 5.1 %RANDOM
Rwork0.1519 ---
obs0.1541 20764 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 101.9 Å2 / Biso mean: 33.8146 Å2 / Biso min: 7.27 Å2
Baniso -1Baniso -2Baniso -3
1--1.9 Å20 Å20 Å2
2--1.37 Å20 Å2
3---0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.861→81.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1835 0 30 242 2107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0211935
X-RAY DIFFRACTIONr_angle_refined_deg1.9481.932629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2055247
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.5623.95386
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96215306
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7411513
X-RAY DIFFRACTIONr_chiral_restr0.1670.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211471
X-RAY DIFFRACTIONr_mcbond_it1.2021.51196
X-RAY DIFFRACTIONr_mcangle_it1.77121923
X-RAY DIFFRACTIONr_scbond_it2.7673739
X-RAY DIFFRACTIONr_scangle_it3.8964.5703
LS refinement shellResolution: 1.861→1.91 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.227 60 -
Rwork0.17 1341 -
all-1401 -
obs--92.54 %
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)
16.64553.6499-1.17027.8197-1.72523.5956-0.05140.2217-0.4899-0.2052-0.0945-0.38390.46090.44880.1460.13830.09580.02250.1452-0.06220.085321.99349.40775.1161
24.2687-0.0981-0.53251.86310.26085.3691-0.0901-0.20180.15180.02850.1156-0.0372-0.12720.3353-0.02550.02490.0239-0.0150.0568-0.0390.040616.404916.194414.7885
34.96521.9172.03369.33981.22894.6972-0.0904-1.3268-0.0390.66230.1169-0.11380.26910.5362-0.02650.15490.1296-0.00430.55410.01440.061517.289110.898229.2104
46.0206-0.4103-0.36641.7070.03052.7639-0.1556-0.3888-0.28020.05460.0215-0.05320.26110.37040.13410.10.06060.02130.07830.00770.05216.41459.865416.5327
517.2371-2.2471-11.55331.56460.228915.2674-0.1811.2262-0.3576-0.3859-0.08810.00970.2788-0.65370.26910.1606-0.0206-0.0250.1234-0.06160.048711.806314.224-0.2005
65.9512-0.59862.4333.4122-1.25134.457-0.055-0.35770.10510.16380.13660.3719-0.1091-0.4437-0.08170.07960.04060.04680.06620.04690.1184-12.66618.660523.2513
76.3764.6361-0.20414.0138-0.92631.3045-0.0135-0.06860.18540.07360.10050.2105-0.03540.0369-0.0870.08770.0540.01750.09190.00970.0695-0.55849.125222.7477
87.58951.1536-0.35885.5233-2.94784.45640.2124-0.67970.51070.4739-0.262-0.1088-0.39050.31350.04960.19170.04680.02290.1635-0.0630.0739-2.178414.352130.3624
96.646-0.65340.10823.769-0.3673.06810.09380.496-0.0302-0.47740.1121-0.18960.01010.0706-0.20590.13750.00630.00330.08150.04220.1669-5.34411.375516.9322
1028.3683-2.83781.099128.27765.64418.05450.906-1.1694-0.94922.395-0.51920.75180.25260.4704-0.38670.35940.02580.08260.3847-0.00660.1161-7.85189.277736.9869
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 20
2X-RAY DIFFRACTION2A21 - 60
3X-RAY DIFFRACTION3A61 - 77
4X-RAY DIFFRACTION4A78 - 113
5X-RAY DIFFRACTION5A114 - 128
6X-RAY DIFFRACTION6B0 - 30
7X-RAY DIFFRACTION7B31 - 56
8X-RAY DIFFRACTION8B57 - 79
9X-RAY DIFFRACTION9B80 - 101
10X-RAY DIFFRACTION10B102 - 107

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