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- PDB-4glv: OBody AM3L09 bound to hen egg-white lysozyme -

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Basic information

Entry
Database: PDB / ID: 4glv
TitleOBody AM3L09 bound to hen egg-white lysozyme
Components
  • Lysozyme C
  • OBody AM3L09
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


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
PHOSPHATE ION / Lysozyme C
Similarity search - Component
Biological speciesPyrobaculum aerophilum (archaea)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.574 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 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2013Group: Experimental preparation
Revision 1.2Feb 12, 2014Group: Database references
Revision 1.3Oct 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
A: Lysozyme C
B: OBody AM3L09
C: Lysozyme C
D: OBody AM3L09
E: Lysozyme C
F: OBody AM3L09
G: Lysozyme C
H: OBody AM3L09
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,32235
Polymers104,6718
Non-polymers2,65127
Water7,350408
1
A: Lysozyme C
B: OBody AM3L09
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,6347
Polymers26,1682
Non-polymers4665
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Lysozyme C
D: OBody AM3L09
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9599
Polymers26,1682
Non-polymers7917
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Lysozyme C
F: OBody AM3L09
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,00311
Polymers26,1682
Non-polymers8369
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Lysozyme C
H: OBody AM3L09
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,7268
Polymers26,1682
Non-polymers5586
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.000, 69.380, 76.360
Angle α, β, γ (deg.)72.170, 69.460, 77.550
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain B and (resseq 10:43 or resseq 49:105) and (name...
21chain D and (resseq 10:43 or resseq 49:105) and (name...
31chain F and (resseq 10:43 or resseq 49:105) and (name...
41chain H and (resseq 10:43 or resseq 49:105) and (name...
12chain A and (resseq 1:124 ) and (name ca or...
22chain C and (resseq 1:124 ) and (name ca or...
32chain E and (resseq 1:124 ) and (name ca or...
42chain G and (resseq 1:124 ) and (name ca or...
13chain B and (resseq 10:43 or resseq 49:105) and not...
23chain D and (resseq 10:43 or resseq 49:105) and not...
33chain F and (resseq 10:43 or resseq 49:105) and not...
43chain H and (resseq 10:43 or resseq 49:105) and not...
14chain A and (resseq 1:124 ) and not (name ca...
24chain C and (resseq 1:124 ) and not (name ca...
34chain E and (resseq 1:124 ) and not (name ca...
44chain G and (resseq 1:124 ) and not (name ca...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain B and (resseq 10:43 or resseq 49:105) and (name...B10 - 43
121chain B and (resseq 10:43 or resseq 49:105) and (name...B49 - 105
211chain D and (resseq 10:43 or resseq 49:105) and (name...D10 - 43
221chain D and (resseq 10:43 or resseq 49:105) and (name...D49 - 105
311chain F and (resseq 10:43 or resseq 49:105) and (name...F10 - 43
321chain F and (resseq 10:43 or resseq 49:105) and (name...F49 - 105
411chain H and (resseq 10:43 or resseq 49:105) and (name...H10 - 43
421chain H and (resseq 10:43 or resseq 49:105) and (name...H49 - 105
112chain A and (resseq 1:124 ) and (name ca or...A0
212chain C and (resseq 1:124 ) and (name ca or...C0
312chain E and (resseq 1:124 ) and (name ca or...E0
412chain G and (resseq 1:124 ) and (name ca or...G0
113chain B and (resseq 10:43 or resseq 49:105) and not...B10 - 43
123chain B and (resseq 10:43 or resseq 49:105) and not...B49 - 105
213chain D and (resseq 10:43 or resseq 49:105) and not...D10 - 43
223chain D and (resseq 10:43 or resseq 49:105) and not...D49 - 105
313chain F and (resseq 10:43 or resseq 49:105) and not...F10 - 43
323chain F and (resseq 10:43 or resseq 49:105) and not...F49 - 105
413chain H and (resseq 10:43 or resseq 49:105) and not...H10 - 43
423chain H and (resseq 10:43 or resseq 49:105) and not...H49 - 105
114chain A and (resseq 1:124 ) and not (name ca...A0
214chain C and (resseq 1:124 ) and not (name ca...C0
314chain E and (resseq 1:124 ) and not (name ca...E0
414chain G and (resseq 1:124 ) and not (name ca...G0

NCS ensembles :
ID
1
2
3
4

NCS oper:
IDCodeMatrixVector
1given(0.999487, -0.009067, 0.030715), (-0.008811, -0.999926, -0.008443), (0.030789, 0.008168, -0.999493)29.9252, -14.1966, -67.621597
2given(0.996385, 0.0182, 0.082975), (-0.030291, 0.988691, 0.146877), (-0.079363, -0.148859, 0.985668)1.53071, 12.9689, -41.267399
3given(0.992646, 0.006388, -0.120883), (-0.010958, -0.989764, -0.14229), (-0.120554, 0.142568, -0.982416)22.4809, -9.96429, -111.646004
4given(0.998705, -0.002236, 0.050826), (-0.001606, -0.999922, -0.012423), (0.05085, 0.012326, -0.99863)30.395901, -13.8827, -66.713799
5given(0.995956, 0.016834, 0.08825), (-0.031527, 0.985308, 0.167853), (-0.084128, -0.169956, 0.981854)1.73641, 13.2459, -41.748402
6given(0.991751, 0.021649, -0.12634), (-0.000942, -0.984378, -0.176065), (-0.128178, 0.174731, -0.976237)22.279499, -11.3462, -111.963997
7given(0.999405, -0.008563, 0.033407), (-0.008334, -0.999941, -0.006981), (0.033465, 0.006698, -0.999417)29.9914, -14.1389, -67.560204
8given(0.996253, 0.024487, 0.082952), (-0.036627, 0.988285, 0.148159), (-0.078352, -0.150642, 0.985478)1.52588, 12.9184, -41.344101
9given(0.993325, 0.004911, -0.115242), (-0.012181, -0.989041, -0.147136), (-0.114702, 0.147558, -0.98238)22.844101, -10.2523, -111.366997
10given(0.998769, -0.001117, 0.049592), (-0.000566, -0.999938, -0.011112), (0.049602, 0.01107, -0.998708)30.3624, -13.8286, -66.765404
11given(0.995607, 0.016116, 0.092234), (-0.031565, 0.985182, 0.168583), (-0.08815, -0.170753, 0.981363)1.75644, 13.192, -41.845001
12given(0.991297, 0.01762, -0.130463), (-0.005573, -0.984499, -0.175303), (-0.131529, 0.174504, -0.975832)22.101, -11.5773, -112.105003

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Components

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Protein , 2 types, 8 molecules ACEGBDFH

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


Mass: 14331.160 Da / Num. of mol.: 4 / 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 AM3L09


Mass: 11836.544 Da / Num. of mol.: 4
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]

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Non-polymers , 5 types, 435 molecules

#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 408 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.64 Å3/Da / Density % sol: 53.45 %
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 / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.95666 Å
DetectorType: ADSC QUANTUM 210r / 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: 7.8 % / Av σ(I) over netI: 4.8 / Number: 254770 / Rsym value: 0.113 / D res high: 2.574 Å / D res low: 69.196 Å / Num. obs: 32670 / % possible obs: 96.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRsym valueRedundancy
8.1448.0194.910.0610.0617.6
5.768.1496.910.0660.0667.7
4.75.7696.910.0680.0687.8
4.074.79710.0650.0657.8
3.644.079710.090.097.8
3.323.6496.710.1060.1067.8
3.083.3296.810.1460.1467.9
2.883.0896.710.2250.2257.9
2.712.8896.310.3120.3127.9
2.572.7193.610.4220.4227.7
ReflectionResolution: 2.574→69.196 Å / Num. all: 32670 / Num. obs: 32670 / % possible obs: 96.2 % / Redundancy: 7.8 % / Rsym value: 0.113 / Net I/σ(I): 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.574-2.717.70.4221.63559846340.42293.6
2.71-2.887.90.3122.43557745250.31296.3
2.88-3.087.90.2253.33338842520.22596.7
3.08-3.327.90.14653141440010.14696.8
3.32-3.647.80.1066.12852336500.10696.7
3.64-4.077.80.094.32570533050.0997
4.07-4.77.80.0659.42273528990.06597
4.7-5.767.80.0688.51941224880.06896.9
5.76-8.147.70.0669.11461618930.06696.9
8.14-48.0097.60.0617.4780210230.06194.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 31.68 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.57 Å48.01 Å
Translation2.57 Å48.01 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
PHASER2.1.4phasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.574→44.826 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8344 / SU ML: 0.39 / σ(F): 0.03 / Phase error: 24.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2448 1617 5.08 %
Rwork0.2014 --
obs0.2036 31849 93.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.43 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 93.76 Å2 / Biso mean: 27.1893 Å2 / Biso min: 3.84 Å2
Baniso -1Baniso -2Baniso -3
1--0.854 Å2-0.2775 Å22.9696 Å2
2--3.5268 Å2-0.7727 Å2
3----2.6729 Å2
Refinement stepCycle: LAST / Resolution: 2.574→44.826 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7301 0 165 408 7874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0037642
X-RAY DIFFRACTIONf_angle_d0.98410333
X-RAY DIFFRACTIONf_chiral_restr0.0531118
X-RAY DIFFRACTIONf_plane_restr0.0021305
X-RAY DIFFRACTIONf_dihedral_angle_d12.7242704
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B362X-RAY DIFFRACTIONPOSITIONAL0.021
12D362X-RAY DIFFRACTIONPOSITIONAL0.021
13F363X-RAY DIFFRACTIONPOSITIONAL0.023
14H363X-RAY DIFFRACTIONPOSITIONAL0.024
21A495X-RAY DIFFRACTIONPOSITIONAL0.016
22C495X-RAY DIFFRACTIONPOSITIONAL0.016
23E495X-RAY DIFFRACTIONPOSITIONAL0.018
24G495X-RAY DIFFRACTIONPOSITIONAL0.019
31B334X-RAY DIFFRACTIONPOSITIONAL0.47
32D334X-RAY DIFFRACTIONPOSITIONAL0.47
33F345X-RAY DIFFRACTIONPOSITIONAL0.78
34H345X-RAY DIFFRACTIONPOSITIONAL0.681
41A460X-RAY DIFFRACTIONPOSITIONAL0.467
42C460X-RAY DIFFRACTIONPOSITIONAL0.467
43E456X-RAY DIFFRACTIONPOSITIONAL0.592
44G460X-RAY DIFFRACTIONPOSITIONAL0.702
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.574-2.6660.31431500.23632736288685
2.666-2.77270.34991420.23952949309191
2.7727-2.89890.28871470.21293006315393
2.8989-3.05170.27021580.20243045320394
3.0517-3.24280.23361760.18563068324495
3.2428-3.49310.21171650.17873057322295
3.4931-3.84450.22211770.17323093327096
3.8445-4.40040.20611510.16853099325096
4.4004-5.54240.20191840.16943108329297
5.5424-44.83270.23781670.20883071323895

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