[English] 日本語
Yorodumi
- PDB-4l99: Structure of the RBP from lactococcal phage 1358 in complex with ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4l99
TitleStructure of the RBP from lactococcal phage 1358 in complex with glycerol
ComponentsReceptor Binding ProteinReceptor (biochemistry)
KeywordsVIRAL PROTEIN / beta sandwich domain / phage receptor binding protein / Lactococcus lactis pellicle surface saccharide
Function / homologyViral head domain of polysaccharide receptor-binding protein-like / Triple-stranded beta-helix / Phage fibre proteins / Jelly Rolls / Sandwich / Mainly Beta / metal ion binding / Putative phage structural protein
Function and homology information
Biological speciesLactococcus phage 1358 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFarenc, C. / Spinelli, S. / Bebeacua, C. / Tremblay, D. / Orlov, I. / Blangy, S. / Klaholz, B.P. / Moineau, S. / Cambillau, C.
CitationJournal: To be Published
Title: A Virulent Siphophage CyoEM Structure and Host Recognition and Infection Mechanism
Authors: Farenc, C. / Spinelli, S. / Bebeacua, C. / Tremblay, D. / Orlov, I. / Blangy, S. / Klaholz, B.P. / Moineau, S. / Cambillau, C.
History
DepositionJun 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Receptor Binding Protein
B: Receptor Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1379
Polymers86,6522
Non-polymers4857
Water13,727762
1
A: Receptor Binding Protein
hetero molecules

A: Receptor Binding Protein
hetero molecules

A: Receptor Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,84315
Polymers129,9783
Non-polymers86512
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_544-z,x-1/2,-y-1/21
crystal symmetry operation11_545y+1/2,-z-1/2,-x1
Buried area16310 Å2
ΔGint-388 kcal/mol
Surface area44060 Å2
MethodPISA
2
B: Receptor Binding Protein
hetero molecules

B: Receptor Binding Protein
hetero molecules

B: Receptor Binding Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,56712
Polymers129,9783
Non-polymers5899
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555-z+1/2,-x,y+1/21
crystal symmetry operation10_545-y,z-1/2,-x+1/21
Buried area15400 Å2
ΔGint-314 kcal/mol
Surface area44050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)166.210, 166.210, 166.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11B-401-

ZN

-
Components

#1: Protein Receptor Binding Protein / Receptor (biochemistry) / RBP


Mass: 43326.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus phage 1358 (virus) / Gene: ORF20 / Plasmid: pETG20A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: D3W0F1
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 762 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 4.42 Å3/Da / Density % sol: 72.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 10 mM zinc sulfate heptahydrate, 100 mM MES, pH 6.5, 25% v/v PEG550 MME, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.921 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 7, 2013 / Details: Kirkpatrick-Baez pair of bi-morph mirrors
RadiationMonochromator: channel cut cryogenically cooled crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.921 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 77461 / Num. obs: 77461 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 51.9 Å2 / Rmerge(I) obs: 0.154 / Net I/σ(I): 9.3
Reflection shellResolution: 2.2→2.33 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.15 / Num. unique all: 12354 / % possible all: 99.6

-
Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
MOLREPphasing
BUSTER2.11.2refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4L9B
Resolution: 2.2→32.21 Å / Cor.coef. Fo:Fc: 0.9477 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.154 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.163 / SU Rfree Blow DPI: 0.137 / SU Rfree Cruickshank DPI: 0.133 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2034 3873 5 %RANDOM
Rwork0.188 ---
all0.1888 77461 --
obs0.1888 77461 99.98 %-
Displacement parametersBiso mean: 56.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.261 Å
Refinement stepCycle: LAST / Resolution: 2.2→32.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6058 0 12 762 6832
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2085SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes178HARMONIC2
X-RAY DIFFRACTIONt_gen_planes914HARMONIC5
X-RAY DIFFRACTIONt_it6226HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion834SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7464SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d6226HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg8485HARMONIC21.12
X-RAY DIFFRACTIONt_omega_torsion3.6
X-RAY DIFFRACTIONt_other_torsion16.79
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2187 282 5 %
Rwork0.1972 5362 -
all0.1983 5644 -
obs--99.98 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.02630.031-0.03130-0.10880.0325-0.0003-0.00110.00090.00590.0003-0.00240.0020.00070-0.0112-0.020.010.0012-0.0023-0.0035-7.3349-102.3845.1649
21.08-0.0479-1.23350.00870.50890.09450.00310.01190.01090.0106-0.00940.0024-0.0017-0.00370.0063-0.0270.00350.02140.0111-0.0394-0.00916.417-80.045120.062
30.1509-0.0701-0.090500.18820.00050.001-0.0032-0.00010.0101-0.00290.0076-0.00510.00020.0019-0.0150.00190.02370.0019-0.00730.00693.6181-82.344924.6481
400.93620.23760-0.81081.2317-0.0028-0.0078-0.00450.0172-0.00250.01690.00660.00850.0054-0.0166-0.02990.03430.01840.0378-0.02724.4418-91.228927.3739
50.2540.437-0.26080-0.23510.0675-0.0005-0.0075-0.00820.0045-0.00750.00360.00790.00370.0081-0.01740.0183-0.01380.02590.0351-0.015316.0577-92.215215.6141
60-0.02530.17690.0264-0.10560.00140.003-0.00860.00080.0096-0.0010.0021-0.00980.006-0.0021-0.0075-0.0156-0.01280.0241-0.0042-0.023117.8065-79.524.0866
70.1287-0.2360.32150.4342-0.26360.3975-0.0033-0.00280.00690.00050.0152-0.0012-0.01840.0292-0.0119-0.05-0.0598-0.0030.00910.00210.018621.5187-67.1187-0.5813
80.1721-0.11650.58690.14450.1810.05710.0018-0.00490.0088-0.00270.0088-0.0038-0.02450.0123-0.0106-0.0319-0.057-0.04130.0138-0.03970.014725.396-61.82623.3356
90.80790.1011-0.25280.016-0.58920.14540.0052-0.00070.0287-0.02170.0021-0.0111-0.00250.0095-0.0073-0.0386-0.0349-0.02540.0362-0.0292-0.001827.7889-67.4445-6.2059
100.8220.2655-0.20630.5274-0.5010.21770.00130.00290.0139-0.01680.0152-0.0363-0.01150.0222-0.0166-0.03580.002-0.00060.03570.0106-0.024631.354-73.1144-10.8528
110.49420.0553-0.10670.0462-0.34010.02440.00220.0050.0198-0.0090.0037-0.0068-0.00360.0081-0.0058-0.0224-0.0197-0.00610.0230.0007-0.008525.2639-69.6513-10.2781
120.1182-0.16860.08330.0196-0.12710.00710.00020.00360.0011-0.00170.0009-0.0033-0.00020.0054-0.001-0.0176-0.01130.02180.01280.01280.005739.2796-63.5937-14.8948
1300.1567-0.156700.05170-0.00040.00060.0020.00160.0011-0.0005-0.00130.0003-0.0008-0.0128-0.03210.0108-0.00030.00780.007238.6926-52.7657-10.9352
140.5907-0.43150.0750.0208-0.144100.00110.00610.0098-0.0041-0.0014-0.00020.00120.00590.0003-0.0257-0.033-0.0116-0.0030.01390.010820.0354-73.0441-6.2855
150-0.0331-0.03590.00320.02440.00990-0.0011-0.0022-0.00050.0002-0.00050.00220.0006-0.0002-0.00210.00070.00780.0064-0.0151-0.004321.6229-89.0752-11.3745
160.087-0.2117-0.05980.05160.12240.0213-0.00040.00020.0014-0.00080.00150.00460.0003-0.0013-0.00110.00270.01040.01450.0009-0.0281-0.000927.7525-14.237555.4211
170.0486-0.061-0.8540.00860.96310.00480.0008-0.00110.00030.004200.00190.025-0.0007-0.0008-0.00430.03370.02680.0073-0.0165-0.004813.7201-38.592144.3501
180.0615-0.1544-0.22500.145400.0004-0.0018-0.00220.0062-0.00090.0040.0078-0.00610.000400.02360.0190.0022-0.0075-0.00538.9724-36.52647.603
191.37-1.10470.13830.00310.848200.00150.01170.00720.01550.00480.008-0.0025-0.0056-0.0063-0.02380.06820.04680.0229-0.0413-0.00435.6862-27.763946.0578
200.2201-0.2855-0.17400.48120.06170.00140.00620.00370.004-0.0054-0.003-0.006-0.00320.004-0.02580.07510.00890.0231-0.01270.00616.6223-26.892533.6133
210.1249-0.224-0.13600.3870-0.00250.0027-0.0038-0.0010.00010.00630.0105-0.00360.0024-0.02580.01990.020.0246-0.0258-0.00449.014-40.269733.3435
220.6892-0.43120.23480.12460.63390.0301-0.00490.0111-0.00030.01860.01370.0089-0.0162-0.0145-0.0088-0.0310.00660.01280.0414-0.0041-0.011434.287-51.228728.7404
230.57320.04160.22180.06661.06350.1221-0.0040.006-0.00060.00570.00990.0056-0.0085-0.033-0.0059-0.0498-0.0068-0.00710.0571-0.0091-0.00230.5163-57.090425.5158
240.2991-0.12230.03820.37580.29230.1882-0.00230.0020.00630-0.0015-0.0061-0.001-0.02210.0038-0.02730.0151-0.01680.0226-0.0121-0.003339.0988-50.522522.2594
250.37730.18330.2280.0494-0.09690.6926-0.00760.024-0.003-0.02410.019-0.005-0.0322-0.0455-0.0115-0.05760.05860.00060.00290.02140.009343.3123-45.137517.8776
260.12860.0115-0.12310.11740.26230.1891-0.00040.00220.00760.00360.00180.0001-0.0104-0.0199-0.0014-0.02140.0124-0.01870.01570.00010.003743.4802-48.260524.1842
270.0696-0.19810.2180-0.20110.171-0.00120.0056-0.0006-0.00510.0019-0.0025-0.00110.0009-0.0006-0.00550.00810.00890.01440.0041-0.008147.1457-55.060310.529
280.03750.07790.070-0.05620.055-0.00040.00270.00140.00090.0033-0.00160.00530.0002-0.0029-0.0134-0.0252-0.03760.0224-0.0208-0.00944.6232-65.997211.9321
290.349-0.1787-0.199800.20850.00180.00010.00060.01180.00510.00480.0022-0.0103-0.0224-0.0049-0.0040.0258-0.00830.0055-0.018-0.001639.5876-44.817729.3982
300.00440.00970.01080.0185-0.01830.0198-0.0001-0.00080.0012-0.0008-0.00010-0.00050.00020.00020.00130.0103-0.0006-0.0030.00750.007543.285-28.627126.328
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{A|2 - A|17}A2 - 17
2X-RAY DIFFRACTION2{A|18 - A|53}A18 - 53
3X-RAY DIFFRACTION3{A|54 - A|78}A54 - 78
4X-RAY DIFFRACTION4{A|79 - A|116}A79 - 116
5X-RAY DIFFRACTION5{A|117 - A|143}A117 - 143
6X-RAY DIFFRACTION6{A|144 - A|170}A144 - 170
7X-RAY DIFFRACTION7{A|171 - A|206}A171 - 206
8X-RAY DIFFRACTION8{A|207 - A|236}A207 - 236
9X-RAY DIFFRACTION9{A|237 - A|269}A237 - 269
10X-RAY DIFFRACTION10{A|270 - A|319}A270 - 319
11X-RAY DIFFRACTION11{A|320 - A|343}A320 - 343
12X-RAY DIFFRACTION12{A|344 - A|355}A344 - 355
13X-RAY DIFFRACTION13{A|356 - A|366}A356 - 366
14X-RAY DIFFRACTION14{A|367 - A|387}A367 - 387
15X-RAY DIFFRACTION15{A|388 - A|393}A388 - 393
16X-RAY DIFFRACTION16{B|2 - B|17}B2 - 17
17X-RAY DIFFRACTION17{B|18 - B|53}B18 - 53
18X-RAY DIFFRACTION18{B|54 - B|78}B54 - 78
19X-RAY DIFFRACTION19{B|79 - B|116}B79 - 116
20X-RAY DIFFRACTION20{B|117 - B|143}B117 - 143
21X-RAY DIFFRACTION21{B|144 - B|170}B144 - 170
22X-RAY DIFFRACTION22{B|171 - B|206}B171 - 206
23X-RAY DIFFRACTION23{B|207 - B|236}B207 - 236
24X-RAY DIFFRACTION24{B|237 - B|269}B237 - 269
25X-RAY DIFFRACTION25{B|270 - B|319}B270 - 319
26X-RAY DIFFRACTION26{B|320 - B|343}B320 - 343
27X-RAY DIFFRACTION27{B|344 - B|355}B344 - 355
28X-RAY DIFFRACTION28{B|356 - B|366}B356 - 366
29X-RAY DIFFRACTION29{B|367 - B|387}B367 - 387
30X-RAY DIFFRACTION30{B|388 - B|393}B388 - 393

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more