[English] 日本語
Yorodumi
- PDB-4ezg: Crystal structure of a putative cell adhesion protein (LMOf2365_1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ezg
TitleCrystal structure of a putative cell adhesion protein (LMOf2365_1307) from Listeria monocytogenes str. 4b F2365 at 1.50 A resolution
ComponentsPutative uncharacterized protein
KeywordsCELL ADHESION / internalin-A / leucine-rich repeat protein / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyLeucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Alpha Beta / Internalin like protein (LPXTG motif) / :
Function and homology information
Biological speciesListeria monocytogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a leucine rich hypothetical protein (LMOf2365_1307) from Listeria monocytogenes str. Li 2 at 1.50 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionMay 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 11, 2012Group: Atomic model
Revision 1.2Dec 24, 2014Group: Structure summary
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Aug 18, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 1, 2023Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,3143
Polymers43,2182
Non-polymers961
Water8,287460
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-14 kcal/mol
Surface area15190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.696, 62.979, 107.201
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Putative uncharacterized protein


Mass: 21608.816 Da / Num. of mol.: 2 / Fragment: UNP residues 30-225
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: Li 2 / Gene: LMOf2365_1307 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q720D2, UniProt: A0A7U9BV03*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O
Sequence details1. THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...1. THE CONSTRUCT WAS EXPRESSED WITH AN N-TERMINAL PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY RESIDUES 30-225 THE TARGET SEQUENCE. 2. THE STRAIN CLONED (ATCC 19115 / 4B / LI 2) DIFFERS FROM THE STRAIN SEQUENCED IN THE DATABASE REFERENCE (SEROTYPE 4B STR. F2365). DNA SEQUENCING OF THE CLONED CONSTRUCT SHOWS AN ASPARAGINE AT POSITION 72 INSTEAD OF AN ASPARTATE AND A LYSINE AT POSITION 126 INSTEAD OF A THREONINE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.17M ammonium sulfate, 15.00% Glycerol, 25.50% polyethylene glycol 4000, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9793
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 10, 2012
Details: Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.5→28.754 Å / Num. obs: 64777 / % possible obs: 98 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 18.318 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 13.87
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.5-1.550.6323147811354197.5
1.55-1.620.4562.63838813824198.1
1.62-1.690.3393.63433211681199
1.69-1.780.244.83589912423198.5
1.78-1.890.1557.13282712065197.7
1.89-2.040.09811.53701512592198.4
2.04-2.240.06516.23475411965198.4
2.24-2.560.04521.63415212045197
2.56-3.230.03229.63672012447198.6
3.23-28.7540.02240.13503912122196.4

-
Phasing

PhasingMethod: SAD

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
SHELXphasing
SHARPphasing
XSCALEDecember 29, 2011data scaling
PHENIX1.7.3refinement
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→28.754 Å / Occupancy max: 1 / Occupancy min: 0.21 / SU ML: 0.21 / σ(F): 1.35 / Phase error: 16.79 / Stereochemistry target values: MLHL
Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 3. A MET- ...Details: 1. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 2. WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET I INCORPORATION. 4. A SULFATE (SO4) FROM THE CRYSTALLIZATION SOLUTION WAS MODELED INTO THE STRUCTURE. 5. THE PROGARM QFIT THAT AUTOMATICALLY IDENTIFIES AND MODELS DISCRETE HETEROGENEITY IN ELECTRON DENSITY MAPS WITH A A CONVEX OPTIMIZATION ALGORITHM WAS IMPLEMENTED DURING REFINEMENT TO MODEL SOME OF THE ALTERNATE CONFORMATIONS.
RfactorNum. reflection% reflection
Rfree0.1929 3257 5.03 %
Rwork0.1706 --
obs0.1717 64700 98.95 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.902 Å2 / ksol: 0.359 e/Å3
Displacement parametersBiso max: 82.06 Å2 / Biso mean: 19.464 Å2 / Biso min: 6.12 Å2
Baniso -1Baniso -2Baniso -3
1-3.3899 Å2-0 Å2-0 Å2
2---1.0921 Å2-0 Å2
3----2.2977 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28.754 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2820 0 5 460 3285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063195
X-RAY DIFFRACTIONf_angle_d1.1614415
X-RAY DIFFRACTIONf_chiral_restr0.086534
X-RAY DIFFRACTIONf_plane_restr0.005582
X-RAY DIFFRACTIONf_dihedral_angle_d10.8911221
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.52240.3211460.28552588273499
1.5224-1.54620.28431350.26842638277399
1.5462-1.57150.26591400.24842664280499
1.5715-1.59860.25121500.22652581273199
1.5986-1.62770.22271390.20226812820100
1.6277-1.6590.24551420.202226882830100
1.659-1.69280.25331440.20482621276599
1.6928-1.72970.20171270.18926672794100
1.7297-1.76990.20271200.17792692281299
1.7699-1.81410.17981580.16782638279699
1.8141-1.86320.17581310.16172651278299
1.8632-1.9180.22691410.18072637277898
1.918-1.97990.19511300.16232678280899
1.9799-2.05060.1771530.15012638279199
2.0506-2.13270.18861460.16182678282499
2.1327-2.22970.18081410.15822685282699
2.2297-2.34720.2141370.17242659279698
2.3472-2.49420.17891350.15852658279398
2.4942-2.68670.19061670.161826812848100
2.6867-2.95680.18841560.161127092865100
2.9568-3.38410.15961440.1682713285799
3.3841-4.26140.17811170.14272748286598
4.2614-28.75950.18361580.1812850300898
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)
10.1092-0.0364-0.09080.4590.17620.33810.022-0.0031-0.01250.0157-0.0176-0.0076-0.0124-0.05630.00070.06210.0096-0.00230.0782-0.00010.072257.00025.71522.481
20.19130.04620.09990.67850.30530.40620.02830.0103-0.01-0.0708-0.0409-0.0264-0.0679-0.0239-0.0110.09780.0017-0.0010.0955-0.00390.105357.4002-0.6733-21.5109
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 35:219)A0
2X-RAY DIFFRACTION2chain 'B' and (resseq 38:219)B0

+
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