[English] 日本語
Yorodumi
- PDB-4nw4: Crystal structure of a DUF4822 family protein (EF0375) from Enter... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4nw4
TitleCrystal structure of a DUF4822 family protein (EF0375) from Enterococcus faecalis V583 at 1.85 A resolution
ComponentsLipoprotein S-layer protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Two lipocain-like domains / PF16103 family (DUF4822) / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY
Function / homologyDomain of unknown function DUF4822 / Domain of unknown function DUF4822 / Domain of unknown function (DUF4822) / Lipocalin / Beta Barrel / Mainly Beta / Unknown ligand / DUF4822 domain-containing protein
Function and homology information
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of a hypothetical protein (EF0375) from Enterococcus faecalis V583 at 1.85 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionDec 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 24, 2014Group: Structure summary
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.3Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 6, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Lipoprotein S-layer protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,68715
Polymers32,6971
Non-polymers99114
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.379, 61.379, 160.389
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein Lipoprotein S-layer protein


Mass: 32696.605 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Strain: V583 / Gene: EF_0375, I574_00797, OO5_02913 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): PB1 / References: UniProt: Q838R0

-
Non-polymers , 5 types, 284 molecules

#2: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY
Sequence detailsTHIS CONSTRUCT (RESIDUES 29-321) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THIS CONSTRUCT (RESIDUES 29-321) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.89 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 2.400M ammonium sulfate, 0.1M TRIS pH 8.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97917
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 21, 2013
Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing)
RadiationMonochromator: single crystal Si(111) bent / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.85→26.731 Å / Num. all: 29118 / Num. obs: 29118 / % possible obs: 99.9 % / Redundancy: 6.6 % / Rsym value: 0.136 / Net I/σ(I): 9.4
Reflection shell

Rmerge(I) obs: 0.013 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.85-1.96.90.61486621401.26499.9
1.9-1.956.90.71439020811.049100
1.95-2.016.711360120390.791100
2.01-2.076.51.31292119970.592100
2.07-2.146.21.61200419260.48399.9
2.14-2.215.52.11022518470.36899.9
2.21-2.296.92.21247117970.35399.9
2.29-2.396.92.61188417160.299100
2.39-2.496.931140416480.25999.9
2.49-2.626.73.61056115720.2199.9
2.62-2.766.14.8936115260.156100
2.76-2.936.15.9877714350.12399.9
2.93-3.137.27.7958613280.094100
3.13-3.3878.9876812440.079100
3.38-3.76.911.3789011460.0699.9
3.7-4.145.610.2579510400.06299.2
4.14-4.7878.364429230.07499.9
4.78-5.857.17.555267740.076100
5.85-8.276.111.436405990.05799.2
8.27-26.7317.416.525263400.03897.3

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
MolProbity3beta29model building
PDB_EXTRACT3.1data extraction
PHASER2.3.0phasing
SCALA3.3.20data scaling
REFMAC5.7.0032refinement
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→26.731 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.615 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2 .A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2 .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 INCORPORATION. 3.ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4.WATERS WERE EXCLUDED FROM AUTOMATIC TLS ASSIGNMENT.5.SULFATES (SO4) FROM THE CRYSTALLIZATION SOLUTION, CHLORIDE (CL),AND GLYCEROL (GOL) USED AS A CRYOPROTECTANT HAVE BEEN MODELED INTO THE STRUCTURE. 6.AN UNKNOWN LIGAND (UNL) HAS BEEN MODELED INTO THE BINDING CAVITY NEAR THE SIDECHAIN OF ARG A108. THE POSITIONING OF THE UNL IS SIMILAR TO AN UNKNOWN LIGAND MODELED INTO THE STRUCTURE OF A HOMOLOG,PDB ID 4KH8.
RfactorNum. reflection% reflectionSelection details
Rfree0.1815 1477 5.1 %RANDOM
Rwork0.1496 ---
obs0.1512 29054 99.86 %-
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: 99.96 Å2 / Biso mean: 29.0028 Å2 / Biso min: 16.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20.72 Å2-0 Å2
2--0.72 Å2-0 Å2
3----2.34 Å2
Refinement stepCycle: LAST / Resolution: 1.85→26.731 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2150 0 57 270 2477
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192233
X-RAY DIFFRACTIONr_bond_other_d0.0010.022016
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9443017
X-RAY DIFFRACTIONr_angle_other_deg0.71634617
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7535272
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.46424.79119
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.04315350
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.741512
X-RAY DIFFRACTIONr_chiral_restr0.0860.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022594
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02556
X-RAY DIFFRACTIONr_mcbond_it2.343.7891091
X-RAY DIFFRACTIONr_mcbond_other2.3383.7881090
X-RAY DIFFRACTIONr_mcangle_it2.8647.0681362
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 116 -
Rwork0.27 2019 -
all-2135 -
obs--99.81 %
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)
10.6902-0.1061-0.68842.52940.50981.9494-0.0136-0.0319-0.01170.0793-0.00370.14370.0151-0.12980.01730.0056-0.00170.00710.0296-0.00640.0244-8.263139.218712.3026
20.7367-0.1985-0.00941.51320.32761.2599-0.0140.04910.0415-0.07060.02550.0197-0.0343-0.0977-0.01160.0136-0.00290.01430.01960.00260.03221.368631.4308-11.2157
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A49 - 171
2X-RAY DIFFRACTION2A172 - 321

+
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