[English] 日本語
Yorodumi
- PDB-3lhn: Crystal structure of putative lipoprotein (NP_718719.1) from Shew... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3lhn
TitleCrystal structure of putative lipoprotein (NP_718719.1) from Shewanella oneidensis at 1.42 A resolution
ComponentsLipoprotein
KeywordsLIPID BINDING PROTEIN / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2
Function / homologyLipocalin - #640 / Copper resistance lipoprotein NlpE / NlpE N-terminal domain / Lipocalin / Beta Barrel / Mainly Beta / Outer membrane lipoprotein NlpE
Function and homology information
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.42 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of putative lipoprotein (NP_718719.1) from Shewanella oneidensis at 1.42 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJan 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_struct_assembly_auth_evidence / software / Item: _software.classification / _software.name
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Feb 1, 2023Group: Database references / Derived calculations / Category: database_2 / 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_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: Lipoprotein
B: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3845
Polymers27,1042
Non-polymers2803
Water4,107228
1
A: Lipoprotein
B: Lipoprotein
hetero molecules

A: Lipoprotein
B: Lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,76810
Polymers54,2074
Non-polymers5616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area7660 Å2
ΔGint-57 kcal/mol
Surface area19140 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-24 kcal/mol
Surface area10840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.185, 50.185, 300.508
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
DetailsANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY SUGGESTS A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION. CRYSTAL PACKING SUPPORTS THE ASSIGNMENT OF A DIMER AS SIGNIFICANT OLIGOMERIZATION STATES.

-
Components

#1: Protein Lipoprotein


Mass: 13551.774 Da / Num. of mol.: 2 / Fragment: sequence database residues 26-150
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis (bacteria) / Gene: SO_3163 / Plasmid: SpeedETS / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q8ECH9
#2: Chemical ChemComp-SO4 / SULFATE ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE CLONED CONSTRUCT CONTAINS RESIDUES 26-150 OF THE FULL LENGTH PROTEIN.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.02 Å3/Da / Density % sol: 38.96 %
Description: DATA WERE SCALED USING XSCALE WITH FRIEDEL PAIRS KEPT AS SEPARATE WHEN COMPUTING R-SYM, COMPLETENESS AND
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 1.6000M ammonium sulfate, 0.1M citric acid pH 5.0, 0.001 M copper (II) chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.91837,0.97932,0.97882
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 7, 2009 / Details: Flat mirror (vertical focusing)
RadiationMonochromator: Single crystal Si(111) bent monochromator (horizontal focusing)
Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979321
30.978821
ReflectionResolution: 1.42→28.421 Å / Num. obs: 43813 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 16.807 Å2 / Rmerge(I) obs: 0.035 / Net I/σ(I): 18.52
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.42-1.470.4921.7163597469194.3
1.47-1.530.3472.8238818004198.3
1.53-1.60.2534.4298647951199.3
1.6-1.680.1786.2286477606199.3
1.68-1.790.1229314268308199.3
1.79-1.930.07214.6305408066199.5
1.93-2.120.04622.4295597724199.6
2.12-2.430.03530.2308388033199.5
2.43-3.060.02739.2306227951199.6
3.06-28.4210.01953.5309087996198.8

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.5.0053refinement
PHENIXrefinement
SOLVEphasing
MolProbity3beta29model building
XSCALEdata scaling
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementMethod to determine structure: MAD / Resolution: 1.42→28.421 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.967 / Occupancy max: 1 / Occupancy min: 0.07 / SU B: 2.231 / SU ML: 0.039 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.063 / ESU R Free: 0.059
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 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 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.A SULFATE ION(SO4) FROM CRYSTALLIZATION AND GLYCEROL MOLECULES(GOL) FROM CRYOPROTECTANT ARE MODELED IN THE STRUCTURE.
RfactorNum. reflection% reflectionSelection details
Rfree0.181 2191 5 %RANDOM
Rwork0.172 ---
obs0.173 43647 99.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 56.82 Å2 / Biso mean: 14.711 Å2 / Biso min: 4.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20.41 Å20 Å2
2--0.82 Å20 Å2
3----1.23 Å2
Refinement stepCycle: LAST / Resolution: 1.42→28.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1622 0 17 228 1867
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0221928
X-RAY DIFFRACTIONr_bond_other_d0.0010.021295
X-RAY DIFFRACTIONr_angle_refined_deg1.7721.9862620
X-RAY DIFFRACTIONr_angle_other_deg0.913.0023202
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6725261
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.70826.75377
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.86415351
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.091152
X-RAY DIFFRACTIONr_chiral_restr0.0840.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022239
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02355
X-RAY DIFFRACTIONr_mcbond_it1.19521218
X-RAY DIFFRACTIONr_mcbond_other0.3032509
X-RAY DIFFRACTIONr_mcangle_it2.02731967
X-RAY DIFFRACTIONr_scbond_it1.8812710
X-RAY DIFFRACTIONr_scangle_it3.0363653
LS refinement shellResolution: 1.421→1.458 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 150 -
Rwork0.286 2950 -
all-3100 -
obs--97.92 %
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)
10.64540.03630.39050.2618-0.26721.0076-0.0055-0.04020.02780.01230.0413-0.043-0.07660.1048-0.03580.0441-0.01160.00270.0824-0.05210.040432.08327.659614.7783
20.68160.31250.31350.47730.55691.6501-0.02460.0452-0.0193-0.0603-0.02550.0826-0.0561-0.12580.05010.00850.0043-0.01380.0376-0.01170.02948.285515.908237.0162
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A44 - 150
2X-RAY DIFFRACTION2B44 - 150

+
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://pdbjlvh1.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