[English] 日本語
Yorodumi
- PDB-3bx8: Engineered Human Lipocalin 2 (LCN2), apo-form -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3bx8
TitleEngineered Human Lipocalin 2 (LCN2), apo-form
ComponentsENGINEERED HUMAN LIPOCALIN 2
KeywordsDE NOVO PROTEIN / PROTEIN BINDING / PROTEIN DESIGN / LIGAND BINDING PROTEIN
Function / homologyCalycin beta-barrel core domain / Lipocalin / Beta Barrel / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 Å
AuthorsSchonfeld, D.L. / Chatwell, L. / Skerra, A.
CitationJournal: To be Published
Title: High affinity molecular recognition and functional blockade of CTLA-4 by an engineered human lipocalin
Authors: Schonfeld, D.L. / Matschiner, G. / Chatwell, L. / Trentmann, S. / Schlehuber, S. / Hohlbaum, A. / Skerra, A.
History
DepositionJan 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ENGINEERED HUMAN LIPOCALIN 2
B: ENGINEERED HUMAN LIPOCALIN 2
C: ENGINEERED HUMAN LIPOCALIN 2
D: ENGINEERED HUMAN LIPOCALIN 2
E: ENGINEERED HUMAN LIPOCALIN 2
F: ENGINEERED HUMAN LIPOCALIN 2
G: ENGINEERED HUMAN LIPOCALIN 2
H: ENGINEERED HUMAN LIPOCALIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)164,24916
Polymers161,5428
Non-polymers2,7078
Water5,891327
1
A: ENGINEERED HUMAN LIPOCALIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4312
Polymers20,1931
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ENGINEERED HUMAN LIPOCALIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5912
Polymers20,1931
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ENGINEERED HUMAN LIPOCALIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5912
Polymers20,1931
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ENGINEERED HUMAN LIPOCALIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5912
Polymers20,1931
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: ENGINEERED HUMAN LIPOCALIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4312
Polymers20,1931
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: ENGINEERED HUMAN LIPOCALIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5912
Polymers20,1931
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: ENGINEERED HUMAN LIPOCALIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4312
Polymers20,1931
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: ENGINEERED HUMAN LIPOCALIN 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,5912
Polymers20,1931
Non-polymers3981
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)61.482, 92.861, 98.825
Angle α, β, γ (deg.)110.77, 90.00, 109.36
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein
ENGINEERED HUMAN LIPOCALIN 2 / ENGINEERED LCN2 / ENGINEERED NEUTROPHIL-GELATINASE ASSOCIATED LIPOCALIN / ENGINEERED SIDEROCALIN


Mass: 20192.723 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pNGAL62 / Production host: Escherichia coli (E. coli) / Strain (production host): W3110
#2: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#3: Chemical
ChemComp-PE5 / 3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL / 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / POLYETHYLENE GLYCOL PEG400


Mass: 398.489 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C18H38O9 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / 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: 3.05 Å3/Da / Density % sol: 59.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.45
Details: 1.45M ammonium sulphate, 0.1M Na-cacodylate, 0.1% (v/v) Anapoe X-405, pH 5.45, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.95373 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 31, 2006 / Details: mirror
RadiationMonochromator: Si-111 crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 129807 / % possible obs: 83.2 % / Redundancy: 1.9 % / Rsym value: 3.2 / Net I/σ(I): 16.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2 / Rsym value: 27.3 / % possible all: 46.9

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.004data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementStarting model: PDB ENTRY 1DFV chain B

1dfv


Resolution: 2→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rfree0.282 5529 4.3 %
Rwork0.251 --
obs-107602 83.4 %
Solvent computationBsol: 46.986 Å2
Displacement parametersBiso mean: 46.56 Å2
Baniso -1Baniso -2Baniso -3
1-7.87 Å2-6.967 Å2-0.737 Å2
2---16.052 Å2-2.51 Å2
3---8.182 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10540 0 172 327 11039
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4591.5
X-RAY DIFFRACTIONc_scbond_it1.8392
X-RAY DIFFRACTIONc_mcangle_it2.4362
X-RAY DIFFRACTIONc_scangle_it2.7252.5
LS refinement shellResolution: 2→2.07 Å /
Rfactor% reflection
Rfree0.374 -
Rwork0.352 -
obs-46.9 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2peg.par
X-RAY DIFFRACTION3peg26.par
X-RAY DIFFRACTION4water_rep.param

+
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