[English] 日本語
Yorodumi
- PDB-3fw4: Crystal structure of Siderocalin (NGAL, Lipocalin 2) complexed wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fw4
TitleCrystal structure of Siderocalin (NGAL, Lipocalin 2) complexed with Ferric Catechol
ComponentsNeutrophil gelatinase-associated lipocalin
KeywordsTRANSPORT PROTEIN / 8-stranded anti-parallel beta barrel / 310-helix / Glycoprotein / Pyrrolidone carboxylic acid / Secreted
Function / homology
Function and homology information


siderophore transport / Metal sequestration by antimicrobial proteins / iron ion sequestering activity / enterobactin binding / small molecule binding / Iron uptake and transport / specific granule lumen / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / defense response to bacterium ...siderophore transport / Metal sequestration by antimicrobial proteins / iron ion sequestering activity / enterobactin binding / small molecule binding / Iron uptake and transport / specific granule lumen / positive regulation of cold-induced thermogenesis / Interleukin-4 and Interleukin-13 signaling / defense response to bacterium / iron ion binding / innate immune response / apoptotic process / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding
Similarity search - Function
Neutrophil gelatinase-associated lipocalin/epididymal-specific lipocalin-12 / Lipocalin / Lipocalin family conserved site / Calycin beta-barrel core domain / Lipocalin / cytosolic fatty-acid binding protein family / Lipocalin/cytosolic fatty-acid binding domain / Calycin / Lipocalin / Lipocalin signature. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
CATECHOL / : / Neutrophil gelatinase-associated lipocalin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsClifton, M.C. / Strong, R.K.
CitationJournal: Nat.Chem.Biol. / Year: 2010
Title: Iron traffics in circulation bound to a siderocalin (Ngal)-catechol complex.
Authors: Bao, G. / Clifton, M. / Hoette, T.M. / Mori, K. / Deng, S.X. / Qiu, A. / Viltard, M. / Williams, D. / Paragas, N. / Leete, T. / Kulkarni, R. / Li, X. / Lee, B. / Kalandadze, A. / Ratner, A.J. ...Authors: Bao, G. / Clifton, M. / Hoette, T.M. / Mori, K. / Deng, S.X. / Qiu, A. / Viltard, M. / Williams, D. / Paragas, N. / Leete, T. / Kulkarni, R. / Li, X. / Lee, B. / Kalandadze, A. / Ratner, A.J. / Pizarro, J.C. / Schmidt-Ott, K.M. / Landry, D.W. / Raymond, K.N. / Strong, R.K. / Barasch, J.
History
DepositionJan 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: 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_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.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
Revision 1.3Sep 6, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Neutrophil gelatinase-associated lipocalin
B: Neutrophil gelatinase-associated lipocalin
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,49233
Polymers61,6693
Non-polymers1,82230
Water4,378243
1
A: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,22213
Polymers20,5561
Non-polymers66512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,6834
Polymers20,5561
Non-polymers1273
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Neutrophil gelatinase-associated lipocalin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,58716
Polymers20,5561
Non-polymers1,03015
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.421, 115.421, 118.801
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

-
Protein , 1 types, 3 molecules ABC

#1: Protein Neutrophil gelatinase-associated lipocalin / NGAL / p25 / 25 kDa alpha-2-microglobulin-related subunit of MMP-9 / Lipocalin-2 / Oncogene 24p3


Mass: 20556.438 Da / Num. of mol.: 3 / Mutation: C87S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HNL, LCN2, NGAL / Plasmid: pGEX-4T3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+RIL / References: UniProt: P80188

-
Non-polymers , 6 types, 273 molecules

#2: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-CAQ / CATECHOL / 1,2-DIHYDROXYBENZENE / Catechol


Mass: 110.111 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6O2
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 3.21 Å3/Da / Density % sol: 61.66 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 1.0-1.4M Ammonium sulfate, 50 mM Sodium Chloride, 200 mM Lithium Sulfate, 100 mM Sodium Acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 30, 2008
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. all: 68321 / Num. obs: 36375 / % possible obs: 99.9 % / Redundancy: 7.9 % / Biso Wilson estimate: 50.4 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 31.5
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 5.09 / Num. unique all: 3562 / % possible all: 100

-
Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.2.0019phasing
RefinementStarting model: 1L6M

1l6m


Resolution: 2.3→40.79 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.896 / SU B: 6.721 / SU ML: 0.168
Isotropic thermal model: Used previously-determined structure
Cross valid method: THROUGHOUT / ESU R: 0.3 / ESU R Free: 0.237 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28376 3443 9.5 %RANDOM
Rwork0.25562 ---
obs0.25827 32869 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.229 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.3→40.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3683 0 99 243 4025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0223884
X-RAY DIFFRACTIONr_bond_other_d0.0020.022618
X-RAY DIFFRACTIONr_angle_refined_deg0.9251.9695258
X-RAY DIFFRACTIONr_angle_other_deg0.8223.0026369
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8655492
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.95724.276152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.84615567
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.8771513
X-RAY DIFFRACTIONr_chiral_restr0.0630.2569
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024279
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02789
X-RAY DIFFRACTIONr_nbd_refined0.1650.2663
X-RAY DIFFRACTIONr_nbd_other0.1760.22673
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21843
X-RAY DIFFRACTIONr_nbtor_other0.0780.22032
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0920.2241
X-RAY DIFFRACTIONr_metal_ion_refined0.1680.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1010.220
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1180.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.110.217
X-RAY DIFFRACTIONr_mcbond_it0.36622458
X-RAY DIFFRACTIONr_mcbond_other0.0342979
X-RAY DIFFRACTIONr_mcangle_it0.69433919
X-RAY DIFFRACTIONr_scbond_it0.74741483
X-RAY DIFFRACTIONr_scangle_it1.24761332
LS refinement shellResolution: 2.297→2.357 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 252 -
Rwork0.303 2348 -
obs--98.93 %

+
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