[English] 日本語
Yorodumi
- PDB-2j4u: E.coli OmpC - camel Lactoferrin complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2j4u
TitleE.coli OmpC - camel Lactoferrin complex
Components
  • LACTOTRANSFERRIN
  • OUTER MEMBRANE PROTEIN C PRECURSOR
KeywordsMEMBRANE PROTEIN/HYDROLASE / MEMBRANE PROTEIN-HYDROLASE COMPLEX / IRON / OMPC / PORIN / COMPLEX / PROTEASE / HYDROLASE / MEMBRANE PROTEIN / ANTIACTERIAL PEPTIDE / ION TRANSPORT / IRON TRANSPORT / SERINE PROTEASE / TRANSPORT / LACTOFERRIN / GLYCOPROTEIN / METAL-BINDING
Function / homology
Function and homology information


intermembrane phospholipid transfer / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism / positive regulation of bone mineralization involved in bone maturation / negative regulation of osteoclast development / antifungal humoral response / specific granule / negative regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of chondrocyte proliferation / regulation of tumor necrosis factor production ...intermembrane phospholipid transfer / negative regulation of tumor necrosis factor (ligand) superfamily member 11 production / negative regulation of single-species biofilm formation in or on host organism / positive regulation of bone mineralization involved in bone maturation / negative regulation of osteoclast development / antifungal humoral response / specific granule / negative regulation of lipopolysaccharide-mediated signaling pathway / positive regulation of chondrocyte proliferation / regulation of tumor necrosis factor production / bone morphogenesis / positive regulation of osteoblast proliferation / porin activity / pore complex / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / positive regulation of osteoblast differentiation / regulation of cytokine production / ossification / innate immune response in mucosa / cell outer membrane / iron ion transport / recycling endosome / antibacterial humoral response / virus receptor activity / monoatomic ion transmembrane transport / early endosome / receptor-mediated virion attachment to host cell / iron ion binding / serine-type endopeptidase activity / DNA damage response / negative regulation of apoptotic process / proteolysis / extracellular space / metal ion binding / identical protein binding / plasma membrane
Similarity search - Function
Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Lactotransferrin / Porin, Gram-negative type / Porin / : / Transferrin-like domain signature 2. / Transferrin family, iron binding site ...Porin, gammaproteobacterial / Porin, Gram-negative type, conserved site / General diffusion Gram-negative porins signature. / Gram-negative porin / Lactotransferrin / Porin, Gram-negative type / Porin / : / Transferrin-like domain signature 2. / Transferrin family, iron binding site / Transferrin-like domain signature 1. / Transferrin-like domain signature 3. / Transferrin / Transferrin-like domain / Transferrin / Transferrin-like domain profile. / Transferrin / Porin domain superfamily / Porin / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Outer membrane porin C / Lactotransferrin
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
CAMELUS DROMEDARIUS (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsBaalaji, S. / Acharya, R.K. / Singh, T.P. / Krishnaswamy, S.
CitationJournal: To be Published
Title: Crystal Structure of the Membrane Protein Ompc Complex with Antibacterial Lactoferrin
Authors: Baalaji, S. / Acharya, R.K. / Singh, T.P. / Krishnaswamy, S.
History
DepositionSep 6, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2013Group: Derived calculations / Refinement description / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "QA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 17-STRANDED BARREL THIS IS REPRESENTED BY A 18-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "UA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 16-STRANDED BARREL THIS IS REPRESENTED BY A 17-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "VA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 16-STRANDED BARREL THIS IS REPRESENTED BY A 17-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "WA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 16-STRANDED BARREL THIS IS REPRESENTED BY A 17-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
P: OUTER MEMBRANE PROTEIN C PRECURSOR
Q: OUTER MEMBRANE PROTEIN C PRECURSOR
R: OUTER MEMBRANE PROTEIN C PRECURSOR
S: LACTOTRANSFERRIN
U: OUTER MEMBRANE PROTEIN C PRECURSOR
V: OUTER MEMBRANE PROTEIN C PRECURSOR
W: OUTER MEMBRANE PROTEIN C PRECURSOR
X: LACTOTRANSFERRIN


Theoretical massNumber of molelcules
Total (without water)240,4248
Polymers240,4248
Non-polymers00
Water00
1
P: OUTER MEMBRANE PROTEIN C PRECURSOR
Q: OUTER MEMBRANE PROTEIN C PRECURSOR
R: OUTER MEMBRANE PROTEIN C PRECURSOR
S: LACTOTRANSFERRIN


Theoretical massNumber of molelcules
Total (without water)120,2124
Polymers120,2124
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9910 Å2
ΔGint-51.4 kcal/mol
Surface area44210 Å2
MethodPISA
2
U: OUTER MEMBRANE PROTEIN C PRECURSOR
V: OUTER MEMBRANE PROTEIN C PRECURSOR
W: OUTER MEMBRANE PROTEIN C PRECURSOR
X: LACTOTRANSFERRIN


Theoretical massNumber of molelcules
Total (without water)120,2124
Polymers120,2124
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9770 Å2
ΔGint-52.8 kcal/mol
Surface area40130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.470, 116.286, 152.280
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11W
21V
31U
41R
51Q
61P
12S
22X

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA

Dom-IDEns-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHE1WG1001 - 13461 - 346
21PHEPHE1VF1001 - 13461 - 346
31PHEPHE1UE1001 - 13461 - 346
41PHEPHE1RC1001 - 13461 - 346
51PHEPHE1QB1001 - 13461 - 346
61PHEPHE1PA1001 - 13461 - 346
12CYSCYS5SD1001 - 10451 - 45
22CYSCYS5XH1001 - 10451 - 45

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.5, 0.866, -0.001), (-0.866, -0.5, -0.001), (-0.001, 1)226.80463, 188.79201, 0.17467
2given(-0.5, -0.866, -0.001), (0.866, -0.5), (-0.001, -0.001, 1)276.84106, -102.00307, 0.13097
3given(-0.5, -0.866), (-0.866, 0.5, -0.001), (0.001, -1)276.83557, 159.88966, 76.06233
4given(1, 0.001, 0.001), (0.001, -1), (0.001, -1)-0.05713, 57.8043, 75.95256
5given(-0.5, 0.866), (0.866, 0.5, 0.001), (0.001, 0.001, -1)226.77521, -130.90002, 76.02821
6given(-1, -0.022, -0.016), (0.022, -1), (-0.016, -0.001, 1)208.94983, 55.56911, 3.17916

-
Components

#1: Protein
OUTER MEMBRANE PROTEIN C PRECURSOR / PORIN OMPC / OUTER MEMBRANE PROTEIN 1B / E.COLI OMPC


Mass: 38336.242 Da / Num. of mol.: 6 / Fragment: RESIDUES 22-367 / Source method: isolated from a natural source / Details: LAB COLLECTION / Source: (natural) ESCHERICHIA COLI (E. coli) / Strain: HB101 / Tissue: OUTER MEMBRANE / References: UniProt: P06996
#2: Protein/peptide LACTOTRANSFERRIN / LACTOFERRIN


Mass: 5203.188 Da / Num. of mol.: 2 / Fragment: N-TERM FRAGMENT, RESIDUES 20-64 / Source method: isolated from a natural source
Details: ONLY 45 RESIDUES SEEN REMAINING COULD NOT BE LOCATED DUE TO DISORDER.
Source: (natural) CAMELUS DROMEDARIUS (Arabian camel) / Tissue: MILK
References: UniProt: Q9TUM0, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
Has protein modificationY
Sequence detailsSIGNAL PEPTIDE NOT PRESENT ONLY THE FIRST 45 RESIDUES ARE SEEN. THE REST COULD NOT BE LOCATED DUE TO DISORDER

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.1 Å3/Da / Density % sol: 59.7 %

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.9795
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 55942 / % possible obs: 79 % / Observed criterion σ(I): 1 / Redundancy: 8.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 12
Reflection shellResolution: 3→3.11 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 3.4 / % possible all: 73

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1OSM, 1DTZ

1osm

1dtz


Resolution: 2.99→152.5 Å / Cor.coef. Fo:Fc: 0.916 / Cor.coef. Fo:Fc free: 0.857 / SU B: 15.655 / SU ML: 0.3 / Cross valid method: THROUGHOUT / ESU R Free: 0.518 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.282 2831 5.1 %RANDOM
Rwork0.215 ---
obs0.218 53110 78.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 2.99→152.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16534 0 0 0 16534
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0470.02216886
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.9011.92422836
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.93252098
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.86724.885954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.655152558
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.0691582
X-RAY DIFFRACTIONr_chiral_restr0.2780.22300
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0213590
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.3490.510119
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3640.511373
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.30211238
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.360.575
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11W2636tight positional0.110.05
12V2636tight positional0.110.05
13U2636tight positional0.110.05
14R2636tight positional0.120.05
15Q2636tight positional0.110.05
16P2636tight positional0.110.05
21S180medium positional0.950.5
21S179loose positional1.445
11W2636tight thermal0.410.5
12V2636tight thermal0.40.5
13U2636tight thermal0.420.5
14R2636tight thermal0.420.5
15Q2636tight thermal0.390.5
16P2636tight thermal0.40.5
21S180medium thermal0.262
21S179loose thermal1.4410
LS refinement shellResolution: 2.99→3.07 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 193 -
Rwork0.247 3421 -
obs--70.04 %

+
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