[English] 日本語
Yorodumi
- PDB-2chu: CeuE in complex with mecam -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2chu
TitleCeuE in complex with mecam
ComponentsENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN
KeywordsBINDING PROTEIN / ENTEROCHELIN UPTAKE / IRON / CAMPYLOBACTER JEJUNI / MECAM / SELF ASSEMBLY / SIDEROPHORE
Function / homology
Function and homology information


outer membrane-bounded periplasmic space / iron ion transport / metal ion binding
Similarity search - Function
FatB domain / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Prokaryotic membrane lipoprotein lipid attachment site profile. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-ECA / : / Enterochelin uptake periplasmic binding protein / :
Similarity search - Component
Biological speciesCAMPYLOBACTER JEJUNI (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMuller, A. / Wilkinson, A.J. / Wilson, K.S. / Duhme-Klair, A.K.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2006
Title: An [{Fe(Mecam)}(2)](6-) Bridge in the Crystal Structure of a Ferric Enterobactin Binding Protein.
Authors: Muller, A. / Wilkinson, A.J. / Wilson, K.S. / Duhme-Klair, A.K.
History
DepositionMar 16, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _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.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET 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
A: ENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN
B: ENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7318
Polymers65,3412
Non-polymers1,3906
Water1,35175
1
A: ENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7362
Polymers32,6711
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: ENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9956
Polymers32,6711
Non-polymers1,3245
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)73.072, 42.445, 57.523
Angle α, β, γ (deg.)91.29, 97.06, 107.34
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein ENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN / CEUE


Mass: 32670.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAMPYLOBACTER JEJUNI (Campylobacter) / Strain: NCTC11168 / Plasmid: PET-YSBLIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9PMU4, UniProt: Q0P8Q4*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-ECA / N,N',N''-[BENZENE-1,3,5-TRIYLTRIS(METHYLENE)]TRIS(2,3-DIHYDROXYBENZAMIDE)


Mass: 573.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H27N3O9
#4: Chemical ChemComp-FE / FE (III) ION / Iron


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHYMOTRYPTIC DIGEST PRODUCT RANGING FROM K15 TO THE C- TERMINAL K310

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.72 Å3/Da / Density % sol: 54.4 %
Crystal growpH: 7.5
Details: 20% PEG 3350, 2.5 MM ZINC ACETATE, MECAM, 10 MM TRIS, 75 MM NACL, pH 7.50

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 1.2823
DetectorDate: Nov 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2823 Å / Relative weight: 1
ReflectionResolution: 2→69.12 Å / Num. obs: 23425 / % possible obs: 91.7 % / Observed criterion σ(I): 3 / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13.2
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.34 / Mean I/σ(I) obs: 3.7 / % possible all: 91.2

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→69.17 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.926 / SU B: 18.202 / SU ML: 0.223 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.443 / ESU R Free: 0.279 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1187 5.1 %RANDOM
Rwork0.17 ---
obs0.174 22237 91.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20.23 Å22.36 Å2
2--1.87 Å20.62 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 2.4→69.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4344 0 88 75 4507
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0224496
X-RAY DIFFRACTIONr_bond_other_d0.0010.024176
X-RAY DIFFRACTIONr_angle_refined_deg1.6932.0086080
X-RAY DIFFRACTIONr_angle_other_deg0.92139765
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9145562
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.5926.778180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.49315819
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.511158
X-RAY DIFFRACTIONr_chiral_restr0.0910.2703
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024949
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02799
X-RAY DIFFRACTIONr_nbd_refined0.2110.2921
X-RAY DIFFRACTIONr_nbd_other0.1840.23979
X-RAY DIFFRACTIONr_nbtor_refined0.1780.22138
X-RAY DIFFRACTIONr_nbtor_other0.0890.22598
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2118
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1280.213
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0750.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.691.52956
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.13824541
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.74631825
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.694.51539
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
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.323 75
Rwork0.234 1634
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)
13.66751.0299-0.01614.61231.79695.49010.0204-0.63590.20870.2845-0.12990.1088-0.36990.41450.1095-0.22180.02930.0182-0.08510.0059-0.2235-0.64296.853410.0054
23.68460.3041-1.86454.95911.89246.4928-0.53370.1559-0.4129-0.34270.2697-0.02070.38960.35150.264-0.201-0.03530.0117-0.21570.0214-0.1720.9555-8.1752-11.6661
35.21-0.19940.45493.8541-1.43874.2224-0.20750.55260.3828-0.34810.16530.02850.0469-0.56710.0422-0.1414-0.08110.0389-0.16440.0098-0.215530.41916.7412-16.8959
43.5319-0.789-0.29643.8604-2.62886.1131-0.2619-0.5363-0.3906-0.09710.1354-0.25070.5171-0.08620.1265-0.23330.00210.0369-0.11380.0096-0.113437.54352.55134.4222
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A37 - 169
2X-RAY DIFFRACTION2A170 - 308
3X-RAY DIFFRACTION3B37 - 169
4X-RAY DIFFRACTION4B170 - 308

+
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