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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


iron ion transport / outer membrane-bounded periplasmic space / 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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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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


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

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Experimental details

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Experiment

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

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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

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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

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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

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