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- PDB-3zkw: Periplasmic Binding Protein CeuE apo form -

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Basic information

Entry
Database: PDB / ID: 3zkw
TitlePeriplasmic Binding Protein CeuE apo form
Components(ENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN) x 2
KeywordsMETAL BINDING PROTEIN / ENTEROBACTIN UPTAKE / 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
Enterochelin uptake periplasmic binding protein
Similarity search - Component
Biological speciesCAMPYLOBACTER JEJUNI (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsRaines, D.J. / Moroz, O.V. / Wilson, K.S. / Duhme-Klair, A.K.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: Interactions of a Periplasmic Binding Protein with a Tetradentate Siderophore Mimic.
Authors: Raines, D.J. / Moroz, O.V. / Wilson, K.S. / Duhme-Klair, A.
History
DepositionJan 25, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Dec 20, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN
B: ENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN
C: ENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)95,1773
Polymers95,1773
Non-polymers00
Water1,946108
1
A: ENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)31,7261
Polymers31,7261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)31,7261
Polymers31,7261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)31,7261
Polymers31,7261
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.950, 62.740, 67.980
Angle α, β, γ (deg.)82.19, 76.74, 75.96
Int Tables number1
Space group name H-MP1

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Components

#1: Protein ENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN / CEUE


Mass: 31725.551 Da / Num. of mol.: 2 / Fragment: RESIDUES 44-330
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL TRUNCATION / Source: (gene. exp.) CAMPYLOBACTER JEJUNI (Campylobacter) / Plasmid: PET-YSBLIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0P8Q4
#2: Protein ENTEROCHELIN UPTAKE PERIPLASMIC BINDING PROTEIN / CEUE


Mass: 31725.551 Da / Num. of mol.: 1 / Fragment: RESIDUES 44-330
Source method: isolated from a genetically manipulated source
Details: N-TERMINAL TRUNCATION / Source: (gene. exp.) CAMPYLOBACTER JEJUNI (Campylobacter) / Plasmid: PET-YSBLIC / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0P8Q4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

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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: 2.46 Å3/Da / Density % sol: 49.9 % / Description: NONE
Crystal growpH: 5
Details: 0.1 M MIB (SODIUM MALONATE, IMIDAZOLE, BORIC ACID) BUFFER, PH 5, 25% (W/V) PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.69→14.7 Å / Num. obs: 95173 / % possible obs: 96.8 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.1
Reflection shellResolution: 1.69→1.74 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.9 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2CHU

2chu


Resolution: 1.71→65.93 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.031 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.11 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.22743 4647 5 %RANDOM
Rwork0.19541 ---
obs0.19699 88200 96.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.407 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.42 Å2-0.02 Å2
2---0.07 Å20.52 Å2
3---0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.71→65.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6655 0 0 108 6763
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.026666
X-RAY DIFFRACTIONr_bond_other_d0.0080.024509
X-RAY DIFFRACTIONr_angle_refined_deg2.0641.9859005
X-RAY DIFFRACTIONr_angle_other_deg1.754311159
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4535854
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.3526.813273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.176151236
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3921511
X-RAY DIFFRACTIONr_chiral_restr0.1520.21057
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0217333
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021158
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
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
LS refinement shellResolution: 1.71→1.754 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 336 -
Rwork0.28 6433 -
obs--95.46 %
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)
10.12310.0935-0.0650.1607-0.21360.74340.01010.02070.02180.0202-0.00420.04170.0557-0.0079-0.00590.0377-0.00250.02090.01840.0030.0278-0.1597-0.80870.3728
20.5322-0.1915-0.10670.3279-0.13470.13770.0310.02130.0005-0.0217-0.0362-0.00070.00230.01880.00520.01840.0075-0.00280.03840.01060.019515.477826.632428.9299
30.43490.28690.11260.66050.20160.0706-0.0055-0.0124-0.05640.02270.0343-0.093-0.0029-0.0022-0.02880.0438-0.0059-0.01070.03050.0070.025233.276425.7875-3.0188
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A24 - 310
2X-RAY DIFFRACTION2B24 - 310
3X-RAY DIFFRACTION3C25 - 310

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