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- PDB-3be5: Crystal structure of FitE (crystal form 1), a group III periplasm... -

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Basic information

Entry
Database: PDB / ID: 3be5
TitleCrystal structure of FitE (crystal form 1), a group III periplasmic siderophore binding protein
ComponentsPutative iron compound-binding protein of ABC transporter family
KeywordsMETAL TRANSPORT / Open form / closed form / group III periplasmic binding protein / Structural Genomics / Montreal-Kingston Bacterial Structural Genomics Initiative / BSGI
Function / homology
Function and homology information


iron coordination entity transport / outer membrane-bounded periplasmic space
Similarity search - Function
: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ferrichrome-binding protein
Similarity search - Component
Biological speciesEscherichia coli O157:H7 EDL933 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsShi, R. / Matte, A. / Cygler, M. / Montreal-Kingston Bacterial Structural Genomics Initiative (BSGI)
CitationJournal: Proteins / Year: 2008
Title: Trapping open and closed forms of FitE-A group III periplasmic binding protein.
Authors: Shi, R. / Proteau, A. / Wagner, J. / Cui, Q. / Purisima, E.O. / Matte, A. / Cygler, M.
History
DepositionNov 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999AUTHORS STATE THAT THIS IS A MUTATION (A259T) BASED ON THE ELECTRON DENSITY MAPS.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative iron compound-binding protein of ABC transporter family
B: Putative iron compound-binding protein of ABC transporter family
C: Putative iron compound-binding protein of ABC transporter family
D: Putative iron compound-binding protein of ABC transporter family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,7216
Polymers130,6504
Non-polymers712
Water10,971609
1
A: Putative iron compound-binding protein of ABC transporter family
B: Putative iron compound-binding protein of ABC transporter family


Theoretical massNumber of molelcules
Total (without water)65,3252
Polymers65,3252
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
MethodPISA
2
C: Putative iron compound-binding protein of ABC transporter family
D: Putative iron compound-binding protein of ABC transporter family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3964
Polymers65,3252
Non-polymers712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.656, 113.633, 224.521
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Putative iron compound-binding protein of ABC transporter family / Putative ferrichrome-binding protein


Mass: 32662.539 Da / Num. of mol.: 4
Fragment: FitE without N-terminal signal sequence: Residues 19-315
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli O157:H7 EDL933 (bacteria)
Strain: O157:H7 EDL933, EHEC / Gene: fite, ECs3913, Z4382 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): DL41(DE3) / References: UniProt: Q8XBR1
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 609 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M Tris-HCl pH 7.5, 0.2 M MgCl2, 22% (w/v) PEG 3350, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 12, 2006
Details: Cryogenically cooled double crystal monochromator with horizontal focusing sagitally bent second mono crystal
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 60135 / Observed criterion σ(I): 5 / Redundancy: 5.2 % / Biso Wilson estimate: 26.4 Å2 / Rsym value: 0.073 / Net I/σ(I): 14.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 4.8 / Num. unique all: 4025 / Rsym value: 0.183 / % possible all: 59.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→47.04 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.911 / SU B: 11.461 / SU ML: 0.155 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.317 / ESU R Free: 0.236 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24488 3042 5.1 %RANDOM
Rwork0.18712 ---
obs0.19008 57016 87.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.43 Å2
Baniso -1Baniso -2Baniso -3
1--1.02 Å20 Å20 Å2
2--3.8 Å20 Å2
3----2.78 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9021 0 2 609 9632
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229246
X-RAY DIFFRACTIONr_angle_refined_deg1.2681.97712574
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.48151188
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.07123.538390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.473151580
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0731580
X-RAY DIFFRACTIONr_chiral_restr0.0820.21458
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026968
X-RAY DIFFRACTIONr_nbd_refined0.2030.24363
X-RAY DIFFRACTIONr_nbtor_refined0.3020.26396
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1510.2658
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1230.27
X-RAY DIFFRACTIONr_mcbond_it0.611.56103
X-RAY DIFFRACTIONr_mcangle_it0.96329563
X-RAY DIFFRACTIONr_scbond_it1.5733510
X-RAY DIFFRACTIONr_scangle_it2.524.53003
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 138 -
Rwork0.198 2697 -
obs--56.6 %
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)
12.261-0.6643-1.69771.5812-0.41392.73560.02330.02240.0748-0.15920.0685-0.0146-0.0540.0341-0.0918-0.0741-0.00740.0310.00180.0458-0.119150.990575.7646-73.4414
20.38890.155-0.33320.79710.26751.47310.04060.09290.0397-0.1058-0.06260.03280.28-0.25170.022-0.0041-0.0005-0.01720.1070.0524-0.105438.697750.8388-66.9709
32.6458-1.70260.21433.3779-0.17181.7824-0.0547-0.27690.24630.40020.0553-0.2298-0.2798-0.0176-0.0005-0.0506-0.02850.02290.04410.0317-0.039353.349273.5434-37.4131
40.80430.24-0.35080.4947-0.0351.96460.04290.1374-0.03130.03870.03570.02260.1096-0.4241-0.0786-0.10380.00160.00690.14840.0607-0.054230.217156.7529-45.5757
50.8463-0.1169-0.78370.75680.49592.41060.09470.03980.0445-0.0977-0.0349-0.0371-0.0120.0575-0.0598-0.07750.01550.0245-0.0040.0143-0.068250.505649.3-20.7796
61.0108-0.2676-0.350.44670.46221.50670.04420.13980.1577-0.0737-0.0028-0.0338-0.2251-0.2543-0.0414-0.06110.02280.00530.05890.0519-0.034428.029958.7238-11.2863
73.8270.61671.94011.8693-0.60242.05720.1089-0.2789-0.15450.1155-0.01360.01820.1059-0.0261-0.0953-0.09020.0253-0.0065-0.0221-0.0063-0.087652.11941.127315.2193
81.7521-0.3843-0.40130.70850.3221.64220.0316-0.08960.04880.0456-0.02360.0264-0.2344-0.1406-0.0081-0.03460.02130.0217-0.01420.0015-0.072534.367264.191111.1783
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA19 - 1521 - 134
2X-RAY DIFFRACTION2AA153 - 312135 - 294
3X-RAY DIFFRACTION3BB19 - 1521 - 134
4X-RAY DIFFRACTION4BB153 - 312135 - 294
5X-RAY DIFFRACTION5CC19 - 1521 - 134
6X-RAY DIFFRACTION6CC153 - 312135 - 294
7X-RAY DIFFRACTION7DD19 - 1521 - 134
8X-RAY DIFFRACTION8DD153 - 312135 - 294

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