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- PDB-3be6: Crystal structure of FitE (crystal form 2), a group III periplasm... -

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Basic information

Entry
Database: PDB / ID: 3be6
TitleCrystal structure of FitE (crystal form 2), 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 / homologyABC 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 / Ferrichrome-binding protein
Function and homology information
Biological speciesEscherichia coli O157:H7 EDL933 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
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)131,19915
Polymers130,6504
Non-polymers54911
Water14,538807
1
A: Putative iron compound-binding protein of ABC transporter family
B: Putative iron compound-binding protein of ABC transporter family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4775
Polymers65,3252
Non-polymers1523
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3750 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)65,72210
Polymers65,3252
Non-polymers3978
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.815, 109.120, 221.992
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 / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 807 / 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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M Tris-HCl pH 7.5, 0.2M 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: 1.82→50 Å / Num. obs: 102274 / Observed criterion σ(I): 4 / Redundancy: 4.6 % / Biso Wilson estimate: 18.9 Å2 / Rsym value: 0.081 / Net I/σ(I): 13.7
Reflection shellResolution: 1.82→1.89 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 4.1 / Num. unique all: 6957 / Rsym value: 0.182 / % possible all: 63.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3BE5

3be5


Resolution: 1.82→49.45 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.932 / SU B: 4.93 / SU ML: 0.078 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.15 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21851 5120 5 %RANDOM
Rwork0.18823 ---
obs0.18975 97076 91.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2--1.96 Å20 Å2
3----1.7 Å2
Refinement stepCycle: LAST / Resolution: 1.82→49.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8992 0 26 807 9825
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0229327
X-RAY DIFFRACTIONr_angle_refined_deg1.0461.97612693
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.64951210
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.50123.384396
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.394151605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6881585
X-RAY DIFFRACTIONr_chiral_restr0.0720.21469
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027041
X-RAY DIFFRACTIONr_nbd_refined0.1930.24509
X-RAY DIFFRACTIONr_nbtor_refined0.3010.26537
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2784
X-RAY DIFFRACTIONr_metal_ion_refined0.0570.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.140.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1640.231
X-RAY DIFFRACTIONr_mcbond_it0.6091.56113
X-RAY DIFFRACTIONr_mcangle_it0.94429628
X-RAY DIFFRACTIONr_scbond_it1.47633553
X-RAY DIFFRACTIONr_scangle_it2.4464.53046
LS refinement shellResolution: 1.82→1.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.236 220 -
Rwork0.214 4311 -
obs--56.1 %
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)
11.2414-0.10330.45760.27480.17290.55720.0260.03730.0146-0.0095-0.00780.0003-0.0050.0017-0.0182-0.0195-0.00650.0022-0.02950.0086-0.0130.922-18.0664-74.7061
20.14880.0374-0.05630.287-0.09660.34790.01590.0046-0.0139-0.0155-0.016-0.0101-0.07540.010600.0118-0.00240.0134-0.0128-0.0017-0.029511.47137.9224-66.6342
30.37-0.0901-0.0941.0467-0.36480.319-0.0169-0.01950.00970.0528-0.016-0.03560.0039-0.02810.0329-0.0042-0.00750.0019-0.0203-0.013-0.0272-1.3827-16.6776-38.3387
40.0213-0.03790.08970.40570.04660.5044-0.02820.0108-0.00060.02560.0230.0104-0.0360.11030.0051-0.0181-0.0070.0030.0206-0.0122-0.033520.42550.7432-45.6563
50.42420.12870.24380.435-0.45440.8450.0157-0.01380.0131-0.0252-0.0122-0.00920.036-0.0255-0.00350.00180.0164-0.0076-0.0225-0.006-0.03360.48585.6051-19.6509
60.3326-0.1241-0.18180.34120.07780.4592-0.03160.0011-0.028-0.01580.00890.00780.00480.0750.0227-0.01590.00730.00070.0146-0.0093-0.034623.4048-4.0668-11.8562
70.44340.045-0.57780.81390.28510.8988-0.0183-0.03150.0144-0.01930.00590.03490.00340.03990.0124-0.03820.0193-0.01440.0116-0.0055-0.03073.13898.941918.4441
80.3907-0.0094-0.11720.0082-0.06420.6005-0.0354-0.03340.0158-0.0019-0.0068-0.00970.12150.060.04220.01610.0271-0.0074-0.00430.0059-0.038618.1561-10.811310.7257
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 DIFFRACTION3BB21 - 1523 - 134
4X-RAY DIFFRACTION4BB153 - 312135 - 294
5X-RAY DIFFRACTION5CC19 - 1521 - 134
6X-RAY DIFFRACTION6CC153 - 312135 - 294
7X-RAY DIFFRACTION7DD21 - 1523 - 134
8X-RAY DIFFRACTION8DD153 - 312135 - 294

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