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- PDB-3nrp: Crystal structure of 'as isolated' uropathogenic E. coli strain F... -

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Basic information

Entry
Database: PDB / ID: 3nrp
TitleCrystal structure of 'as isolated' uropathogenic E. coli strain F11 FetP recombinantly expressed in the periplasm of E. coli BL21(DE3)
ComponentsPeriplasmic protein-probably involved in high-affinity Fe2+ transport
KeywordsTRANSPORT PROTEIN / Immunoglobulin-like fold / Iron transporter / Copper binding
Function / homologyPeriplasmic metal-binding protein Tp34-type / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsChan, A.C.K. / Murphy, M.E.P.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Characterization of a Dipartite Iron Uptake System from Uropathogenic Escherichia coli Strain F11.
Authors: Koch, D. / Chan, A.C. / Murphy, M.E. / Lilie, H. / Grass, G. / Nies, D.H.
History
DepositionJun 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Periplasmic protein-probably involved in high-affinity Fe2+ transport
B: Periplasmic protein-probably involved in high-affinity Fe2+ transport
C: Periplasmic protein-probably involved in high-affinity Fe2+ transport
D: Periplasmic protein-probably involved in high-affinity Fe2+ transport


Theoretical massNumber of molelcules
Total (without water)70,6444
Polymers70,6444
Non-polymers00
Water6,395355
1
A: Periplasmic protein-probably involved in high-affinity Fe2+ transport
B: Periplasmic protein-probably involved in high-affinity Fe2+ transport


Theoretical massNumber of molelcules
Total (without water)35,3222
Polymers35,3222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3180 Å2
ΔGint-22 kcal/mol
Surface area13980 Å2
MethodPISA
2
C: Periplasmic protein-probably involved in high-affinity Fe2+ transport
D: Periplasmic protein-probably involved in high-affinity Fe2+ transport


Theoretical massNumber of molelcules
Total (without water)35,3222
Polymers35,3222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-20 kcal/mol
Surface area14050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.852, 134.852, 45.422
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein
Periplasmic protein-probably involved in high-affinity Fe2+ transport


Mass: 17660.945 Da / Num. of mol.: 4 / Fragment: UNP residues 25-175
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: F11 / Gene: EcF11_1994 / Plasmid: pET22b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B3HWD5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 3.38 Å3/Da / Density % sol: 63.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20% PEG 3350, 0.2 M ammonium citrate pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97964 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 23, 2008 / Details: Rh coated mirror
RadiationMonochromator: Double crystal monochromator Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97964 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.408
11h+k,-k,-l20.088
11K, H, -L30.089
11-h,-k,l40.415
ReflectionResolution: 1.6→116.786 Å / Num. all: 114166 / Num. obs: 114166 / % possible obs: 93.6 % / Redundancy: 4.1 % / Rsym value: 0.08 / Net I/σ(I): 8.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.6-1.693.60.3931.956301157020.39388.1
1.69-1.793.50.2672.850828147150.26787.3
1.79-1.913.40.2023.446548138360.20287.3
1.91-2.073.30.1454.444553136550.14592.5
2.07-2.263.50.1343.946765132930.13497.9
2.26-2.534.30.1195.252466122480.11999.9
2.53-2.925.30.1065.856820107500.106100
2.92-3.585.60.08285153591450.082100
3.58-5.065.70.05711.94003370590.05799.6
5.06-42.3335.60.05511.82124437630.05597.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å42.33 Å
Translation2.5 Å42.33 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.15data scaling
MOLREPphasing
REFMACrefmac_5.5.0102refinement
PDB_EXTRACT3.1data extraction
Blu-Icedata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→50.01 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 2.572 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.016 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2075 5760 5.1 %RANDOM
Rwork0.1707 ---
obs0.1726 114016 93.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 49.98 Å2 / Biso mean: 21.067 Å2 / Biso min: 7.57 Å2
Baniso -1Baniso -2Baniso -3
1-6.53 Å20 Å20 Å2
2--6.53 Å20 Å2
3----13.05 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4704 0 0 355 5059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224993
X-RAY DIFFRACTIONr_angle_refined_deg1.4331.9486792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4445629
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.36424.693228
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.83215794
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0021514
X-RAY DIFFRACTIONr_chiral_restr0.0910.2677
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213956
X-RAY DIFFRACTIONr_mcbond_it0.6671.53081
X-RAY DIFFRACTIONr_mcangle_it1.08324959
X-RAY DIFFRACTIONr_scbond_it1.89731912
X-RAY DIFFRACTIONr_scangle_it2.6284.51833
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 449 -
Rwork0.295 7387 -
all-7836 -
obs--86.83 %

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