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- PDB-3e3k: Structural characterization of a putative endogenous metal chelat... -

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Basic information

Entry
Database: PDB / ID: 3e3k
TitleStructural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA (butane-1,2,4-tricarboxylate without nickel form)
ComponentsNickel-binding periplasmic protein
KeywordsMETAL TRANSPORT / Nickel / nickellophore / butane-1 / 2 / 4-tricarboxylate / transport
Function / homology
Function and homology information


nickel cation import across plasma membrane / metal cluster binding / peptide transport / peptide transmembrane transporter activity / negative chemotaxis / nickel cation binding / transition metal ion binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space / periplasmic space / heme binding
Similarity search - Function
Nickel ABC transporter, substrate-binding protein NikA / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II ...Nickel ABC transporter, substrate-binding protein NikA / Solute-binding protein family 5, conserved site / Bacterial extracellular solute-binding proteins, family 5 signature. / Dipeptide-binding Protein; domain 3 / Dipeptide-binding Protein; Domain 3 / Peptide/nickel binding protein, MppA-type / Solute-binding protein family 5 domain / Solute-binding protein family 5 / Bacterial extracellular solute-binding proteins, family 5 Middle / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / (2R)-butane-1,2,4-tricarboxylic acid / Nickel-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsCherrier, M.V. / Cavazza, C. / Bochot, C. / Lemaire, D. / Fontecilla-Camps, J.C.
CitationJournal: Biochemistry / Year: 2008
Title: Structural characterization of a putative endogenous metal chelator in the periplasmic nickel transporter NikA
Authors: Cherrier, M.V. / Cavazza, C. / Bochot, C. / Lemaire, D. / Fontecilla-Camps, J.C.
History
DepositionAug 7, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nickel-binding periplasmic protein
B: Nickel-binding periplasmic protein
C: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)170,52120
Polymers169,0823
Non-polymers1,43917
Water1,856103
1
A: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8906
Polymers56,3611
Non-polymers5295
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,8567
Polymers56,3611
Non-polymers4956
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7757
Polymers56,3611
Non-polymers4156
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)158.700, 158.700, 134.600
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Nickel-binding periplasmic protein / NikA


Mass: 56360.734 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: nikA, b3476, JW3441 / Plasmid: pET28B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P33590

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Non-polymers , 6 types, 120 molecules

#2: 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
#3: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-HCT / (2R)-butane-1,2,4-tricarboxylic acid


Mass: 190.151 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H10O6
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.89 Å3/Da / Density % sol: 57.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 1.5M ammonium sulfate, 0.1M sodium acetate, pH4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 20, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionHighest resolution: 2.8 Å / % possible obs: 93.6 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 64.602 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 24.9
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5 % / Rmerge(I) obs: 0.348 / Mean I/σ(I) obs: 5.3 / Num. measured obs: 45255 / Num. unique all: 4202 / Num. unique obs: 9081 / % possible all: 89.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZLQ

1zlq


Resolution: 2.8→48.45 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.85 / Occupancy min: 0 / SU B: 18.96 / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.36 / ESU R Free: 0.472 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32087 2356 5 %RANDOM
Rwork0.24475 ---
obs0.24853 44771 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 86.29 Å2 / Biso mean: 61.426 Å2 / Biso min: 19.93 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20.16 Å20 Å2
2--0.33 Å20 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.8→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11879 0 90 103 12072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.02211981
X-RAY DIFFRACTIONr_angle_refined_deg2.1821.9616343
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.97251493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.19824.709550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.252151801
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7081557
X-RAY DIFFRACTIONr_chiral_restr0.140.21795
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029359
X-RAY DIFFRACTIONr_nbd_refined0.320.36645
X-RAY DIFFRACTIONr_nbtor_refined0.3520.58152
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2560.5861
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2570.351
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.59
X-RAY DIFFRACTIONr_mcbond_it1.29227637
X-RAY DIFFRACTIONr_mcangle_it2.164312088
X-RAY DIFFRACTIONr_scbond_it2.06534904
X-RAY DIFFRACTIONr_scangle_it3.12344255
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.537 174 -
Rwork0.389 3310 -
all-4504 -
obs--100 %

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