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- PDB-4i8c: X-ray structure of NikA in complex with Ni-(L-His)2 -

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Basic information

Entry
Database: PDB / ID: 4i8c
TitleX-ray structure of NikA in complex with Ni-(L-His)2
ComponentsNickel-binding periplasmic protein
KeywordsTRANSPORT PROTEIN
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 ...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 / membrane
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 / HISTIDINE / NICKEL (II) ION / Nickel-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.503 Å
AuthorsLebrette, H. / Iannello, M. / Fontecilla-Camps, J.C. / Cavazza, C.
CitationJournal: J.Inorg.Biochem. / Year: 2012
Title: The binding mode of Ni-((L)-His)(2) in NikA revealed by X-ray crystallography.
Authors: Lebrette, H. / Iannello, M. / Fontecilla-Camps, J.C. / Cavazza, C.
History
DepositionDec 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)172,10439
Polymers169,0823
Non-polymers3,02236
Water5,927329
1
A: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,42114
Polymers56,3611
Non-polymers1,06113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,49415
Polymers56,3611
Non-polymers1,13314
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,18910
Polymers56,3611
Non-polymers8289
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)158.630, 158.630, 135.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
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


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 / Production host: Escherichia coli (E. coli) / References: UniProt: P33590

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Non-polymers , 7 types, 365 molecules

#2: Chemical
ChemComp-HIS / HISTIDINE / Histidine


Type: L-peptide linking / Mass: 156.162 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H10N3O2
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ni
#4: Chemical
ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 329 / 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: 2.92 Å3/Da / Density % sol: 57.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 1.5M Ammonium sulfate, 0.1M sodium acetate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 28, 2012 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.5→48.5 Å / Num. obs: 66527 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 2.58 % / Rsym value: 0.053
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 2.58 % / Mean I/σ(I) obs: 2.34 / Rsym value: 0.401 / % possible all: 96.4

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Processing

Software
NameVersionClassification
MXCUBEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3DP8

3dp8


Resolution: 2.503→48.5 Å / SU ML: 0.31 / σ(F): 1.06 / Phase error: 25.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2339 3324 4.99 %
Rwork0.1885 --
obs0.1907 66526 98.29 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.503→48.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11859 0 192 329 12380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00912390
X-RAY DIFFRACTIONf_angle_d1.09116849
X-RAY DIFFRACTIONf_dihedral_angle_d13.6764581
X-RAY DIFFRACTIONf_chiral_restr0.0721829
X-RAY DIFFRACTIONf_plane_restr0.0052214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.503-2.53140.30652190.25844121X-RAY DIFFRACTION98
2.5314-2.56120.28762210.25534205X-RAY DIFFRACTION99
2.5612-2.59250.33332190.25714118X-RAY DIFFRACTION99
2.5925-2.62530.34652150.26044121X-RAY DIFFRACTION99
2.6253-2.65980.29032150.24494186X-RAY DIFFRACTION99
2.6598-2.69620.29972170.24964039X-RAY DIFFRACTION98
2.6962-2.73480.2992210.25364177X-RAY DIFFRACTION99
2.7348-2.77560.35172210.25884173X-RAY DIFFRACTION99
2.7756-2.81890.31172170.24544109X-RAY DIFFRACTION99
2.8189-2.86520.32162180.24534137X-RAY DIFFRACTION99
2.8652-2.91450.27162160.23734129X-RAY DIFFRACTION100
2.9145-2.96750.29712180.23064147X-RAY DIFFRACTION99
2.9675-3.02460.2822210.24514163X-RAY DIFFRACTION99
3.0246-3.08630.33992180.23444152X-RAY DIFFRACTION99
3.0863-3.15340.31612180.22214111X-RAY DIFFRACTION99
3.1534-3.22680.29952170.23234126X-RAY DIFFRACTION99
3.2268-3.30750.26592160.22834117X-RAY DIFFRACTION99
3.3075-3.39690.30532150.21494088X-RAY DIFFRACTION99
3.3969-3.49680.23392130.20544044X-RAY DIFFRACTION97
3.4968-3.60960.26522160.20784140X-RAY DIFFRACTION98
3.6096-3.73860.28092100.19434011X-RAY DIFFRACTION97
3.7386-3.88820.23522160.18484053X-RAY DIFFRACTION97
3.8882-4.06510.20032110.17124067X-RAY DIFFRACTION97
4.0651-4.27930.20992130.15764079X-RAY DIFFRACTION98
4.2793-4.54720.1822150.14554103X-RAY DIFFRACTION98
4.5472-4.8980.17472090.14684052X-RAY DIFFRACTION98
4.898-5.39030.16082140.14194136X-RAY DIFFRACTION98
5.3903-6.1690.20152190.14924114X-RAY DIFFRACTION98
6.169-7.76710.15642070.1414057X-RAY DIFFRACTION98
7.7671-48.50950.14762000.14413840X-RAY DIFFRACTION92

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