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- PDB-3mw0: X-ray structure of the doubly hydroxylated iron complex-NikA spec... -

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Basic information

Entry
Database: PDB / ID: 3mw0
TitleX-ray structure of the doubly hydroxylated iron complex-NikA species, NikA1/O2
ComponentsNickel-binding periplasmic protein
KeywordsTRANSPORT PROTEIN / protein-bound iron complex
Function / homology
Function and homology information


nickel cation import across plasma membrane / metal cluster binding / nickel cation transport / peptide transmembrane transporter activity / peptide transport / negative chemotaxis / nickel cation binding / transition metal ion binding / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / outer membrane-bounded periplasmic space ...nickel cation import across plasma membrane / metal cluster binding / nickel cation transport / peptide transmembrane transporter activity / peptide transport / 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
Chem-BHR / DITHIANE DIOL / : / Nickel-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCavazza, C. / Bochot, C. / Rousselot-Pailley, P. / Carpentier, P. / Cherrier, M.V. / Martin, L. / Marchi-Delapierre, C. / Fontecilla-Camps, J.C. / Menage, S.
CitationJournal: NAT.CHEM. / Year: 2010
Title: Crystallographic snapshots of the reaction of aromatic C-H with O(2) catalysed by a protein-bound iron complex
Authors: Cavazza, C. / Bochot, C. / Rousselot-Pailley, P. / Carpentier, P. / Cherrier, M.V. / Martin, L. / Marchi-Delapierre, C. / Fontecilla-Camps, J.C. / Menage, S.
History
DepositionMay 5, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / 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_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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_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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)113,9468
Polymers112,7212
Non-polymers1,2256
Water8,593477
1
A: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9734
Polymers56,3611
Non-polymers6123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,9734
Polymers56,3611
Non-polymers6123
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.983, 94.511, 125.105
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 Nickel-binding periplasmic protein / NikA


Mass: 56360.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: nikA / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P33590, EC: 3.6.3.24
#2: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe
#3: Chemical ChemComp-BHR / 2-[2-[carboxymethyl-[(2-hydroxyphenyl)methyl]amino]ethyl-[(2,3-dihydroxyphenyl)methyl]amino]ethanoic acid


Mass: 404.414 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N2O7
#4: Chemical ChemComp-DTD / DITHIANE DIOL


Mass: 152.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 477 / 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: 2.28 Å3/Da / Density % sol: 46.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: 1.8M ammonium sulfate, 0.1M sodium acetate, pH 4.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorDate: Nov 6, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.3→47.6 Å / Num. obs: 46496 / % possible obs: 98 % / Redundancy: 7.2 % / Biso Wilson estimate: 26.6 Å2 / Rsym value: 0.106 / Net I/σ(I): 13.1
Reflection shellHighest resolution: 2.3 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 5.7 / Num. unique all: 5316 / Rsym value: 0.335 / % possible all: 94

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Processing

Software
NameVersionClassification
MxCuBEdata collection
PHASERphasing
REFMAC5.5.0102refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ZLQ

1zlq


Resolution: 2.3→47.26 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.901 / SU B: 6.506 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.349 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24436 2377 5 %RANDOM
Rwork0.17424 ---
obs0.17762 45153 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.154 Å2
Baniso -1Baniso -2Baniso -3
1-0.25 Å20 Å20 Å2
2---0.43 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 2.3→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7869 0 76 477 8422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0228130
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.321.96911076
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.125993
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97824.717371
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.403151307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6271540
X-RAY DIFFRACTIONr_chiral_restr0.090.21211
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216256
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6071.55006
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.17528098
X-RAY DIFFRACTIONr_scbond_it1.82733124
X-RAY DIFFRACTIONr_scangle_it3.0684.52978
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 173 -
Rwork0.19 3296 -
obs--100 %

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