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- PDB-3mvy: X-ray structure of the diatomic oxo-intermediate NikA/1-Int', pri... -

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Basic information

Entry
Database: PDB / ID: 3mvy
TitleX-ray structure of the diatomic oxo-intermediate NikA/1-Int', prior hydroxylation
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 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 ...nickel cation import across plasma membrane / metal cluster binding / nickel cation transport / 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 / Chem-BHZ / : / PEROXIDE ION / Nickel-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 / 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_comp_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_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_comp_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.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

Downloads & links

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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)114,95926
Polymers112,7212
Non-polymers2,23824
Water6,305350
1
A: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,77717
Polymers56,3611
Non-polymers1,41616
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,1829
Polymers56,3611
Non-polymers8228
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.985, 95.172, 125.049
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 8 types, 374 molecules

#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-FE / FE (III) ION


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


Mass: 372.415 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H24N2O5
#7: Chemical ChemComp-PER / PEROXIDE ION


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.3 Å3/Da / Density % sol: 46.43 %
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: BM30A / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 2009 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.5→43.5 Å / Num. obs: 34625 / % possible obs: 94 % / Redundancy: 2.3 % / Biso Wilson estimate: 36.9 Å2 / Rsym value: 0.106 / Net I/σ(I): 7.86
Reflection shellHighest resolution: 2.5 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 6716 / Rsym value: 0.313 / % possible all: 88

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Processing

SoftwareName: REFMAC / Version: 5.5.0109 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1ZLQ

1zlq


Resolution: 2.5→43.49 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.882 / SU B: 9.515 / SU ML: 0.214 / Cross valid method: THROUGHOUT / ESU R: 1.176 / ESU R Free: 0.311 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1823 5 %RANDOM
Rwork0.17262 ---
obs0.17645 34625 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: 21.989 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---0.16 Å20 Å2
3---0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.5→43.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7864 0 143 350 8357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0228176
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7161.97111123
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8095995
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.58724.545374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.486151298
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5621543
X-RAY DIFFRACTIONr_chiral_restr0.1060.21209
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0216295
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_it0.6691.55028
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.27628115
X-RAY DIFFRACTIONr_scbond_it2.13233148
X-RAY DIFFRACTIONr_scangle_it3.4934.53007
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 132 -
Rwork0.198 2508 -
obs--100 %

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