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- PDB-4i9d: X-ray structure of NikA in complex with Fe-N,N'-Bis(2-pyridylmeth... -

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Basic information

Entry
Database: PDB / ID: 4i9d
TitleX-ray structure of NikA in complex with Fe-N,N'-Bis(2-pyridylmethyl)-N-carboxymethyl-N'-methyl
ComponentsNickel-binding periplasmic protein
KeywordsMETAL TRANSPORT / TRANSPORT PROTEIN / PROTEIN-BOUND IRON COMPLEX
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 / Chem-L4D / Nickel-binding periplasmic protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsCherrier, M.V. / Amara, P. / Iannello, M. / Cavazza, C.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2013
Title: An artificial oxygenase built from scratch: substrate binding site identified using a docking approach.
Authors: Esmieu, C. / Cherrier, M.V. / Amara, P. / Girgenti, E. / Marchi-Delapierre, C. / Oddon, F. / Iannello, M. / Jorge-Robin, A. / Cavazza, C. / Menage, S.
History
DepositionDec 5, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 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 / 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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)117,06252
Polymers112,7212
Non-polymers4,34150
Water21,5641197
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A: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,18235
Polymers56,3611
Non-polymers2,82134
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nickel-binding periplasmic protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,88017
Polymers56,3611
Non-polymers1,51916
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.670, 94.730, 124.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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


Mass: 56360.734 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: BL21(DE3) / Gene: b3476, JW3441, nikA / Plasmid: Pet22b / 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 , 5 types, 1247 molecules

#2: Chemical...
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-L4D / {(S)-N-(2-{methyl[(pyridin-2-yl-kappaN)methyl]amino-kappaN}ethyl)-N-[(pyridin-2-yl-kappaN)methyl]glycinato-kappa~2~N,O}iron(2+) / {N,N'-Bis(2-pyridylmethyl)-N-carboxymethyl-N'-methyl}iron(2+)


Mass: 369.219 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21FeN4O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1197 / 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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.7
Details: 1.8 M ammonium sulfate, 100 mM sodium acetate pH 4.7, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.27985 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 18, 2010 / Details: Mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27985 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 113057 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 25.693 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 19.33
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique allNum. unique obs% possible all
1.7-1.86.40.3585.84112764176081760899.7
1.8-1.96.60.2378.5693171141441414499.8
1.9-26.70.16211.9976997114321143299.9
2-2.16.80.11915.41645629424942499.9
2.1-2.570.08420.31171338243972439799.9
2.5-36.90.05826.15104269150631506399.9
3-470.04235.1284967120571205799.9
4-66.80.03641.21430946298629899.8
6-106.40.03541.67134762116211698.1
10-504.80.03536.5248451851879.3

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ZLQ

1zlq


Resolution: 1.7→40.94 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8856 / SU ML: 0.17 / σ(F): 1.99 / Phase error: 18.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1945 5652 5 %RANDOM
Rwork0.1524 ---
obs0.1545 113053 99.68 %-
all-113413 --
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 51.419 Å2 / ksol: 0.379 e/Å3
Displacement parametersBiso max: 89.28 Å2 / Biso mean: 24.0375 Å2 / Biso min: 7.11 Å2
Baniso -1Baniso -2Baniso -3
1--0.1689 Å2-0 Å20 Å2
2---1.0582 Å2-0 Å2
3---1.2271 Å2
Refinement stepCycle: LAST / Resolution: 1.7→40.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7899 0 284 1197 9380
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0238846
X-RAY DIFFRACTIONf_angle_d2.25212059
X-RAY DIFFRACTIONf_chiral_restr0.1651293
X-RAY DIFFRACTIONf_plane_restr0.0131584
X-RAY DIFFRACTIONf_dihedral_angle_d15.1863375
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.71930.25061860.20353539372599
1.7193-1.73950.25651850.194235223707100
1.7395-1.76070.27441880.188935683756100
1.7607-1.7830.2331850.179335113696100
1.783-1.80650.24041870.180235613748100
1.8065-1.83120.22721870.181635383725100
1.8312-1.85740.22721870.167435583745100
1.8574-1.88510.21321880.168135723760100
1.8851-1.91460.21421840.165335073691100
1.9146-1.94590.20061880.164635583746100
1.9459-1.97950.22211880.167535723760100
1.9795-2.01550.21851870.169935683755100
2.0155-2.05430.21681880.156735573745100
2.0543-2.09620.19161860.153635443730100
2.0962-2.14180.19911880.152535603748100
2.1418-2.19160.2031860.154735523738100
2.1916-2.24640.18671890.152835913780100
2.2464-2.30710.18641880.153535713759100
2.3071-2.3750.22941900.151735933783100
2.375-2.45170.19541880.149235733761100
2.4517-2.53930.20921880.15935843772100
2.5393-2.64090.1991900.15635963786100
2.6409-2.76110.21071880.157735793767100
2.7611-2.90660.19271910.152636233814100
2.9066-3.08870.20371890.149236043793100
3.0887-3.3270.18121910.146336193810100
3.327-3.66170.17341920.137136603852100
3.6617-4.19110.15871920.120536363828100
4.1911-5.27850.15171940.128536893883100
5.2785-40.95160.19631940.17423696389096
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.08520.489-0.06281.4326-0.14081.115-0.0028-0.0383-0.0337-0.0614-0.05520.11820.0776-0.10640.05210.08920.0051-0.0160.094-0.02760.115-14.7735-12.0006-40.6326
21.85871.51770.69682.79820.75741.0641-0.10750.2771-0.0077-0.45990.16480.0661-0.14430.0579-0.04450.20440.0117-0.01210.1531-0.01840.1146-10.03277.4071-51.4893
30.631-0.06970.18520.546-0.22410.5164-0.0211-0.01590.05550.0288-0.0082-0.0334-0.09880.05050.02460.1123-0.00570.00470.0937-0.01760.0927-0.307812.4284-22.4611
41.70240.02980.83591.48290.40264.5130.08290.1732-0.1221-0.08110.0374-0.2889-0.02061.0137-0.12510.15210.0094-0.00760.2724-0.01790.183620.7117.1172-15.1435
50.91380.6191-0.18440.8119-0.40210.4401-0.06230.0833-0.1432-0.11940.0104-0.1570.06810.10780.0580.11830.01290.01510.1267-0.01890.12877.7083.5073-25.6671
60.5191-0.06260.08111.0806-0.49391.01290.00770.0103-0.0941-0.05120.01350.06630.1017-0.0673-0.0190.1013-0.00370.0080.0938-0.02170.1121-7.4252-0.5117-24.0073
71.7981-0.04250.54190.5769-0.26461.4218-0.00820.2879-0.1739-0.13410.11750.25490.1516-0.2176-0.09860.1685-0.0511-0.02850.2067-0.00650.2208-40.12519.2236-25.1249
80.6475-0.0634-0.271.4805-0.15970.83270.0824-0.02120.05510.0941-0.05210.0417-0.1048-0.037-0.03050.099-0.00410.01430.12950.00560.0978-21.787727.9966-17.483
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 3:164)A3 - 164
2X-RAY DIFFRACTION2chain 'A' and (resseq 165:211)A165 - 211
3X-RAY DIFFRACTION3chain 'A' and (resseq 212:321)A212 - 321
4X-RAY DIFFRACTION4chain 'A' and (resseq 322:350)A322 - 350
5X-RAY DIFFRACTION5chain 'A' and (resseq 351:412)A351 - 412
6X-RAY DIFFRACTION6chain 'A' and (resseq 413:500)A413 - 500
7X-RAY DIFFRACTION7chain 'B' and (resseq 4:234)B4 - 234
8X-RAY DIFFRACTION8chain 'B' and (resseq 235:500)B235 - 500

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