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- PDB-4oi3: Crystal structure analysis of SCO4226 from Streptomyces coelicolo... -

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Basic information

Entry
Database: PDB / ID: 4oi3
TitleCrystal structure analysis of SCO4226 from Streptomyces coelicolor A3(2)
ComponentsNickel responsive protein
KeywordsMETAL BINDING PROTEIN / nickel responsive protein / Structural Genomics / ferredoxin-like fold / a nickel responsive protein / nickel binding
Function / homologyORF SCO4226, nickel-binding ferredoxin-like monomer / SCO4226-like / SCO4226, nickel-binding ferredoxin-like monomer / Nickel responsive protein SCO4226-like / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / SCO4226 family nickel-binding protein
Function and homology information
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsLu, M. / Jiang, Y.L. / Wang, S. / Cheng, W. / Zhang, R.G. / Virolle, M.J. / Chen, Y. / Zhou, C.Z.
CitationJournal: Plos One / Year: 2014
Title: Streptomyces coelicolor SCO4226 Is a Nickel Binding Protein.
Authors: Lu, M. / Jiang, Y.L. / Wang, S. / Jin, H. / Zhang, R.G. / Virolle, M.J. / Chen, Y. / Zhou, C.Z.
History
DepositionJan 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 17, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 22, 2014Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nickel responsive protein
B: Nickel responsive protein


Theoretical massNumber of molelcules
Total (without water)20,4232
Polymers20,4232
Non-polymers00
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-14 kcal/mol
Surface area7780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.574, 66.982, 34.265
Angle α, β, γ (deg.)90.00, 95.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nickel responsive protein


Mass: 10211.600 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Strain: A3(2) / Gene: SCO4226 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q9FCE4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 1.66 Å3/Da / Density % sol: 25.7 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6 M sodium citrate dehydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9794 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 13, 2008
RadiationMonochromator: Si(III) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.3→34.14 Å / Num. all: 32680 / Num. obs: 30687 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 1.3→1.32 Å / Rmerge(I) obs: 0.317 / % possible all: 66.6

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
SOLVEphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.3→34.14 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.964 / SU B: 1.497 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.051 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16926 1550 5.1 %RANDOM
Rwork0.15237 ---
all0.15237 31002 --
obs0.15327 29092 93.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.945 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å2-0.32 Å2
2---0.58 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.3→34.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1256 0 0 158 1414
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0211314
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0731.8911790
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8725168
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.5424.59574
X-RAY DIFFRACTIONr_dihedral_angle_3_deg1115198
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.037156
X-RAY DIFFRACTIONr_chiral_restr0.0780.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021062
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.2556
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.290.2871
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1120.2120
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.240
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.190.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9291.5842
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.11721304
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6153520
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2064.5482
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr0.98231362
X-RAY DIFFRACTIONr_sphericity_free2.8063158
X-RAY DIFFRACTIONr_sphericity_bonded2.00831276
LS refinement shellResolution: 1.301→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 80 -
Rwork0.192 1614 -
obs--70.12 %

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