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- PDB-6oby: The nucleotide-binding protein AF_226 in complex with ADP from Ar... -

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Basic information

Entry
Database: PDB / ID: 6oby
TitleThe nucleotide-binding protein AF_226 in complex with ADP from Archaeoglobus fulgidus with Co found by PIXE. Based on 3KB1.
ComponentsIron-sulfur cluster carrier protein
KeywordsMETAL TRANSPORT / ALPHA-BETA PROTEIN / PIXE
Function / homology
Function and homology information


ATP-dependent FeS chaperone activity / iron-sulfur cluster assembly / 4 iron, 4 sulfur cluster binding / ATP hydrolysis activity / ATP binding / metal ion binding
Similarity search - Function
Mrp, conserved site / Mrp family signature. / Iron-sulfur protein NUBPL-like / Mrp/NBP35 ATP-binding protein / Flagellum site-determining protein YlxH/ Fe-S cluster assembling factor NBP35 / NUBPL iron-transfer P-loop NTPase / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / Iron-sulfur cluster carrier protein
Similarity search - Component
Biological speciesArchaeoglobus fulgidus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.87 Å
AuthorsSnell, E.H. / Garman, E.F. / Lowe, E.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1231306 United States
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: High-Throughput PIXE as an Essential Quantitative Assay for Accurate Metalloprotein Structural Analysis: Development and Application.
Authors: Grime, G.W. / Zeldin, O.B. / Snell, M.E. / Lowe, E.D. / Hunt, J.F. / Montelione, G.T. / Tong, L. / Snell, E.H. / Garman, E.F.
History
DepositionMar 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Remark 0THIS ENTRY 6OBY REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 3KB1, DETERMINED BY F. ...THIS ENTRY 6OBY REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL DATA IN 3KB1, DETERMINED BY F.FOROUHAR,S.LEW,M.ABASHIDZE,J.SEETHARAMAN,M.MAO,R.XIAO, C.CICCOSANTI,H.WANG,J.K.EVERETT,R.NAIR,T.B.ACTON,B.ROST,.T.MONTELIONE,J.F.HUNT,L.TONG,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Iron-sulfur cluster carrier protein
B: Iron-sulfur cluster carrier protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,8395
Polymers58,9262
Non-polymers9133
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3350 Å2
ΔGint-48 kcal/mol
Surface area21380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.440, 67.682, 79.403
Angle α, β, γ (deg.)90.00, 90.09, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: _ / Auth seq-ID: 4 - 258 / Label seq-ID: 4 - 258

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Iron-sulfur cluster carrier protein


Mass: 29462.975 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus (archaea) / Plasmid: PET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)+ MAGIC / References: UniProt: O28015
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.35 Å3/Da / Density % sol: 47.56 % / Description: Authors used the sf data from the entry 3KB1
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: PROTEIN SOLUTION: 100MM NACL, 5MM DTT, 0.02% NAN3, 10MM TRIS-HCL (PH 7.5). RESERVOIR SOLUTION: 100 MM NAACETATE (PH 4.6), 30% MPD, AND 200 MM NACL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97899 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 7, 2009 / Details: MIRRORS
RadiationMonochromator: SI 111 CHANNEL MIRRORS / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97899 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 26385 / % possible obs: 98.3 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.093 / Rsym value: 0.076 / Net I/σ(I): 15
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.254 / Num. unique obs: 0 / Rsym value: 0.22 / % possible all: 88.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0241refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.87→28.54 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.859 / SU B: 23.812 / SU ML: 0.43 / Cross valid method: THROUGHOUT / ESU R Free: 0.481 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28395 587 4.8 %RANDOM
Rwork0.21711 ---
obs0.22036 11606 96.72 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Displacement parametersBiso mean: 49.987 Å2
Baniso -1Baniso -2Baniso -3
1--7.61 Å2-0 Å2-0.23 Å2
2--3.81 Å20 Å2
3---3.81 Å2
Refinement stepCycle: LAST / Resolution: 2.87→28.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3764 0 55 8 3827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0133894
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173750
X-RAY DIFFRACTIONr_angle_refined_deg1.4341.6485276
X-RAY DIFFRACTIONr_angle_other_deg1.1381.5768706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5925482
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.44623.103174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.64115650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2211518
X-RAY DIFFRACTIONr_chiral_restr0.0560.2510
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024254
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02758
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_it3.2685.1281940
X-RAY DIFFRACTIONr_mcbond_other3.2685.1281939
X-RAY DIFFRACTIONr_mcangle_it5.267.6812418
X-RAY DIFFRACTIONr_mcangle_other5.2597.6812419
X-RAY DIFFRACTIONr_scbond_it3.55.4711954
X-RAY DIFFRACTIONr_scbond_other3.55.4711954
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7288.0252859
X-RAY DIFFRACTIONr_long_range_B_refined9.9797.0815924
X-RAY DIFFRACTIONr_long_range_B_other9.9797.07515925
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 7544 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.872→2.947 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 29 -
Rwork0.31 718 -
obs--80.24 %

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