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- PDB-4rb2: Crystal structure of Magnetospirillum gryphiswaldense MSR-1 SeMet... -

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Basic information

Entry
Database: PDB / ID: 4rb2
TitleCrystal structure of Magnetospirillum gryphiswaldense MSR-1 SeMet-Fur-Mn2+-feoAB1 operator
Components
  • (DNA (25-MER)) x 2
  • DNA-binding transcriptional dual regulator of siderophore biosynthesis and transport(Fur family)
KeywordsMETAL BINDING PROTEIN/DNA / ferric uptake regulator (FUR) / metal ion activation / operator recognition / cooperativity / broad substrate recognition / DNA shape readout / METAL BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


negative regulation of siderophore biosynthetic process / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / zinc ion binding / cytosol
Similarity search - Function
Ferric-uptake regulator, C-terminal dimerisarion domain / Ferric-uptake regulator, C-terminal domain / Ferric-uptake regulator / Ferric uptake regulator family / Dna Ligase; domain 1 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich ...Ferric-uptake regulator, C-terminal dimerisarion domain / Ferric-uptake regulator, C-terminal domain / Ferric-uptake regulator / Ferric uptake regulator family / Dna Ligase; domain 1 / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Ferric uptake regulation protein
Similarity search - Component
Biological speciesMagnetospirillum gryphiswaldense (magnetotactic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.82 Å
AuthorsDeng, Z. / Chen, Z.
CitationJournal: Nat Commun
Title: Mechanistic insights into metal ion activation and operator recognition by the ferric uptake regulator.
Authors: Deng, Z. / Wang, Q. / Liu, Z. / Zhang, M. / Machado, A.C. / Chiu, T.P. / Feng, C. / Zhang, Q. / Yu, L. / Qi, L. / Zheng, J. / Wang, X. / Huo, X. / Qi, X. / Li, X. / Wu, W. / Rohs, R. / Li, Y. / Chen, Z.
History
DepositionSep 12, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 15, 2015Provider: 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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.ptnr1_label_seq_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (25-MER)
B: DNA (25-MER)
C: DNA-binding transcriptional dual regulator of siderophore biosynthesis and transport(Fur family)
D: DNA-binding transcriptional dual regulator of siderophore biosynthesis and transport(Fur family)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,1868
Polymers48,9674
Non-polymers2204
Water25214
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8470 Å2
ΔGint-70 kcal/mol
Surface area20060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.301, 68.669, 82.646
Angle α, β, γ (deg.)90.00, 109.25, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-305-

HOH

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Components

#1: DNA chain DNA (25-MER) / feoAB1 operator


Mass: 7646.970 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (25-MER) / feoAB1 operator


Mass: 7705.022 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein DNA-binding transcriptional dual regulator of siderophore biosynthesis and transport(Fur family)


Mass: 16807.314 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Magnetospirillum gryphiswaldense (magnetotactic)
Strain: MSR-1 v2 / Gene: Fur, MGMSRv2_3137 / Production host: Escherichia coli (E. coli) / References: UniProt: V6F4Q0
#4: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 14 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.58 Å3/Da / Density % sol: 52.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6
Details: pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 1W2B / Wavelength: 0.9793, 0.9795, 1.000
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 11, 2012
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97951
311
ReflectionResolution: 2.82→50 Å / Num. all: 12295 / Num. obs: 11230 / % possible obs: 91.4 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 2.82→2.87 Å / % possible all: 92.4

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD
Starting model: PDB entry 4RAY

4ray


Resolution: 2.82→45.73 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.897 / SU B: 17.896 / SU ML: 0.341 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R Free: 0.44 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27541 580 5.2 %RANDOM
Rwork0.23811 ---
obs0.24013 10544 91.36 %-
all-11230 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 85.68 Å2
Baniso -1Baniso -2Baniso -3
1--6.48 Å2-0 Å25.08 Å2
2---1.46 Å20 Å2
3---4.96 Å2
Refinement stepCycle: LAST / Resolution: 2.82→45.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2033 1019 4 14 3070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0163213
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8661.6574574
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6885265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.75422.52599
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.88215307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0161522
X-RAY DIFFRACTIONr_chiral_restr0.0580.2475
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212127
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.82→2.893 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 38 -
Rwork0.396 772 -
obs--92.36 %

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