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- PDB-2w57: Crystal structure of the Vibrio cholerae ferric uptake regulator ... -

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Basic information

Entry
Database: PDB / ID: 2w57
TitleCrystal structure of the Vibrio cholerae ferric uptake regulator (Fur) reveals structural rearrangement of the DNA-binding domains
ComponentsFERRIC UPTAKE REGULATION PROTEIN
KeywordsMETAL TRANSPORT / GENE REGULATION / VIBRIO CHOLERAE / TRANSCRIPTION REGULATION / IRON / REPRESSOR / DNA-BINDING / TRANSCRIPTION / METAL-BINDING / FERRIC UPTAKE
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
Ferric uptake regulation protein
Similarity search - Component
Biological speciesVIBRIO CHOLERAE (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsSheikh, M.A. / Taylor, G.L.
CitationJournal: Mol.Microbiol. / Year: 2009
Title: Crystal Structure of the Vibrio Cholerae Ferric Uptake Regulator (Fur) Reveals Insights Into Metal Co-Ordination.
Authors: Sheikh, M.A. / Taylor, G.L.
History
DepositionDec 5, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.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_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_conn.ptnr2_label_seq_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

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Assembly

Deposited unit
A: FERRIC UPTAKE REGULATION PROTEIN
B: FERRIC UPTAKE REGULATION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1386
Polymers33,8762
Non-polymers2624
Water1,42379
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3030 Å2
ΔGint-29.9 kcal/mol
Surface area16910 Å2
MethodPQS
Unit cell
Length a, b, c (Å)88.880, 88.880, 85.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein FERRIC UPTAKE REGULATION PROTEIN / FERRIC UPTAKE REGULATOR


Mass: 16938.133 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) VIBRIO CHOLERAE (bacteria) / Strain: N16961 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0C6C8
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 79 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.47 Å3/Da / Density % sol: 50 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU SATURN 944 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→18 Å / Num. obs: 10961 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 8.6 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 16.6
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 8.6 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1MZB,2FU4

1mzb

2fu4


Resolution: 2.6→62.87 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.889 / SU B: 21.18 / SU ML: 0.244 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.66 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 522 4.8 %RANDOM
Rwork0.216 ---
obs0.218 10383 99.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 2.6→62.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2100 0 4 79 2183
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0212138
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.9542888
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4675260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.47525.536112
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.69115390
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.05158
X-RAY DIFFRACTIONr_chiral_restr0.0690.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021608
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1990.2874
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21418
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3210.2100
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0640.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.220.225
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.140.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6741.51334
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.1922086
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.4553882
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.3834.5802
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: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 42 -
Rwork0.268 756 -
obs--100 %
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)
11.55310.36150.89760.30340.31960.5747-0.0510.0998-0.0909-0.0770.1555-0.10880.01120.1043-0.10450.0280.00790.00660.0811-0.04250.0169-26.6060.562-2.5829
21.87870.5719-1.19340.3507-0.07791.21930.02330.0337-0.00480.02090.0274-0.0763-0.0209-0.0285-0.05070.0343-0.0305-0.01280.0460.00140.0057-23.34688.435919.0153
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 133
2X-RAY DIFFRACTION2B3 - 133

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