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- PDB-1mzb: Ferric uptake regulator -

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Basic information

Entry
Database: PDB / ID: 1mzb
TitleFerric uptake regulator
Componentsferric uptake regulation protein
KeywordsGENE REGULATION / ferric uptake regulator / iron / dtxr
Function / homology
Function and homology information


negative regulation of siderophore biosynthetic process / siderophore biosynthetic process / DNA-binding transcription repressor activity / protein-DNA complex / ferrous iron binding / 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 speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsPohl, E. / Vasil, M.L. / Haller, J.C.
CitationJournal: Mol.Microbiol. / Year: 2003
Title: Architecture of a protein central to iron homeostatis: Crystal structure and spectroscopic analysis of the Ferric uptake regulator
Authors: Pohl, E. / Haller, J.C. / Mijovilovich, A. / Meyer-Klaucke, W. / Garman, E. / Vasil, M.L.
History
DepositionOct 7, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / 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 / _diffrn_source.pdbx_synchrotron_site / _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.ptnr1_symmetry / _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_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.ptnr3_symmetry / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6655
Polymers15,4041
Non-polymers2624
Water2,270126
1
A: ferric uptake regulation protein
hetero molecules

A: ferric uptake regulation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,33110
Polymers30,8072
Non-polymers5238
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555x,-y+1/2,-z+1/41
2
A: ferric uptake regulation protein
hetero molecules

A: ferric uptake regulation protein
hetero molecules

A: ferric uptake regulation protein
hetero molecules

A: ferric uptake regulation protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,66120
Polymers61,6154
Non-polymers1,04716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
crystal symmetry operation10_655-x+1,-y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area10490 Å2
ΔGint-304 kcal/mol
Surface area24990 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)63.300, 63.300, 180.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Components on special symmetry positions
IDModelComponents
11A-204-

ZN

21A-1088-

HOH

Detailsthe functional unit is a dimer

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Components

#1: Protein ferric uptake regulation protein / ferric uptake regulator


Mass: 15403.638 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q03456
#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.: 126 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 57.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ethyleneglycol, ZnSO4, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
140 %ethylene glycol1reservoir
2100 mMTris1reservoirpH7.0
310 mM1reservoirZnSO4
410 mg/mlprotein1drop
510 mMTris1droppH7.5
6100 mM1dropNaBr
710 %glycerol1drop
81 mMascorbic acid1drop

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONEMBL/DESY, HAMBURG BW7A11.2837, 1.2828, 1.1310
SYNCHROTRONEMBL/DESY, HAMBURG BW7B20.8459
Detector
TypeIDDetectorDate
MARRESEARCH1CCDNov 20, 2001
MARRESEARCH2IMAGE PLATENov 11, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1focusing double crystalsMADMx-ray1
2S channel cutSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.28371
21.28281
31.1311
40.84591
ReflectionResolution: 1.8→12 Å / Num. all: 17412 / Num. obs: 17153 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.8→1.86 Å / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 30 Å / Num. obs: 17481 / % possible obs: 99.8 % / Redundancy: 12.8 % / Num. measured all: 223710 / Rmerge(I) obs: 0.049
Reflection shell
*PLUS
Highest resolution: 1.8 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.425 / Mean I/σ(I) obs: 6.2

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Processing

Software
NameClassification
MAR345data collection
DENZOdata reduction
SHELXSphasing
CNSrefinement
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→12 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2536 828 random
Rwork0.2257 --
all-17412 -
obs-17153 -
Refinement stepCycle: LAST / Resolution: 1.8→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1038 0 4 126 1168
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.49415
X-RAY DIFFRACTIONc_bond_d0.013765
Refinement
*PLUS
Rfactor Rfree: 0.254 / Rfactor Rwork: 0.226
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.49

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