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- PDB-2xig: The structure of the Helicobacter pylori ferric uptake regulator ... -

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Basic information

Entry
Database: PDB / ID: 2xig
TitleThe structure of the Helicobacter pylori ferric uptake regulator Fur reveals three functional metal binding sites
ComponentsFERRIC UPTAKE REGULATION PROTEIN
KeywordsTRANSCRIPTION / HPFUR / HOMEOSTASIS
Function / homology
Function and homology information


negative regulation of siderophore biosynthetic process / regulation of secondary metabolite biosynthetic process / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / DNA binding / 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
CITRIC ACID / Ferric uptake regulation protein
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsDian, C. / Vitale, S. / Leonard, G.A. / Fauquant, F. / Muller, C. / Bahlawane, C. / de Reuse, H. / Michaud-Soret, I. / Terradot, L.
CitationJournal: Mol.Microbiol. / Year: 2011
Title: The Structure of the Helicobacter Pylori Ferric Uptake Regulator Fur Reveals Three Functional Metal Binding Sites.
Authors: Dian, C. / Vitale, S. / Leonard, G.A. / Bahlawane, C. / Fauquant, C. / Leduc, D. / Muller, C. / De Reuse, H. / Michaud-Soret, I. / Terradot, L.
History
DepositionJun 29, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2011Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)71,70617
Polymers70,7294
Non-polymers97713
Water6,792377
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9140 Å2
ΔGint-49.7 kcal/mol
Surface area29820 Å2
MethodPISA
2
A: FERRIC UPTAKE REGULATION PROTEIN
B: FERRIC UPTAKE REGULATION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9499
Polymers35,3652
Non-polymers5857
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-21.5 kcal/mol
Surface area16250 Å2
MethodPISA
3
C: FERRIC UPTAKE REGULATION PROTEIN
D: FERRIC UPTAKE REGULATION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7578
Polymers35,3652
Non-polymers3926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-19.1 kcal/mol
Surface area16990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.150, 48.290, 72.250
Angle α, β, γ (deg.)83.32, 77.82, 87.65
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 17682.359 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Strain: 26695 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O25671
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 377 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, CYS 78 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 78 TO SER ...ENGINEERED RESIDUE IN CHAIN A, CYS 78 TO SER ENGINEERED RESIDUE IN CHAIN B, CYS 78 TO SER ENGINEERED RESIDUE IN CHAIN C, CYS 78 TO SER ENGINEERED RESIDUE IN CHAIN D, CYS 78 TO SER

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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: 2.34 Å3/Da / Density % sol: 45.76 % / Description: NONE
Crystal growpH: 7.4
Details: HPFUR2M PRE-LOADED WITH ZINC (2 EQ) AT 30 MG/ML WAS CRYSTALLIZED FROM 20% PEG 3350, 100 MM NA CITRATE, pH 7.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 15, 2009 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.85→47.96 Å / Num. obs: 51362 / % possible obs: 95.2 % / Observed criterion σ(I): 6 / Redundancy: 4.1 % / Biso Wilson estimate: 23.58 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.5
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.8 / % possible all: 94.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: ZN-SAD MODEL AT 2.15A

Resolution: 1.85→35.097 Å / SU ML: 0.21 / σ(F): 1.96 / Phase error: 25.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2339 5032 5.1 %
Rwork0.1981 --
obs0.1999 99642 92.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.921 Å2 / ksol: 0.386 e/Å3
Displacement parametersBiso mean: 35.66 Å2
Baniso -1Baniso -2Baniso -3
1-5.3609 Å23.9897 Å2-2.2187 Å2
2--4.5069 Å2-2.4059 Å2
3----9.8678 Å2
Refinement stepCycle: LAST / Resolution: 1.85→35.097 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4780 0 25 377 5182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054888
X-RAY DIFFRACTIONf_angle_d0.876564
X-RAY DIFFRACTIONf_dihedral_angle_d17.2331870
X-RAY DIFFRACTIONf_chiral_restr0.061733
X-RAY DIFFRACTIONf_plane_restr0.003843
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.91610.31195540.28219397X-RAY DIFFRACTION93
1.9161-1.99280.30755170.24749541X-RAY DIFFRACTION93
1.9928-2.08350.2614350.2219534X-RAY DIFFRACTION93
2.0835-2.19340.27145020.21699586X-RAY DIFFRACTION93
2.1934-2.33070.27174870.20949482X-RAY DIFFRACTION93
2.3307-2.51070.22924860.21029569X-RAY DIFFRACTION93
2.5107-2.76320.26894950.20549519X-RAY DIFFRACTION93
2.7632-3.16280.22925780.19519503X-RAY DIFFRACTION93
3.1628-3.9840.20285330.16989350X-RAY DIFFRACTION92
3.984-35.10290.18644450.17249129X-RAY DIFFRACTION89
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)
10.28040.27160.22080.7015-0.01120.91560.10850.05530.0170.0681-0.0016-0.00270.16860.1168-0.09590.16250.0168-0.02330.1835-0.02370.132623.93121.948261.3133
20.4660.0270.10110.34430.06220.56830.0450.01090.0039-0.03940.037-0.0190.13820.1003-0.0640.13460.02030.01460.1069-0.00630.115925.71693.78131.119
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A OR CHAIN B
2X-RAY DIFFRACTION2CHAIN C OR CHAIN D

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