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- PDB-2o03: Crystal structure of FurB from M. tuberculosis- a Zinc uptake reg... -

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Basic information

Entry
Database: PDB / ID: 2o03
TitleCrystal structure of FurB from M. tuberculosis- a Zinc uptake regulator
Componentsprobable Zinc uptake regulation protein FurB
KeywordsGENE REGULATION / Zinc uptake / DNA-binding / helix-turn-helix / Zinc binding
Function / homology
Function and homology information


regulation of secondary metabolite biosynthetic process / DNA-binding transcription repressor activity / response to zinc ion / protein-DNA complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein homodimerization activity / DNA binding ...regulation of secondary metabolite biosynthetic process / DNA-binding transcription repressor activity / response to zinc ion / protein-DNA complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein homodimerization activity / DNA binding / zinc ion binding / metal ion binding / plasma membrane / cytosol / cytoplasm
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
Zinc uptake regulation protein / Zinc uptake regulation protein
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.699 Å
AuthorsLucarelli, D. / Russo, S. / Pohl, E.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Crystal structure and function of the zinc uptake regulator FurB from Mycobacterium tuberculosis.
Authors: Lucarelli, D. / Russo, S. / Garman, E. / Milano, A. / Meyer-Klaucke, W. / Pohl, E.
History
DepositionNov 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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

Downloads & links

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Assembly

Deposited unit
A: probable Zinc uptake regulation protein FurB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,6884
Polymers14,4921
Non-polymers1963
Water1448
1
A: probable Zinc uptake regulation protein FurB
hetero molecules

A: probable Zinc uptake regulation protein FurB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3768
Polymers28,9842
Non-polymers3926
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area2780 Å2
ΔGint-20 kcal/mol
Surface area14830 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)51.600, 51.600, 133.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
DetailsThe second part of the biological assembly is generated by the two fold axis: -y,-x,1/2-z.

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Components

#1: Protein probable Zinc uptake regulation protein FurB / Ferric uptake regulation protein


Mass: 14492.003 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: furB / Plasmid: pETM11 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O05839, UniProt: P9WN85*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 8 / 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: 3.1 Å3/Da / Density % sol: 60.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.3 M ammonium phosphate, 14% glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSLS X06SA11.28087
SYNCHROTRONSLS X06SA21.28358, 1.28441, 1.26924
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDApr 29, 2006
MARMOSAIC 225 mm CCD2CCDApr 29, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1LN2 cooled fixed-exit Si(111) monochromatorSINGLE WAVELENGTHMx-ray1
2LN2 cooled fixed-exit Si(111) monochromatorMADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.280871
21.283581
31.284411
41.269241
ReflectionResolution: 2.69→40 Å / Num. all: 5464 / Num. obs: 5344 / % possible obs: 97.8 % / Observed criterion σ(I): 3 / Redundancy: 16.76 % / Rmerge(I) obs: 0.069 / Rsym value: 0.107 / Net I/σ(I): 18.85
Reflection shellResolution: 2.69→2.85 Å / Redundancy: 16.7 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 4.4 / Num. unique all: 775 / Rsym value: 0.64 / % possible all: 92.8

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT2data extraction
GCLIENTdata collection
XDSdata reduction
XSCALEdata scaling
SHELXCDphasing
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: MAD / Resolution: 2.699→33.69 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.914 / SU B: 26.548 / SU ML: 0.277 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.563 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.239 268 5 %RANDOM
Rwork0.23 ---
obs0.23 5344 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.712 Å2
Baniso -1Baniso -2Baniso -3
1-1.92 Å20 Å20 Å2
2--1.92 Å20 Å2
3----3.84 Å2
Refinement stepCycle: LAST / Resolution: 2.699→33.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms954 0 3 8 965
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.021982
X-RAY DIFFRACTIONr_angle_refined_deg1.3891.9021317
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6625128
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.01122.09343
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.20915144
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.251159
X-RAY DIFFRACTIONr_chiral_restr0.0960.2156
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02736
X-RAY DIFFRACTIONr_nbd_refined0.220.2329
X-RAY DIFFRACTIONr_nbtor_refined0.2860.2651
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.217
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1650.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1410.24
X-RAY DIFFRACTIONr_mcbond_it0.5261.5647
X-RAY DIFFRACTIONr_mcangle_it0.92621004
X-RAY DIFFRACTIONr_scbond_it2.263364
X-RAY DIFFRACTIONr_scangle_it2.7074.5313
LS refinement shellResolution: 2.699→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.38 19 -
Rwork0.298 350 -
obs-369 100 %
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)
16.37574.2195-1.833411.3459-2.13610.9668-0.1671-0.0109-0.2160.39460.3284-0.00280.18420.2271-0.1613-0.02390.07240.006-0.18880.0001-0.258765.9814.17811.9713
24.078-0.2313-3.56814.2073-1.94747.48730.37010.18770.86830.44150.23250.7107-1.2-0.4872-0.60260.13770.09330.21260.07120.17850.196148.95458.149430.3024
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDAuth seq-IDLabel seq-ID
112 - 752 - 75
2276 - 13076 - 130

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