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- PDB-2fyi: Crystal Structure of the Cofactor-Binding Domain of the Cbl Trans... -

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Basic information

Entry
Database: PDB / ID: 2fyi
TitleCrystal Structure of the Cofactor-Binding Domain of the Cbl Transcriptional Regulator
ComponentsHTH-type transcriptional regulator cbl
KeywordsTRANSCRIPTION / Transcriptional regulator / LYS-R family / cofactor-binding domain / cysteine biosynthesis
Function / homology
Function and homology information


positive regulation of sulfur utilization / cysteine biosynthetic process / transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
HTH-type transcriptional regulator cbl, PBP2 domain / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily ...HTH-type transcriptional regulator cbl, PBP2 domain / LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
HTH-type transcriptional regulator cbl
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsStec, E. / Neumann, P. / Wilkinson, A.J. / Brzozowski, A.M. / Bujacz, G.D.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Structural Basis of the Sulphate Starvation Response in E. coli: Crystal Structure and Mutational Analysis of the Cofactor-binding Domain of the Cbl Transcriptional Regulator.
Authors: Stec, E. / Witkowska-Zimny, M. / Hryniewicz, M.M. / Neumann, P. / Wilkinson, A.J. / Brzozowski, A.M. / Verma, C.S. / Zaim, J. / Wysocki, S. / D Bujacz, G.
History
DepositionFeb 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 21, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details
Remark 999SEQUENCE These cloning artifacts come from the pET-28a vector sequence, between the His-tag and the ...SEQUENCE These cloning artifacts come from the pET-28a vector sequence, between the His-tag and the native sequence of the Cbl cofactor-binding domain

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HTH-type transcriptional regulator cbl
B: HTH-type transcriptional regulator cbl
C: HTH-type transcriptional regulator cbl
D: HTH-type transcriptional regulator cbl


Theoretical massNumber of molelcules
Total (without water)102,6374
Polymers102,6374
Non-polymers00
Water6,846380
1
A: HTH-type transcriptional regulator cbl
B: HTH-type transcriptional regulator cbl


Theoretical massNumber of molelcules
Total (without water)51,3182
Polymers51,3182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-1 kcal/mol
Surface area19490 Å2
MethodPISA
2
C: HTH-type transcriptional regulator cbl

C: HTH-type transcriptional regulator cbl


Theoretical massNumber of molelcules
Total (without water)51,3182
Polymers51,3182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
3
D: HTH-type transcriptional regulator cbl

D: HTH-type transcriptional regulator cbl


Theoretical massNumber of molelcules
Total (without water)51,3182
Polymers51,3182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)169.686, 242.373, 101.626
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91A
101B
111C
121D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILETHRTHR3AA97 - 17918 - 100
21ILEILETHRTHR3BB97 - 17918 - 100
31ILEILETHRTHR3CC97 - 17918 - 100
41ILEILETHRTHR3DD97 - 17918 - 100
52THRTHRGLNGLN5AA185 - 246106 - 167
62THRTHRGLNGLN5BB185 - 246106 - 167
72THRTHRGLNGLN5CC185 - 246106 - 167
82THRTHRGLNGLN5DD185 - 246106 - 167
93ARGARGVALVAL5AA262 - 304183 - 225
103ARGARGVALVAL5BB262 - 304183 - 225
113ARGARGVALVAL5CC262 - 304183 - 225
123ARGARGVALVAL5DD262 - 304183 - 225

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Components

#1: Protein
HTH-type transcriptional regulator cbl


Mass: 25659.154 Da / Num. of mol.: 4 / Fragment: cofactor-binding domain, residues 88-307
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: cbl / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Codon Plus / References: UniProt: Q47083
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 1

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Sample preparation

CrystalDensity Matthews: 5.09 Å3/Da / Density % sol: 75.83 %
Crystal growTemperature: 292 K / pH: 7.5
Details: 3.8 M NaCl, 10 mM Adenosine 5'-Phosphosulphate, 0.1M Hepes, pH 7.50, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8042
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 7, 2004 / Details: TRIANGULAR MONOCHROMATOR, BENT MIRROR
RadiationMonochromator: SAGITALLY FOCUSED SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8042 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 51701 / % possible obs: 99.6 % / Observed criterion σ(I): -1.5 / Redundancy: 3.9 % / Biso Wilson estimate: 39.6 Å2 / Rmerge(I) obs: 0.124 / Rsym value: 0.092 / Net I/σ(I): 10.4
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 2.4 / Rsym value: 0.639 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AL3

1al3


Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.913 / SU B: 18.401 / SU ML: 0.188 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.335 / ESU R Free: 0.254 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.226 2577 5 %RANDOM
Rwork0.184 ---
obs0.187 46596 99.7 %-
all-49173 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 39.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.98 Å20 Å20 Å2
2--2.4 Å20 Å2
3----0.42 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a-0.23 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7125 0 0 380 7505
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0227386
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8031.95510061
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0555917
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.30923.909353
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.774151271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5671561
X-RAY DIFFRACTIONr_chiral_restr0.1120.21154
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025615
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2530.33322
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3370.55175
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.5619
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.3125
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3010.538
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.26124585
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.23237353
X-RAY DIFFRACTIONr_scbond_it1.26623072
X-RAY DIFFRACTIONr_scangle_it2.13332708
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A316tight positional0.080.05
2B316tight positional0.090.05
3C316tight positional0.080.05
4D316tight positional0.080.05
1A404medium positional0.340.5
2B404medium positional0.270.5
3C404medium positional0.30.5
4D404medium positional0.380.5
1A717loose positional0.575
2B717loose positional0.535
3C717loose positional0.525
4D717loose positional0.545
1A316tight thermal0.120.5
2B316tight thermal0.160.5
3C316tight thermal0.160.5
4D316tight thermal0.120.5
1A404medium thermal0.952
2B404medium thermal1.082
3C404medium thermal1.012
4D404medium thermal0.862
1A717loose thermal1.7810
2B717loose thermal2.2510
3C717loose thermal2.210
4D717loose thermal1.6410
LS refinement shellResolution: 2.8→2.87 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 191 -
Rwork0.321 3468 -
obs--96.95 %
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)
11.5359-1.9871-0.78294.39491.24911.3667-0.1799-0.2444-0.12330.25280.1273-0.25770.34080.13630.05260.04960.0636-0.0028-0.10390.0662-0.070751.44840.6125.714
23.9393-1.5702-0.9281.08870.36261.5427-0.01980.22530.01860.0536-0.0667-0.03580.1421-0.25420.0866-0.0496-0.02160.0088-0.20090.0148-0.150142.73651.0252.925
36.45240.8808-1.06760.54540.06620.4491-0.17980.43820.1707-0.12010.10280.03860.20660.15030.077-0.04340.0489-0.00930.06820.0704-0.1417-6.72665.02813.971
41.17611.45090.45776.57781.49991.18040.0902-0.0995-0.13450.5855-0.0598-0.47970.2248-0.106-0.03030.15870.0258-0.0672-0.18870.0141-0.000466.781-7.49611.088
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA85 - 3076 - 228
2X-RAY DIFFRACTION2BB85 - 3076 - 228
3X-RAY DIFFRACTION3CC80 - 3071 - 228
4X-RAY DIFFRACTION4DD85 - 3076 - 228

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