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- PDB-5c8a: Crystal structure of a truncated form of Thermus thermophilus Car... -

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Basic information

Entry
Database: PDB / ID: 5c8a
TitleCrystal structure of a truncated form of Thermus thermophilus CarH bound to adenosylcobalamin (dark state)
ComponentsLight-dependent transcriptional regulator CarH
KeywordsTRANSCRIPTIONAL REGULATOR / Transcription factor / light sensor / adenosylcobalamin-binding / DNA-binding / TRANSCRIPTION
Function / homology
Function and homology information


cobalamin binding / DNA-binding transcription factor activity / DNA binding / identical protein binding / metal ion binding
Similarity search - Function
Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methionine synthase domain / : / MerR HTH family regulatory protein / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance / Cobalamin-binding domain superfamily / MerR-type HTH domain / B12-binding domain profile. ...Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methionine synthase domain / : / MerR HTH family regulatory protein / MerR-type HTH domain profile. / helix_turn_helix, mercury resistance / Cobalamin-binding domain superfamily / MerR-type HTH domain / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain / Putative DNA-binding domain superfamily
Similarity search - Domain/homology
5'-DEOXYADENOSINE / COBALAMIN / Probable transcriptional regulator
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsJost, M. / Drennan, C.L.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM069857 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2015
Title: Structural basis for gene regulation by a B12-dependent photoreceptor.
Authors: Jost, M. / Fernandez-Zapata, J. / Polanco, M.C. / Ortiz-Guerrero, J.M. / Chen, P.Y. / Kang, G. / Padmanabhan, S. / Elias-Arnanz, M. / Drennan, C.L.
History
DepositionJun 25, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Nov 4, 2015Group: Database references
Revision 1.3Sep 20, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 1, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.5Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Light-dependent transcriptional regulator CarH
B: Light-dependent transcriptional regulator CarH
C: Light-dependent transcriptional regulator CarH
D: Light-dependent transcriptional regulator CarH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,88913
Polymers88,4704
Non-polymers6,4189
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19310 Å2
ΔGint-60 kcal/mol
Surface area27360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.430, 99.680, 143.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsTetramer according to Size exclusion chromatography, analytical ultracentrifugation

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Components

#1: Protein
Light-dependent transcriptional regulator CarH


Mass: 22117.543 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB27 / ATCC BAA-163 / DSM 7039 / Gene: TT_P0056 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star pLysS / References: UniProt: Q746J7
#2: Chemical
ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#3: Chemical
ChemComp-5AD / 5'-DEOXYADENOSINE / Deoxyadenosine


Mass: 251.242 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H13N5O3
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
Compound detailssample was proteolytically degraded during crystallization

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.95 Å3/Da / Density % sol: 36.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350, 0.2 M KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 22, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→100 Å / Num. obs: 40511 / % possible obs: 98.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 36.72 Å2 / Rsym value: 0.062 / Net I/σ(I): 15.2
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 2.1 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAD solution from different space group

Resolution: 2.15→81.958 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / Phase error: 26.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2268 2042 5.04 %Random selection
Rwork0.1832 ---
obs0.1853 40477 98.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.2 Å2
Refinement stepCycle: LAST / Resolution: 2.15→81.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5755 0 442 259 6456
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046397
X-RAY DIFFRACTIONf_angle_d0.8198788
X-RAY DIFFRACTIONf_dihedral_angle_d11.7512512
X-RAY DIFFRACTIONf_chiral_restr0.031982
X-RAY DIFFRACTIONf_plane_restr0.0041279
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1501-2.20010.3371440.28382539X-RAY DIFFRACTION100
2.2001-2.25510.31841270.27342523X-RAY DIFFRACTION99
2.2551-2.31610.33071330.25332500X-RAY DIFFRACTION97
2.3161-2.38430.3291360.23472552X-RAY DIFFRACTION100
2.3843-2.46120.30091440.22522555X-RAY DIFFRACTION100
2.4612-2.54920.30441400.2222525X-RAY DIFFRACTION98
2.5492-2.65130.28051510.20872508X-RAY DIFFRACTION99
2.6513-2.77190.29071560.21212532X-RAY DIFFRACTION98
2.7719-2.91810.25511430.21032531X-RAY DIFFRACTION99
2.9181-3.10090.2331180.20482610X-RAY DIFFRACTION99
3.1009-3.34030.21991250.18512579X-RAY DIFFRACTION98
3.3403-3.67650.21471320.17242551X-RAY DIFFRACTION97
3.6765-4.20850.2031340.14962593X-RAY DIFFRACTION99
4.2085-5.30210.15621320.1452604X-RAY DIFFRACTION97
5.3021-82.01710.18141270.15882733X-RAY DIFFRACTION97
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)
11.5904-1.0983-0.0042.33310.16243.14030.030.0801-0.0792-0.1366-0.02990.07830.4022-0.08870.02490.5323-0.02280.00990.36640.01180.349315.998893.1426-3.1212
20.7796-0.53780.49362.2682-1.62673.8728-0.012-0.12970.00930.1021-0.0216-0.233-0.19530.33360.04270.52-0.04870.01270.449-0.01280.422530.3924110.3172-5.6035
30.6875-0.2828-0.14292.782-0.78852.7131-0.0141-0.09810.0457-0.03180.0171-0.20270.0880.35470.00960.41810.0103-0.02120.4633-0.01110.370620.597397.218731.4835
40.7782-0.1797-0.04232.880.67482.7267-0.0059-0.0033-0.06640.04180.06490.1791-0.0442-0.222-0.0710.45870.0343-0.02720.37290.03660.3767-1.1508102.011131.9499
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' )
2X-RAY DIFFRACTION2(chain 'B' )
3X-RAY DIFFRACTION3(chain 'C' )
4X-RAY DIFFRACTION4(chain 'D' )

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