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- PDB-5c8e: Crystal structure of Thermus thermophilus CarH bound to adenosylc... -

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Basic information

Entry
Database: PDB / ID: 5c8e
TitleCrystal structure of Thermus thermophilus CarH bound to adenosylcobalamin and a 26-bp DNA segment
Components
  • 26-mer DNA segment containing the CarH operator sequence (antisense strand)
  • 26-mer DNA segment containing the CarH operator sequence (sense strand)
  • Light-dependent transcriptional regulator CarH
KeywordsTranscription regulator/DNA / Transcription factor / light sensor / adenosylcobalamin-binding / DNA-binding / Transcription regulator-DNA complex
Function / homology
Function and homology information


cobalamin binding / DNA-binding transcription factor activity / DNA binding / identical protein binding / metal ion binding
Similarity search - Function
Methionine synthase domain / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / Cobalamin-binding domain / Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Methionine synthase domain / : / MerR HTH family regulatory protein ...Methionine synthase domain / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 - #10 / Cobalamin-binding domain / Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / 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 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
5'-DEOXYADENOSINE / COBALAMIN / DNA / DNA (> 10) / Probable transcriptional regulator
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
Thermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.89 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 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
E: Light-dependent transcriptional regulator CarH
F: Light-dependent transcriptional regulator CarH
G: Light-dependent transcriptional regulator CarH
H: Light-dependent transcriptional regulator CarH
I: 26-mer DNA segment containing the CarH operator sequence (antisense strand)
J: 26-mer DNA segment containing the CarH operator sequence (sense strand)
K: 26-mer DNA segment containing the CarH operator sequence (antisense strand)
L: 26-mer DNA segment containing the CarH operator sequence (sense strand)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)311,18028
Polymers298,52712
Non-polymers12,65316
Water0
1
A: Light-dependent transcriptional regulator CarH
B: Light-dependent transcriptional regulator CarH
C: Light-dependent transcriptional regulator CarH
D: Light-dependent transcriptional regulator CarH
I: 26-mer DNA segment containing the CarH operator sequence (antisense strand)
J: 26-mer DNA segment containing the CarH operator sequence (sense strand)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,59014
Polymers149,2636
Non-polymers6,3268
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26740 Å2
ΔGint-117 kcal/mol
Surface area46530 Å2
MethodPISA
2
E: Light-dependent transcriptional regulator CarH
F: Light-dependent transcriptional regulator CarH
G: Light-dependent transcriptional regulator CarH
H: Light-dependent transcriptional regulator CarH
K: 26-mer DNA segment containing the CarH operator sequence (antisense strand)
L: 26-mer DNA segment containing the CarH operator sequence (sense strand)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,59014
Polymers149,2636
Non-polymers6,3268
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26210 Å2
ΔGint-107 kcal/mol
Surface area47010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)177.940, 141.820, 162.690
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
12
22
32
42
13
23
14
24
15
25

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'A' and (resseq 81:103 or resseq 106:107 or resseq...
211chain 'B' and (resseq 81:103 or resseq 106:107 or resseq...
311chain 'D' and (resseq 81:103 or resseq 106:107 or resseq...
411chain 'C' and (resseq 81:103 or resseq 106:107 or resseq...
511chain 'E' and (resseq 81:103 or resseq 106:107 or resseq...
611chain 'F' and (resseq 81:103 or resseq 106:107 or resseq...
711chain 'H' and (resseq 81:103 or resseq 106:107 or resseq...
811chain 'G' and (resseq 81:103 or resseq 106:107 or resseq...
112chain 'A' and (resseq 5:28 or resseq 30:36 or resseq 44:74)
212chain 'C' and (resseq 5:36 or resseq 44:57 or resseq 59:74)
312chain 'E' and (resseq 5:36 or resseq 44:74)
412chain 'G' and (resseq 5:36 or resseq 44:74)
113chain 'B' and (resseq 5:36 or resseq 44:74)
213chain 'F' and (resseq 5:36 or resseq 44:74)
114(chain 'I' and (resseq 2:25) and (name P or name...
214(chain 'K' and (resseq 2:25) and (name P or name...
115(chain 'J' and (resseq 2:25) and (name P or name...
215(chain 'L' and (resseq 2:25) and (name P or name...

NCS ensembles :
ID
1
2
3
4
5

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Components

#1: Protein
Light-dependent transcriptional regulator CarH


Mass: 33323.250 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039) (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: DNA chain 26-mer DNA segment containing the CarH operator sequence (antisense strand)


Mass: 7998.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus HB27 (bacteria)
#3: DNA chain 26-mer DNA segment containing the CarH operator sequence (sense strand)


Mass: 7972.207 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus HB27 (bacteria)
#4: Chemical
ChemComp-B12 / COBALAMIN / Vitamin B12


Mass: 1330.356 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C62H89CoN13O14P
#5: Chemical
ChemComp-5AD / 5'-DEOXYADENOSINE / Deoxyadenosine


Mass: 251.242 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H13N5O3

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.44 Å3/Da / Density % sol: 64.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 16% PEG 3350, 0.2 M L-Proline, 0.1 M HEPES pH 7.5

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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: Nov 23, 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: 3.89→100 Å / Num. obs: 38480 / % possible obs: 99.9 % / Redundancy: 12.2 % / Rsym value: 0.098 / Net I/σ(I): 15.7
Reflection shellResolution: 3.89→3.99 Å / Redundancy: 12.4 % / Mean I/σ(I) obs: 2 / % possible all: 100

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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: 3 different models were used for MR: residues 83-270 of PDB ID 5C8A; residues 6-75 of PDB ID 5C8F, and a model of a 26-bp DNA segment with ideal geometry, generated using 3D-DART

5c8a

5c8f


Resolution: 3.89→91.638 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / Phase error: 33.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2573 1863 4.86 %Random selection
Rwork0.2502 ---
obs0.2505 38338 99.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 172 Å2
Refinement stepCycle: LAST / Resolution: 3.89→91.638 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14500 2120 872 0 17492
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00518329
X-RAY DIFFRACTIONf_angle_d0.78925519
X-RAY DIFFRACTIONf_dihedral_angle_d15.4346821
X-RAY DIFFRACTIONf_chiral_restr0.0372893
X-RAY DIFFRACTIONf_plane_restr0.0073290
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1362X-RAY DIFFRACTIONPOSITIONAL
12B1362X-RAY DIFFRACTIONPOSITIONAL0.055
13D1358X-RAY DIFFRACTIONPOSITIONAL0.058
14C1355X-RAY DIFFRACTIONPOSITIONAL0.024
15E1372X-RAY DIFFRACTIONPOSITIONAL0.003
16F1368X-RAY DIFFRACTIONPOSITIONAL0.061
17H1355X-RAY DIFFRACTIONPOSITIONAL0.058
18G1361X-RAY DIFFRACTIONPOSITIONAL0.024
21A378X-RAY DIFFRACTIONPOSITIONAL
22C378X-RAY DIFFRACTIONPOSITIONAL0.008
23E378X-RAY DIFFRACTIONPOSITIONAL0.005
24G384X-RAY DIFFRACTIONPOSITIONAL0.007
31B387X-RAY DIFFRACTIONPOSITIONAL
32F387X-RAY DIFFRACTIONPOSITIONAL0.003
41I264X-RAY DIFFRACTIONPOSITIONAL
42K264X-RAY DIFFRACTIONPOSITIONAL0.004
51J264X-RAY DIFFRACTIONPOSITIONAL
52L264X-RAY DIFFRACTIONPOSITIONAL0.004
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.89-3.99520.37991510.36282758X-RAY DIFFRACTION100
3.9952-4.11280.36451660.34512714X-RAY DIFFRACTION100
4.1128-4.24550.30031360.32382795X-RAY DIFFRACTION100
4.2455-4.39720.3081330.29552776X-RAY DIFFRACTION100
4.3972-4.57330.33931380.28062785X-RAY DIFFRACTION100
4.5733-4.78140.26441350.26492774X-RAY DIFFRACTION100
4.7814-5.03350.27781390.27542799X-RAY DIFFRACTION100
5.0335-5.34880.25641290.2782800X-RAY DIFFRACTION100
5.3488-5.76180.27391400.27632816X-RAY DIFFRACTION100
5.7618-6.34150.30511580.2862814X-RAY DIFFRACTION100
6.3415-7.25880.28371510.25932817X-RAY DIFFRACTION100
7.2588-9.1440.18551390.19982880X-RAY DIFFRACTION100
9.144-91.6630.2131480.19852947X-RAY DIFFRACTION98
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)
17.84783.25121.73082.29071.4121.4838-0.20420.46160.7898-0.6560.141-0.2803-0.1004-0.24990.05411.85480.05380.17071.46610.13721.6435213.710763.2295-91.4571
21.3869-0.27630.0091.0998-0.79840.93960.2315-0.0060.7995-0.0787-0.2307-0.23580.01920.0054-0.01211.7025-0.03160.10251.4951-0.18641.6225203.046165.9482-64.6931
33.8087-1.0326-1.35770.51121.15730.60050.11610.2191-0.21840.006-0.1614-0.38560.2605-0.22720.1221.64730.02650.1561.57640.05821.9591213.504137.5455-77.0905
43.32251.8190.16594.5621-1.6451.81320.08350.6132-0.5208-1.0696-0.07280.1418-0.09520.00130.06952.12990.17710.04852.0647-0.21821.902216.30530.406-102.6438
56.12651.72590.2942.774-1.11851.0494-0.02870.3211-0.5535-0.06310.142-0.0939-0.25280.4526-0.161.5482-0.1573-0.02211.1651-0.1251.1323141.875629.8015-172.9145
63.036-0.7168-0.83253.67271.96181.03870.3884-0.6665-0.59870.6627-0.1699-0.5014-0.2710.437-0.20421.5039-0.1637-0.12871.18470.23541.1585152.263127.1478-147.3151
73.6185-1.13150.64421.314-0.08141.13660.20960.0140.02850.25290.01260.10590.24030.2387-0.2461.4867-0.0064-0.03931.1819-0.01251.2955142.27856.0495-158.4116
82.74052.3301-0.08434.07280.29981.27850.12980.48780.4565-1.0155-0.13260.76410.23330.0934-0.05051.73140.0004-0.07711.41140.19431.3143139.301663.154-183.7668
92.16860.55280.26951.17571.87692.74270.19750.2119-0.6149-0.30060.39820.08830.8513-2.8167-0.55432.1067-0.59190.12642.68750.05321.705176.076639.5569-60.7171
102.6471-0.2495-0.96892.3897-0.63817.41810.518-0.59890.7237-0.01360.6542-0.0264-0.61130.8839-1.12282.1499-0.3889-0.22582.4053-0.06932.0189180.371653.5499-142.1709
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H
9X-RAY DIFFRACTION9(chain I or chain J)
10X-RAY DIFFRACTION10(chain K or chain L)

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