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- PDB-8c36: Light-adapted 2.0 Angstrom crystal structure of H132A variant of ... -

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Basic information

Entry
Database: PDB / ID: 8c36
TitleLight-adapted 2.0 Angstrom crystal structure of H132A variant of cobalamin binding domain belonging to a light-dependent transcription regulator TtCarH obtained under aerobic conditions
ComponentsProbable transcriptional regulator
KeywordsTRANSCRIPTION / CarH / cobalamin / light-activated / transcription regulator
Function / homology
Function and homology information


cobalamin binding / DNA-binding transcription factor activity / DNA binding / metal ion binding / identical protein binding
Similarity search - Function
Methionine synthase domain / Cobalamin-binding domain / Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Methionine synthase domain / : / MerR HTH family regulatory protein / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. ...Methionine synthase domain / Cobalamin-binding domain / Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 / Methionine synthase domain / : / MerR HTH family regulatory protein / helix_turn_helix, mercury resistance / MerR-type HTH domain profile. / MerR-type HTH domain / Cobalamin-binding domain superfamily / 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
COBALAMIN / Probable transcriptional regulator
Similarity search - Component
Biological speciesThermus thermophilus HB27 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPoddar, H. / Leys, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/S030336/1 United Kingdom
CitationJournal: Nat Commun / Year: 2023
Title: Redox driven B 12 -ligand switch drives CarH photoresponse.
Authors: Poddar, H. / Rios-Santacruz, R. / Heyes, D.J. / Shanmugam, M. / Brookfield, A. / Johannissen, L.O. / Levy, C.W. / Jeffreys, L.N. / Zhang, S. / Sakuma, M. / Colletier, J.P. / Hay, S. / ...Authors: Poddar, H. / Rios-Santacruz, R. / Heyes, D.J. / Shanmugam, M. / Brookfield, A. / Johannissen, L.O. / Levy, C.W. / Jeffreys, L.N. / Zhang, S. / Sakuma, M. / Colletier, J.P. / Hay, S. / Schiro, G. / Weik, M. / Scrutton, N.S. / Leys, D.
History
DepositionDec 23, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Refinement description / Category: pdbx_refine_tls / pdbx_refine_tls_group
Item: _pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y ..._pdbx_refine_tls.origin_x / _pdbx_refine_tls.origin_y / _pdbx_refine_tls.origin_z / _pdbx_refine_tls_group.beg_auth_seq_id / _pdbx_refine_tls_group.end_auth_seq_id
Revision 1.2Aug 30, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Probable transcriptional regulator
B: Probable transcriptional regulator
C: Probable transcriptional regulator
D: Probable transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,0928
Polymers92,7714
Non-polymers5,3214
Water8,557475
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16560 Å2
ΔGint-80 kcal/mol
Surface area29340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.405, 70.664, 203.687
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Probable transcriptional regulator


Mass: 23192.730 Da / Num. of mol.: 4 / Mutation: H132A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB27 (bacteria) / Gene: TT_P0056 / Production host: Escherichia coli (E. coli) / References: UniProt: Q746J7
#2: Chemical
ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 475 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.8
Details: 0.1 M ammonium sulfate, 0.1 M sodium citrate pH 5.8, 16% w/v PEG 4000, 20% v/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2→67.9 Å / Num. obs: 62906 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 1 / Net I/σ(I): 10.3
Reflection shellResolution: 2→2.05 Å / Redundancy: 13.5 % / Mean I/σ(I) obs: 1 / Num. unique obs: 4599 / CC1/2: 0.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
xia2data reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8C35

8c35


Resolution: 2→66.85 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 10.797 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.169 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2183 3060 4.9 %RANDOM
Rwork0.18113 ---
obs0.18293 59761 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.436 Å2
Baniso -1Baniso -2Baniso -3
1-2.79 Å2-0 Å20 Å2
2---0.16 Å20 Å2
3----2.63 Å2
Refinement stepCycle: 1 / Resolution: 2→66.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5838 0 364 475 6677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0126499
X-RAY DIFFRACTIONr_bond_other_d0.0020.0156367
X-RAY DIFFRACTIONr_angle_refined_deg1.9331.7448964
X-RAY DIFFRACTIONr_angle_other_deg0.541.63414590
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9925792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.218572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30310959
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.110.2981
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027720
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021500
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2873.1043130
X-RAY DIFFRACTIONr_mcbond_other2.2873.1043130
X-RAY DIFFRACTIONr_mcangle_it3.245.5693909
X-RAY DIFFRACTIONr_mcangle_other3.245.573910
X-RAY DIFFRACTIONr_scbond_it3.4823.6523369
X-RAY DIFFRACTIONr_scbond_other3.4823.6523370
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3736.5035047
X-RAY DIFFRACTIONr_long_range_B_refined8.14434.857455
X-RAY DIFFRACTIONr_long_range_B_other8.04833.067277
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 227 -
Rwork0.317 4357 -
obs--99.83 %
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)
11.94980.01970.32841.2184-0.17733.171-0.06980.1397-0.2943-0.00290.09130.16640.7246-0.3458-0.02150.2007-0.08890.04580.0577-0.01360.0919-11.863-17.84141.313
21.2107-0.23710.4351.1214-0.81884.3905-0.05790.21270.14430.03280.09270.2516-0.2378-0.4756-0.03480.05150.02290.02750.11170.05250.1248-19.911-0.68954.51
30.80870.28220.4341.40970.20943.51830.01020.12070.1458-0.1281-0.03840.27520.0998-0.34370.02820.0164-0.0027-0.02250.07290.01540.0658-9.1475.64616.394
41.1641.5455-0.14774.3724-0.03881.2959-0.01740.0966-0.2199-0.01420.0453-0.14070.16560.2006-0.02790.03420.03660.00540.0564-0.02670.062913.3223.06418.229
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A82 - 274
2X-RAY DIFFRACTION2B82 - 276
3X-RAY DIFFRACTION3C83 - 275
4X-RAY DIFFRACTION4D82 - 275

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