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- PDB-8jbt: B12-binding domain from Chloracidobacterium thermophilum MerR fam... -

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Basic information

Entry
Database: PDB / ID: 8jbt
TitleB12-binding domain from Chloracidobacterium thermophilum MerR family protein, anaerobic light state
ComponentsPutative cobalamin binding protein
KeywordsTRANSCRIPTION / B12-dependent transcription regulators from the MerR superfamily
Function / homologyCOBALAMIN
Function and homology information
Biological speciesChloracidobacterium thermophilum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhang, S. / Yu, Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/S030336/1 United Kingdom
CitationJournal: Febs J. / Year: 2025
Title: SignatureFinder enables sequence mining to identify cobalamin-dependent photoreceptor proteins.
Authors: Yu, Y. / Jeffreys, L.N. / Poddar, H. / Hill, A. / Johannissen, L. / Dai, F. / Sakuma, M. / Leys, D. / Heyes, D.J. / Zhang, S. / Scrutton, N.S.
History
DepositionMay 9, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 13, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2025Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Feb 19, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative cobalamin binding protein
B: Putative cobalamin binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,7239
Polymers72,2502
Non-polymers3,4747
Water1,18966
1
A: Putative cobalamin binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8604
Polymers36,1251
Non-polymers1,7353
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-10 kcal/mol
Surface area11860 Å2
MethodPISA
2
B: Putative cobalamin binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8645
Polymers36,1251
Non-polymers1,7394
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-14 kcal/mol
Surface area11150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.485, 123.485, 73.105
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-435-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Putative cobalamin binding protein


Mass: 36124.918 Da / Num. of mol.: 2 / Fragment: B12 binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chloracidobacterium thermophilum (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)

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Non-polymers , 6 types, 73 molecules

#2: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.23 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.1M Tris pH 8.5, 20% v/v Ethanol / Temp details: cold room

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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 XE 16M / Detector: PIXEL / Date: Jan 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.299→106.941 Å / Num. obs: 28905 / % possible obs: 100 % / Redundancy: 20.6 % / CC1/2: 1 / Rmerge(I) obs: 0.2803 / Rrim(I) all: 0.287 / Net I/σ(I): 8.08
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 19.7 % / Rmerge(I) obs: 2.463 / Mean I/σ(I) obs: 0.72 / Num. unique obs: 2852 / CC1/2: 0.5 / Rrim(I) all: 2.75 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
DIALSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→106.94 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.946 / SU B: 11.065 / SU ML: 0.197 / Cross valid method: THROUGHOUT / ESU R: 0.277 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22527 1426 4.9 %RANDOM
Rwork0.20636 ---
obs0.20733 27458 99.99 %-
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.3 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.694 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å2-0.08 Å2-0 Å2
2---0.17 Å20 Å2
3---0.55 Å2
Refinement stepCycle: LAST / Resolution: 2.3→106.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3591 0 236 66 3893
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0163944
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163696
X-RAY DIFFRACTIONr_angle_refined_deg0.9291.85400
X-RAY DIFFRACTIONr_angle_other_deg0.3751.5628434
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0435.424495
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.83718.63622
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.49810567
X-RAY DIFFRACTIONr_chiral_restr0.0430.2593
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.024667
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02959
X-RAY DIFFRACTIONr_mcbond_it2.9333.7111817
X-RAY DIFFRACTIONr_mcbond_other2.9013.7091815
X-RAY DIFFRACTIONr_mcangle_it4.2086.6762267
X-RAY DIFFRACTIONr_mcangle_other4.2076.6792268
X-RAY DIFFRACTIONr_scbond_it3.9394.0622127
X-RAY DIFFRACTIONr_scbond_other3.9384.0632128
X-RAY DIFFRACTIONr_scangle_other5.7917.293134
X-RAY DIFFRACTIONr_long_range_B_refined7.22237.874290
X-RAY DIFFRACTIONr_long_range_B_other7.22337.774286
LS refinement shellResolution: 2.3→2.359 Å
RfactorNum. reflection% reflection
Rfree0.307 111 -
Rwork0.337 2017 -
obs--99.81 %
Refinement TLS params.Method: refined / Origin x: -10.652 Å / Origin y: -41.476 Å / Origin z: -20.303 Å
111213212223313233
T0.0447 Å20.0169 Å20.0361 Å2-0.0819 Å20.0241 Å2--0.0581 Å2
L1.6413 °20.2641 °2-0.2006 °2-1.615 °20.4986 °2--1.4396 °2
S0.0747 Å °0.1838 Å °0.0643 Å °-0.1971 Å °0.0546 Å °-0.2443 Å °-0.0646 Å °0.0896 Å °-0.1293 Å °

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