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- PDB-8j2x: Saccharothrix syringae photocobilins protein, light state -

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Basic information

Entry
Database: PDB / ID: 8j2x
TitleSaccharothrix syringae photocobilins protein, light state
ComponentsCobalamin-binding protein
KeywordsUNKNOWN FUNCTION / cobalamin binding / biliverdin binding / B12-dependent photoreceptor protein / photocobilins
Function / homology
Function and homology information


cobalamin binding / methyltransferase activity / metal ion binding
Similarity search - Function
Cobalamin (vitamin B12)-binding module, cap domain / B12 binding domain / Methionine synthase domain / B12 binding domain / Cobalamin-binding domain superfamily / B12-binding domain profile. / Cobalamin (vitamin B12)-binding domain
Similarity search - Domain/homology
COBALAMIN / BILIVERDINE IX ALPHA / DI(HYDROXYETHYL)ETHER / Cobalamin-binding protein
Similarity search - Component
Biological speciesSaccharothrix syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsZhang, S. / Poddar, H. / Levy, C. / Leys, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Engineering and Physical Sciences Research CouncilEP/S030336/1 United Kingdom
CitationJournal: Nat Commun / Year: 2024
Title: Photocobilins integrate B12 and bilin photochemistry for enzyme control.
Authors: Zhang, S. / Jeffreys, L.N. / Poddar, H. / Yu, Y. / Liu, C. / Patel, K. / Johannissen, L.O. / Zhu, L. / Cliff, M.J. / Yan, C. / Schiro, G. / Weik, M. / Sakuma, M. / Levy, C.W. / Leys, D. / ...Authors: Zhang, S. / Jeffreys, L.N. / Poddar, H. / Yu, Y. / Liu, C. / Patel, K. / Johannissen, L.O. / Zhu, L. / Cliff, M.J. / Yan, C. / Schiro, G. / Weik, M. / Sakuma, M. / Levy, C.W. / Leys, D. / Heyes, D.J. / Scrutton, N.S.
History
DepositionApr 15, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 10, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cobalamin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,4264
Polymers36,4071
Non-polymers2,0193
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-25 kcal/mol
Surface area15050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.667, 109.667, 98.074
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Cobalamin-binding protein


Mass: 36407.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharothrix syringae (bacteria) / Gene: EKG83_22740 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A5Q0H231
#2: Chemical ChemComp-B12 / COBALAMIN


Mass: 1330.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C62H89CoN13O14P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H34N4O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 4.68 Å3/Da / Density % sol: 73.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2M Potassium citrate tribasic monohydrate 20% w/v PEG 3350

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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: Jul 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.98→98.07 Å / Num. obs: 47811 / % possible obs: 99.92 % / Redundancy: 20.6 % / CC1/2: 1 / Rmerge(I) obs: 0.07186 / Rrim(I) all: 0.074 / Net I/σ(I): 20.64
Reflection shellResolution: 1.98→2.01 Å / Rmerge(I) obs: 2.404 / Mean I/σ(I) obs: 0.67 / Num. unique obs: 4716 / CC1/2: 0.6 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5refinement
DIALSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→94.97 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.959 / SU B: 7.104 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.105 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20029 2271 4.7 %RANDOM
Rwork0.18316 ---
obs0.18394 45541 100 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.837 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0.11 Å2-0 Å2
2---0.21 Å20 Å2
3---0.69 Å2
Refinement stepCycle: LAST / Resolution: 1.98→94.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2538 0 141 80 2759
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0162788
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152543
X-RAY DIFFRACTIONr_angle_refined_deg1.5511.8283850
X-RAY DIFFRACTIONr_angle_other_deg0.4811.6115853
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0395.441374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg1.74559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.36410369
X-RAY DIFFRACTIONr_chiral_restr0.0930.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023354
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02587
X-RAY DIFFRACTIONr_mcbond_it2.4053.5361358
X-RAY DIFFRACTIONr_mcbond_other2.4053.5361358
X-RAY DIFFRACTIONr_mcangle_it3.6245.2761698
X-RAY DIFFRACTIONr_mcangle_other3.6235.2811699
X-RAY DIFFRACTIONr_scbond_it3.1563.9291430
X-RAY DIFFRACTIONr_scbond_other3.1553.931431
X-RAY DIFFRACTIONr_scangle_other4.7585.7752152
X-RAY DIFFRACTIONr_long_range_B_refined7.54249.753047
X-RAY DIFFRACTIONr_long_range_B_other7.53748.7223040
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 177 -
Rwork0.352 3314 -
obs--99.97 %
Refinement TLS params.Method: refined / Origin x: -44.685 Å / Origin y: 27.747 Å / Origin z: 46.752 Å
111213212223313233
T0.2615 Å20.0085 Å2-0.0146 Å2-0.2074 Å20.008 Å2--0.0094 Å2
L2.2941 °21.8211 °2-1.2289 °2-1.7737 °2-0.9209 °2--1.2565 °2
S-0.0416 Å °-0.0082 Å °-0.1155 Å °-0.0293 Å °-0.0069 Å °-0.0701 Å °0.0066 Å °0.0617 Å °0.0485 Å °

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