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- PDB-8j2w: Saccharothrix syringae photocobilins protein, dark state -

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Basic information

Entry
Database: PDB / ID: 8j2w
TitleSaccharothrix syringae photocobilins protein, dark state
ComponentsCobalamin-binding protein
KeywordsUNKNOWN FUNCTION / cobalamin binding / biliverdin binding / B12-dependent photoreceptor protein / photocobilins
Function / homology
Function and homology information


methionine synthase activity / homocysteine metabolic process / cobalamin binding / tetrahydrofolate metabolic process / metal ion binding / cytosol
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
5'-DEOXYADENOSINE / COBALAMIN / BILIVERDINE IX ALPHA / 1,4-DIETHYLENE DIOXIDE / DI(HYDROXYETHYL)ETHER / Cobalamin-binding protein
Similarity search - Component
Biological speciesSaccharothrix syringae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsZhang, S. / Poddar, H. / Levy, W.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

Downloads & links

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Assembly

Deposited unit
A: Cobalamin-binding protein
B: Cobalamin-binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,14513
Polymers72,3402
Non-polymers4,80511
Water7,314406
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12460 Å2
ΔGint-38 kcal/mol
Surface area26480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.111, 97.539, 72.662
Angle α, β, γ (deg.)90.00, 116.72, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Cobalamin-binding protein


Mass: 36169.895 Da / Num. of mol.: 2
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

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Non-polymers , 6 types, 417 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-5AD / 5'-DEOXYADENOSINE


Mass: 251.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H13N5O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-BLA / BILIVERDINE IX ALPHA


Mass: 582.646 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C33H34N4O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H8O2
#6: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.98 Å3/Da / Density % sol: 58.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 38% v/v 1,4-Dioxane

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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: May 14, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.7→75.18 Å / Num. obs: 90363 / % possible obs: 99.8 % / Redundancy: 6.9 % / CC1/2: 1 / Rrim(I) all: 0.083 / Net I/σ(I): 15
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4348 / CC1/2: 0.7 / Rrim(I) all: 0.953 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
DIALSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→75.18 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.635 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.096 / ESU R Free: 0.095 / 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
Rfree0.21176 4537 5 %RANDOM
Rwork0.18286 ---
obs0.1843 85824 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.958 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20.07 Å2
2--0.02 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.7→75.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4955 0 336 406 5697
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0165483
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154996
X-RAY DIFFRACTIONr_angle_refined_deg1.6221.837561
X-RAY DIFFRACTIONr_angle_other_deg0.4941.61311493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7195.426727
X-RAY DIFFRACTIONr_dihedral_angle_2_deg2.863518
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.73910723
X-RAY DIFFRACTIONr_chiral_restr0.140.2838
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026555
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021141
X-RAY DIFFRACTIONr_mcbond_it2.3862.0122657
X-RAY DIFFRACTIONr_mcbond_other2.3862.0122657
X-RAY DIFFRACTIONr_mcangle_it3.3062.9923323
X-RAY DIFFRACTIONr_mcangle_other3.3062.9953324
X-RAY DIFFRACTIONr_scbond_it3.3942.3562826
X-RAY DIFFRACTIONr_scbond_other3.3932.3572827
X-RAY DIFFRACTIONr_scangle_other4.7413.394239
X-RAY DIFFRACTIONr_long_range_B_refined6.94928.5946283
X-RAY DIFFRACTIONr_long_range_B_other6.89927.7026180
LS refinement shellResolution: 1.7→1.743 Å
RfactorNum. reflection% reflection
Rfree0.317 319 -
Rwork0.302 6228 -
obs--97.21 %
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)
11.29330.09120.28710.8489-0.08971.5665-0.01450.06020.0667-0.0085-0.00160.1264-0.0053-0.14110.01620.0248-0.0003-0.0060.03560.01720.038910.321.77216.591
21.57090.12570.07461.17240.47261.06530.02190.0095-0.11260.13980.0918-0.20220.09770.1278-0.11370.0620.0277-0.03760.024-0.030.059833.085-3.73128.508
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 404
2X-RAY DIFFRACTION2B7 - 404

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