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- PDB-5nvd: Crystal structure of hexameric CBS-CP12 protein from bloom-formin... -

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Basic information

Entry
Database: PDB / ID: 5nvd
TitleCrystal structure of hexameric CBS-CP12 protein from bloom-forming cyanobacteria at 2.5 A resolution in P6322 crystal form
ComponentsCBS-CP12
KeywordsPHOTOSYNTHESIS / Cystathionine beta synthase domain / fusion protein / redox-regulation of photosynthesis
Function / homology
Function and homology information


CP12 domain / CP12 domain / CP12 / : / Domain in cystathionine beta-synthase and other proteins. / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile.
Similarity search - Domain/homology
Biological speciesMicrocystis aeruginosa PCC 7806 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHackenberg, C. / Hakanpaa, J. / Eigner, C. / Antonyuk, S.V. / Dittmann, E. / Lamzin, V.S.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Structural and functional insights into the unique CBS-CP12 fusion protein family in cyanobacteria.
Authors: Hackenberg, C. / Hakanpaa, J. / Cai, F. / Antonyuk, S. / Eigner, C. / Meissner, S. / Laitaoja, M. / Janis, J. / Kerfeld, C.A. / Dittmann, E. / Lamzin, V.S.
History
DepositionMay 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 6, 2018Group: Data collection / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value
Revision 1.2Jun 20, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.3Jul 11, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.4Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CBS-CP12


Theoretical massNumber of molelcules
Total (without water)23,1551
Polymers23,1551
Non-polymers00
Water55831
1
A: CBS-CP12
x 6


Theoretical massNumber of molelcules
Total (without water)138,9276
Polymers138,9276
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation10_444-y-1,-x-1,-z-1/21
crystal symmetry operation11_554-x+y,y,-z-1/21
crystal symmetry operation12_544x,x-y-1,-z-1/21
Buried area19810 Å2
ΔGint-110 kcal/mol
Surface area46810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.235, 98.235, 100.619
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein CBS-CP12


Mass: 23154.561 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: First four residues in the sequence are EXPRESSION TAG
Source: (gene. exp.) Microcystis aeruginosa PCC 7806 (bacteria)
Gene: IPF_2164 / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR / References: UniProt: A8YJ50
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.03 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein at 6.08 mg/ml in 50 mM Bicine/KOH pH 7.8, 40 mM KCl, 0.132 mM AMP solution was mixed with reservoir solution containing 0.15 M KSCN, 0.1 M HEPES pH 7.0 and 18% PEG3350 containing 0.1 ...Details: Protein at 6.08 mg/ml in 50 mM Bicine/KOH pH 7.8, 40 mM KCl, 0.132 mM AMP solution was mixed with reservoir solution containing 0.15 M KSCN, 0.1 M HEPES pH 7.0 and 18% PEG3350 containing 0.1 mM Guanidine hydrochloride. Cryoprotector - reservoir solution with 25% ethylene glycol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.5→100.62 Å / Num. obs: 10477 / % possible obs: 99.9 % / Redundancy: 18.5 % / Biso Wilson estimate: 59.721 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.027 / Net I/σ(I): 23.4
Reflection shellResolution: 2.5→2.6 Å / Redundancy: 17.6 % / Rmerge(I) obs: 1.354 / Mean I/σ(I) obs: 2.6 / Num. unique obs: 1142 / CC1/2: 0.881 / Rpim(I) all: 0.462 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NMU

5nmu


Resolution: 2.5→85.07 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.937 / SU B: 20.157 / SU ML: 0.205 / Cross valid method: THROUGHOUT / ESU R: 0.284 / ESU R Free: 0.223 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23446 495 4.8 %RANDOM
Rwork0.19866 ---
obs0.20038 9924 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 74.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.1 Å20.55 Å20 Å2
2--1.1 Å20 Å2
3----3.57 Å2
Refinement stepCycle: 1 / Resolution: 2.5→85.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1351 0 0 31 1382
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191379
X-RAY DIFFRACTIONr_bond_other_d0.0020.021382
X-RAY DIFFRACTIONr_angle_refined_deg1.7321.9731868
X-RAY DIFFRACTIONr_angle_other_deg1.01233179
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9875175
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.89224.13858
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.74815254
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.7231511
X-RAY DIFFRACTIONr_chiral_restr0.0920.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211528
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02283
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_it2.6215.159698
X-RAY DIFFRACTIONr_mcbond_other2.625.165699
X-RAY DIFFRACTIONr_mcangle_it4.27.732872
X-RAY DIFFRACTIONr_mcangle_other4.2037.733872
X-RAY DIFFRACTIONr_scbond_it3.4425.726681
X-RAY DIFFRACTIONr_scbond_other3.445.731682
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6438.34995
X-RAY DIFFRACTIONr_long_range_B_refined7.69460.5741466
X-RAY DIFFRACTIONr_long_range_B_other7.70260.5121463
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 29 -
Rwork0.353 709 -
obs--99.86 %
Refinement TLS params.Method: refined / Origin x: -12.203 Å / Origin y: -40.942 Å / Origin z: -21.059 Å
111213212223313233
T0.0276 Å20.032 Å2-0.0734 Å2-0.065 Å2-0.0698 Å2--0.4181 Å2
L1.1366 °2-0.0168 °2-1.2211 °2-0.5727 °2-0.5923 °2--2.5636 °2
S-0.0544 Å °0.0078 Å °0.1332 Å °-0.0092 Å °-0.1114 Å °0.1023 Å °-0.0183 Å °0.0475 Å °0.1658 Å °

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