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- PDB-5nmu: Structure of hexameric CBS-CP12 protein from bloom-forming cyanob... -

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Basic information

Entry
Database: PDB / ID: 5nmu
TitleStructure of hexameric CBS-CP12 protein from bloom-forming cyanobacteria
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 / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsHackenberg, C. / Hakanpaa, J. / 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
DepositionApr 7, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 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 1.2Jul 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 1.3Jan 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 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CBS-CP12
B: CBS-CP12
C: CBS-CP12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,6057
Polymers69,4643
Non-polymers1424
Water3,441191
1
A: CBS-CP12
B: CBS-CP12
C: CBS-CP12
hetero molecules

A: CBS-CP12
B: CBS-CP12
C: CBS-CP12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)139,21114
Polymers138,9276
Non-polymers2848
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area21010 Å2
ΔGint-196 kcal/mol
Surface area44680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.607, 124.021, 118.447
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein CBS-CP12


Mass: 23154.561 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: Extra residues are left after TAG cleavage
Source: (gene. exp.) Microcystis aeruginosa PCC 7806 (bacteria)
Gene: IPF_2164 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LOBSTR / References: UniProt: A8YJ50
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 2.13 Å3/Da / Density % sol: 44 % / Description: hanging drop
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 8
Details: 300 mM Na Acetate, 25% PEG2000 MME, 100 mM HEPES buffer, pH 8.0, Vapor diffusion, Temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 17, 2015 / Details: KB mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.15→68.7 Å / Num. obs: 32084 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 39.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.039 / Rpim(I) all: 0.038 / Net I/σ(I): 14.8
Reflection shellResolution: 2.15→2.22 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.384 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 2725 / CC1/2: 0.811 / Rpim(I) all: 0.366 / % possible all: 96.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
Aimlessdata scaling
CRANK2phasing
ARP/wARPmodel building
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5NPL

5npl


Resolution: 2.15→38.58 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 11.801 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.192 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23419 1643 5.1 %RANDOM
Rwork0.1783 ---
obs0.18105 30438 97.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 53.779 Å2
Baniso -1Baniso -2Baniso -3
1--2.42 Å20 Å20 Å2
2--2.24 Å20 Å2
3---0.18 Å2
Refinement stepCycle: 1 / Resolution: 2.15→38.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4001 0 4 191 4196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194061
X-RAY DIFFRACTIONr_bond_other_d0.0020.024049
X-RAY DIFFRACTIONr_angle_refined_deg1.6951.9725491
X-RAY DIFFRACTIONr_angle_other_deg1.01639308
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9615516
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.71424.121165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.8415735
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.3911530
X-RAY DIFFRACTIONr_chiral_restr0.0960.2651
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214486
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02830
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_it1.6063.2822079
X-RAY DIFFRACTIONr_mcbond_other1.6033.2812078
X-RAY DIFFRACTIONr_mcangle_it2.5614.9032590
X-RAY DIFFRACTIONr_mcangle_other2.5614.9052591
X-RAY DIFFRACTIONr_scbond_it1.9793.4831981
X-RAY DIFFRACTIONr_scbond_other1.9763.481979
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2735.1282901
X-RAY DIFFRACTIONr_long_range_B_refined6.20239.3474433
X-RAY DIFFRACTIONr_long_range_B_other6.18239.1314401
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.151→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 124 -
Rwork0.243 2180 -
obs--95.76 %
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)
11.15380.1410.01440.6656-0.08961.74570.1128-0.03910.08460.0407-0.01430.1014-0.243-0.1877-0.09850.30850.04650.05660.13990.00640.0274-8.854-25.195-23.746
21.6345-0.5750.44680.976-0.36641.18990.0541-0.0185-0.14430.1586-0.01130.18370.0294-0.2374-0.04270.1928-0.02080.01660.19220.02860.0479-15.095-41.791-16.344
30.8429-0.28230.05410.938-0.30351.8919-0.0660.0452-0.27580.096-0.01240.13410.3553-0.00680.07840.2896-0.0422-0.03930.08490.04120.1598-3.123-62.673-21.345
47.03270.28744.77342.045-1.45076.1166-0.11670.0610.03540.17060.1196-0.0523-0.32670.0596-0.00290.2835-0.0689-0.0930.1250.0080.038814.668-40.3874.667
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 135
2X-RAY DIFFRACTION1A190 - 191
3X-RAY DIFFRACTION2B1 - 190
4X-RAY DIFFRACTION3C1 - 190
5X-RAY DIFFRACTION4A136 - 180

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