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

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Basic information

Entry
Database: PDB / ID: 5npl
TitleCrystal structure of hexameric CBS-CP12 protein from bloom-forming cyanobacteria, Yb-derivative at 2.8 A resolution
ComponentsSimilar to tr|Q8YYT1|Q8YYT1
KeywordsPHOTOSYNTHESIS / Cystathionine beta synthase domain / fusion protein / redox-regulation of photosynthesis
Function / homology
Function and homology information


CP12 domain / CP12 domain / CP12 / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile.
Similarity search - Domain/homology
Chem-DO3 / YTTERBIUM (III) ION / Similar to tr
Similarity search - Component
Biological speciesMicrocystis aeruginosa PCC 7806 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.79 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 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Similar to tr|Q8YYT1|Q8YYT1
B: Similar to tr|Q8YYT1|Q8YYT1
C: Similar to tr|Q8YYT1|Q8YYT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,21422
Polymers69,4643
Non-polymers3,75119
Water91951
1
A: Similar to tr|Q8YYT1|Q8YYT1
B: Similar to tr|Q8YYT1|Q8YYT1
C: Similar to tr|Q8YYT1|Q8YYT1
hetero molecules

A: Similar to tr|Q8YYT1|Q8YYT1
B: Similar to tr|Q8YYT1|Q8YYT1
C: Similar to tr|Q8YYT1|Q8YYT1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,42944
Polymers138,9276
Non-polymers7,50138
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area24130 Å2
ΔGint-192 kcal/mol
Surface area49960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.890, 120.734, 117.548
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13B
23C

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A3 - 178
2010B3 - 178
1020A2 - 178
2020C2 - 178
1030B3 - 178
2030C3 - 178

NCS ensembles :
ID
1
2
3

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Components

#1: Protein Similar to tr|Q8YYT1|Q8YYT1


Mass: 23154.561 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
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: Chemical
ChemComp-YB / YTTERBIUM (III) ION


Mass: 173.040 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: Yb
#3: Chemical ChemComp-DO3 / 10-((2R)-2-HYDROXYPROPYL)-1,4,7,10-TETRAAZACYCLODODECANE 1,4,7-TRIACETIC ACID


Mass: 404.459 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H32N4O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsUn-modelled atoms are due to lack of electron density support.

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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 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 8
Details: 300 MM NA ACETATE, 20% PEG2000 MME, REMARK 280 100 MM HEPES BUFFER, PH 8.0; before data collection crystals were soaked for 30 min in a solution containing 25% PEG2000MME, 0.2 M sodium ...Details: 300 MM NA ACETATE, 20% PEG2000 MME, REMARK 280 100 MM HEPES BUFFER, PH 8.0; before data collection crystals were soaked for 30 min in a solution containing 25% PEG2000MME, 0.2 M sodium acetate, 0.1 M HEPES, pH 8.0 and 0.1 M Yb-HPDO3A

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 1.385 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 10, 2015 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.385 Å / Relative weight: 1
ReflectionResolution: 2.79→66 Å / Num. obs: 13464 / % possible obs: 97.8 % / Redundancy: 6.5 % / Biso Wilson estimate: 51.1 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.5
Reflection shellResolution: 2.79→2.87 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.77 / % possible all: 61.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XDSdata scaling
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 2.79→10 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.926 / SU B: 25.935 / SU ML: 0.259 / Cross valid method: THROUGHOUT / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21948 677 4.9 %RANDOM
Rwork0.18593 ---
obs0.18764 13151 95.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 53.449 Å2
Baniso -1Baniso -2Baniso -3
1-5.23 Å20 Å20 Å2
2--2.17 Å20 Å2
3----7.4 Å2
Refinement stepCycle: LAST / Resolution: 2.79→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4120 0 73 51 4244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0194243
X-RAY DIFFRACTIONr_bond_other_d0.0020.024211
X-RAY DIFFRACTIONr_angle_refined_deg1.7791.9825744
X-RAY DIFFRACTIONr_angle_other_deg1.02739688
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5955534
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.8324.035171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.40415746
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3641532
X-RAY DIFFRACTIONr_chiral_restr0.1220.2683
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0214672
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02864
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_it2.1393.842145
X-RAY DIFFRACTIONr_mcbond_other2.1393.8382144
X-RAY DIFFRACTIONr_mcangle_it3.6625.7472676
X-RAY DIFFRACTIONr_mcangle_other3.6615.7492677
X-RAY DIFFRACTIONr_scbond_it2.2584.1772097
X-RAY DIFFRACTIONr_scbond_other2.2574.1762095
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8686.1373068
X-RAY DIFFRACTIONr_long_range_B_refined6.24745.6954436
X-RAY DIFFRACTIONr_long_range_B_other6.24545.6974436
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A104700.05
12B104700.05
21A105480.05
22C105480.05
31B104420.06
32C104420.06
LS refinement shellResolution: 2.792→2.858 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 33 -
Rwork0.333 659 -
obs--70.54 %
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)
11.1284-0.42251.06980.7774-0.8491.69460.0079-0.00870.00530.1110.01460.0698-0.1169-0.0614-0.02250.02570.00470.00960.075-0.02510.2235-3.615-27.087-17.071
20.6994-0.15330.8780.7172-0.59611.50180.0492-0.02720.01120.12120.02850.09960.0122-0.0991-0.07770.0354-0.01260.03050.0657-0.01220.231-16.469-40.227-17.56
32.0549-0.61530.78710.6248-0.16511.3266-0.1034-0.01060.08570.07030.0094-0.00570.2277-0.04910.0940.077-0.0124-0.00090.00470.01710.1666-1.785-61.003-20.612
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 190
2X-RAY DIFFRACTION2B1 - 190
3X-RAY DIFFRACTION3C1 - 190

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