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- PDB-5y2w: Structure of Synechocystis PCC6803 CcmR regulatory domain in comp... -

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Basic information

Entry
Database: PDB / ID: 5y2w
TitleStructure of Synechocystis PCC6803 CcmR regulatory domain in complex with 2-PG
ComponentsRubisco operon transcriptional regulator
KeywordsTRANSCRIPTION / LysR-type transcription factor
Function / homology
Function and homology information


transcription cis-regulatory region binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription
Similarity search - Function
LysR, substrate-binding / LysR substrate binding domain / LysR-type HTH domain profile. / Transcription regulator HTH, LysR / Bacterial regulatory helix-turn-helix protein, lysR family / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
2-PHOSPHOGLYCOLIC ACID / Rubisco operon transcriptional regulator
Similarity search - Component
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsJiang, Y.L. / Wang, X.P. / Sun, H. / Cheng, W. / Cao, D.D. / Han, S.J. / Li, W.F. / Chen, Y. / Zhou, C.Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31630001, 31500598 China
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018
Title: Coordinating carbon and nitrogen metabolic signaling through the cyanobacterial global repressor NdhR.
Authors: Jiang, Y.L. / Wang, X.P. / Sun, H. / Han, S.J. / Li, W.F. / Cui, N. / Lin, G.M. / Zhang, J.Y. / Cheng, W. / Cao, D.D. / Zhang, Z.Y. / Zhang, C.C. / Chen, Y. / Zhou, C.Z.
History
DepositionJul 27, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed
Revision 1.2Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Nov 22, 2023Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rubisco operon transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,8062
Polymers26,6501
Non-polymers1561
Water70339
1
A: Rubisco operon transcriptional regulator
hetero molecules

A: Rubisco operon transcriptional regulator
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6114
Polymers53,2992
Non-polymers3122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area3380 Å2
ΔGint-19 kcal/mol
Surface area18790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.965, 58.965, 123.958
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Rubisco operon transcriptional regulator


Mass: 26649.672 Da / Num. of mol.: 1 / Fragment: UNP residues 91-316
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Strain: PCC 6803 / Kazusa / Gene: rbcR / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / References: UniProt: P73862
#2: Chemical ChemComp-PGA / 2-PHOSPHOGLYCOLIC ACID


Mass: 156.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C2H5O6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 39 / Source method: isolated from a natural source / Formula: H2O

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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: 2.33 Å3/Da / Density % sol: 47.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M MgCl2, 0.1 M HEPES, pH 7.5, 30% (v/v) Polyethylene glycol 400, 5 mM 2-PG

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97861 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 13083 / % possible obs: 98.7 % / Redundancy: 4.8 % / Net I/σ(I): 11.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 1289 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5Y2V

5y2v


Resolution: 2.2→47.26 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.928 / SU B: 6.362 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.25 / ESU R Free: 0.212 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25476 643 4.9 %RANDOM
Rwork0.2006 ---
obs0.20308 12432 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 52.827 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.02 Å2-0 Å2
2--0.02 Å2-0 Å2
3----0.08 Å2
Refinement stepCycle: 1 / Resolution: 2.2→47.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1661 0 9 39 1709
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191701
X-RAY DIFFRACTIONr_bond_other_d0.0010.021678
X-RAY DIFFRACTIONr_angle_refined_deg1.7431.9752303
X-RAY DIFFRACTIONr_angle_other_deg0.82233843
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9595207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.19223.62580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.68915301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9141515
X-RAY DIFFRACTIONr_chiral_restr0.0960.2263
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211905
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02390
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_it4.1524.948831
X-RAY DIFFRACTIONr_mcbond_other4.1424.945830
X-RAY DIFFRACTIONr_mcangle_it5.6837.3991037
X-RAY DIFFRACTIONr_mcangle_other5.6817.4041038
X-RAY DIFFRACTIONr_scbond_it5.0265.52870
X-RAY DIFFRACTIONr_scbond_other4.9925.519870
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.4968.0511267
X-RAY DIFFRACTIONr_long_range_B_refined9.43639.5091897
X-RAY DIFFRACTIONr_long_range_B_other9.4439.5171898
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 53 -
Rwork0.249 908 -
obs--99.07 %

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