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- PDB-3hx1: Crystal structure of the Slr1951 protein from Synechocystis sp. N... -

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Basic information

Entry
Database: PDB / ID: 3hx1
TitleCrystal structure of the Slr1951 protein from Synechocystis sp. Northeast Structural Genomics Consortium Target SgR167A
ComponentsSlr1951 protein
KeywordsStructural Genomics / Unknown function / P74513_SYNY3 / Slr1951 / Adenylate cyclase-like protein / NESG / SgR167A / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homology
Function and homology information


Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsVorobiev, S. / Chen, Y. / Seetharaman, J. / Janjua, J. / Xiao, R. / Ciccosanti, C. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. ...Vorobiev, S. / Chen, Y. / Seetharaman, J. / Janjua, J. / Xiao, R. / Ciccosanti, C. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the Slr1951 protein from Synechocystis sp.
Authors: Vorobiev, S. / Chen, Y. / Seetharaman, J. / Janjua, J. / Xiao, R. / Ciccosanti, C. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJun 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Author supporting evidence / Category: pdbx_struct_assembly_auth_evidence
Revision 1.3Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Slr1951 protein
B: Slr1951 protein


Theoretical massNumber of molelcules
Total (without water)30,4492
Polymers30,4492
Non-polymers00
Water82946
1
A: Slr1951 protein


Theoretical massNumber of molelcules
Total (without water)15,2251
Polymers15,2251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Slr1951 protein


Theoretical massNumber of molelcules
Total (without water)15,2251
Polymers15,2251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.130, 56.130, 290.868
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
DetailsMonomer according to aggregation screening.

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Components

#1: Protein Slr1951 protein


Mass: 15224.563 Da / Num. of mol.: 2 / Fragment: residues 1-123
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: slr1951 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: P74513
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.17 Å3/Da / Density % sol: 43.37 %
Crystal growTemperature: 291 K / Method: microbatch under oil / pH: 8
Details: 40 % PEG 1000, 0.1M potassium phosphate monobasic, 0.1M TrisHCl, pH 8.0, Microbatch under oil, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97931, 0.97907, 0.91162
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 14, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979311
20.979071
30.911621
ReflectionResolution: 2.5→50 Å / Num. all: 17900 / Num. obs: 17793 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.141 / Net I/σ(I): 21.8
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.629 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1753 / % possible all: 99.6

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDEphasing
REFMACrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.5→37.3 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 234852.875 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 802 5.1 %RANDOM
Rwork0.232 ---
obs-15877 89.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.346 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 54.5 Å2
Baniso -1Baniso -2Baniso -3
1--11.66 Å20 Å20 Å2
2---11.66 Å20 Å2
3---23.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.5→37.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1647 0 0 46 1693
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d27.4
X-RAY DIFFRACTIONc_improper_angle_d0.71
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.269 102 4.9 %
Rwork0.308 1977 -
obs-2079 70 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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