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- PDB-3c4s: Crystal structure of the Ssl0352 protein from Synechocystis sp. N... -

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Basic information

Entry
Database: PDB / ID: 3c4s
TitleCrystal structure of the Ssl0352 protein from Synechocystis sp. Northeast Structural Genomics Consortium target SgR42
ComponentsSsl0352 protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / P74795_SYNY3 / Ssl0352 / NESG / SgR42 / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium
Function / homologyNADH dehydrogenase-like complex, subunit S / NAD(P)H dehydrogenase subunit S / photosynthetic electron transport chain / SH3 type barrels. - #140 / SH3 type barrels. / Roll / Mainly Beta / Ssl0352 protein
Function and homology information
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsVorobiev, S.M. / Chen, Y. / Seetharaman, J. / Wang, D. / Maglaqui, M. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. ...Vorobiev, S.M. / Chen, Y. / Seetharaman, J. / Wang, D. / Maglaqui, M. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the Ssl0352 protein from Synechocystis sp.
Authors: Vorobiev, S.M. / Chen, Y. / Seetharaman, J. / Wang, D. / Maglaqui, M. / Janjua, H. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJan 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2008Provider: 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 1.3Aug 30, 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 / 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: Ssl0352 protein
B: Ssl0352 protein


Theoretical massNumber of molelcules
Total (without water)15,3112
Polymers15,3112
Non-polymers00
Water2,684149
1
A: Ssl0352 protein


Theoretical massNumber of molelcules
Total (without water)7,6561
Polymers7,6561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Ssl0352 protein


Theoretical massNumber of molelcules
Total (without water)7,6561
Polymers7,6561
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.606, 44.606, 65.100
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS A MONOMER ACCORDING TO AGGREGATION SCREENING.

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Components

#1: Protein Ssl0352 protein


Mass: 7655.642 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (bacteria) / Strain: PCC 6803 / Gene: ssl0352 / Plasmid: pET21-23C / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: P74795
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.44 Å3/Da / Density % sol: 49.63 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 291 K / Method: microbatch under oil / pH: 6.5
Details: 30% Jeffamine M-600, 0.05M Cesium chloride, 0.1M MES pH 6.5, MICROBATCH UNDER OIL, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jan 25, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 31765 / Num. obs: 31765 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 14.1 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 17.36
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 6 / Num. unique all: 3200 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2JZ2, chain A

2jz2


Resolution: 1.7→24.89 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1019206.95 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: The Friedel pairs were used in phasing
RfactorNum. reflection% reflectionSelection details
Rfree0.194 1462 4.8 %RANDOM
Rwork0.186 ---
obs0.186 30233 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.6645 Å2 / ksol: 0.421479 e/Å3
Displacement parametersBiso mean: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.48 Å20.82 Å20 Å2
2--0.37 Å20 Å2
3----0.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.05 Å-0.04 Å
Refinement stepCycle: LAST / Resolution: 1.7→24.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms894 0 0 149 1043
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.207 219 4.8 %
Rwork0.199 4302 -
obs--85.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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