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- PDB-1sqs: X-Ray Crystal Structure Protein SP1951 of Streptococcus pneumonia... -

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Basic information

Entry
Database: PDB / ID: 1sqs
TitleX-Ray Crystal Structure Protein SP1951 of Streptococcus pneumoniae. Northeast Structural Genomics Consortium Target SpR27.
Componentsconserved hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha beta protein / PSI / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


oxidoreductase activity / nucleotide binding
Similarity search - Function
NADPH-dependent FMN reductase-like / NADPH-dependent FMN reductase / Flavodoxin domain / Flavoprotein-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
L(+)-TARTARIC ACID / NADPH-dependent FMN reductase-like domain-containing protein / FMN_red domain-containing protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsForouhar, F. / Lee, I. / Vorobiev, S.M. / Xiao, R. / Acton, T.B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.STRUCT.FUNCT.GENOM / Year: 2007
Title: Functional insights from structural genomics.
Authors: Forouhar, F. / Kuzin, A. / Seetharaman, J. / Lee, I. / Zhou, W. / Abashidze, M. / Chen, Y. / Yong, W. / Janjua, H. / Fang, Y. / Wang, D. / Cunningham, K. / Xiao, R. / Acton, T.B. / ...Authors: Forouhar, F. / Kuzin, A. / Seetharaman, J. / Lee, I. / Zhou, W. / Abashidze, M. / Chen, Y. / Yong, W. / Janjua, H. / Fang, Y. / Wang, D. / Cunningham, K. / Xiao, R. / Acton, T.B. / Pichersky, E. / Klessig, D.F. / Porter, C.W. / Montelione, G.T. / Tong, L.
History
DepositionMar 19, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Dec 20, 2017Group: Database references / Category: pdbx_database_related

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: conserved hypothetical protein
B: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0293
Polymers56,8792
Non-polymers1501
Water9,656536
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2990 Å2
ΔGint-11 kcal/mol
Surface area20920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.161, 81.994, 63.450
Angle α, β, γ (deg.)90, 94.62, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein conserved hypothetical protein


Mass: 28439.254 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP1951 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q97NR6, UniProt: A0A0H2URW2*PLUS
#2: Chemical ChemComp-TLA / L(+)-TARTARIC ACID / Tartaric acid


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 536 / 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: 2.257 Å3/Da / Density % sol: 45.55 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Protein solution: 10mM Tris (pH 7.5), 5mM DTT. Well solution: 10% PEG 3350, 100mM Sodium Tartrate, 200mM NaCl., VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 28, 2004 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.5→28.76 Å / Num. obs: 154553 / % possible obs: 96.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.061 / Net I/σ(I): 19.74
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.277 / Mean I/σ(I) obs: 3.8 / Num. unique all: 14629 / Rsym value: 0.25 / % possible all: 92

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: SAD
Starting model: None

Resolution: 1.5→28.76 Å / Isotropic thermal model: anisotropic overall / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
Details: Used weighted full matrix least squares procedure. Friedel pairs were used.
RfactorNum. reflection% reflectionSelection details
Rfree0.22 13944 -Random
Rwork0.2 ---
obs-137508 89.9 %-
Displacement parametersBiso mean: 20 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å2-1.08 Å2
2--1.85 Å20 Å2
3----2.5 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.09 Å0.05 Å
Refinement stepCycle: LAST / Resolution: 1.5→28.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3796 0 10 536 4342
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d1
X-RAY DIFFRACTIONc_dihedral_angle_d22
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.005
RfactorNum. reflection% reflection
Rfree0.232 1846 -
Rwork0.205 --
obs-17191 72.2 %

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