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- PDB-2fi0: The crystal structure of the conserved domain protein from Strept... -

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Basic information

Entry
Database: PDB / ID: 2fi0
TitleThe crystal structure of the conserved domain protein from Streptococcus pneumoniae TIGR4
Componentsconserved domain protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Streptococcus pneumoniae / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologySP0561-like / SP0561-like / Domain of unknown function DUF1858 / Domain of unknown function (DUF1858) / ScdA-like, N-terminal domain superfamily / Orthogonal Bundle / Mainly Alpha / : / DUF1858 domain-containing protein
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsZhang, R. / Li, H. / Abdullah, J. / Collart, F. / Cymborowski, M. / Minor, W. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of the conserved domain protein from Streptococcus pneumoniae TIGR4
Authors: Zhang, R. / Li, H. / Abdullah, J. / Collart, F. / Cymborowski, M. / Minor, W. / Joachimiak, A.
History
DepositionDec 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Apr 13, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / database_2
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: conserved domain protein


Theoretical massNumber of molelcules
Total (without water)8,8651
Polymers8,8651
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.420, 92.420, 41.343
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein conserved domain protein


Mass: 8865.405 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: GenBank: 14972036, UniProt: Q8CZ42*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 3.83 Å3/Da / Density % sol: 67.89 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.5 M NaCl, 0.1M Tris-HCl, 0.2M MgCl2, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 287K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9798 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 18, 2005 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. all: 7362 / Num. obs: 6747 / % possible obs: 91.64 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 13.77
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.155 / Mean I/σ(I) obs: 3.2 / Num. unique all: 1572 / % possible all: 43.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.1→46.23 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.943 / SU B: 8.944 / SU ML: 0.131 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.178 / ESU R Free: 0.162
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23627 319 4.5 %RANDOM
Rwork0.20281 ---
obs0.20438 6747 91.64 %-
all-7362 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.344 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å2-0.28 Å20 Å2
2---0.56 Å20 Å2
3---0.84 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.038 Å0.034 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.035 Å
Refinement stepCycle: LAST / Resolution: 2.1→46.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms601 0 0 57 658
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022608
X-RAY DIFFRACTIONr_bond_other_d0.0010.02605
X-RAY DIFFRACTIONr_angle_refined_deg1.2772.014824
X-RAY DIFFRACTIONr_angle_other_deg0.85431411
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.811578
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.67225.90922
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.70215116
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.807153
X-RAY DIFFRACTIONr_chiral_restr0.0710.2103
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02651
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0296
X-RAY DIFFRACTIONr_nbd_refined0.1920.2140
X-RAY DIFFRACTIONr_nbd_other0.1780.2632
X-RAY DIFFRACTIONr_nbtor_refined0.1590.2310
X-RAY DIFFRACTIONr_nbtor_other0.0830.2355
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.239
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1780.216
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0660.23
X-RAY DIFFRACTIONr_mcbond_it0.7831.5511
X-RAY DIFFRACTIONr_mcbond_other0.1061.5161
X-RAY DIFFRACTIONr_mcangle_it0.9682643
X-RAY DIFFRACTIONr_scbond_it1.7063232
X-RAY DIFFRACTIONr_scangle_it2.624.5181
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 12 -
Rwork0.209 308 -
obs--53.16 %
Refinement TLS params.Method: refined / Origin x: 36.321 Å / Origin y: 12.599 Å / Origin z: 19.019 Å
111213212223313233
T-0.143 Å20.0214 Å20.0314 Å2--0.2145 Å2-0.0557 Å2--0.1547 Å2
L5.5506 °21.0705 °2-1.629 °2-6.4194 °2-1.3628 °2--3.1587 °2
S0.0717 Å °0.0365 Å °0.3742 Å °0.2656 Å °-0.004 Å °-0.245 Å °-0.317 Å °-0.0228 Å °-0.0676 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 303 - 30
2X-RAY DIFFRACTION1AA31 - 5631 - 56
3X-RAY DIFFRACTION1AA57 - 8157 - 81

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