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- PDB-3ge2: Crystal structure of putative lipoprotein SP_0198 from Streptococ... -

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Basic information

Entry
Database: PDB / ID: 3ge2
TitleCrystal structure of putative lipoprotein SP_0198 from Streptococcus pneumoniae
ComponentsLipoprotein, putative
KeywordsLIPOPROTEIN / beta-barrel / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


Domain of unknown function DUF3642, lipoprotein / Bacterial lipoprotein / Lipocalin - #50 / D-aminopeptidase/lipoprotein domain superfamily / Lipocalin / Prokaryotic membrane lipoprotein lipid attachment site profile. / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
: / DUF3642 domain-containing protein / Lipoprotein, putative
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.203 Å
AuthorsKim, Y. / Zhang, R. / Joachimiak, G. / Gornicki, P. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal Structure of Putative Lipoprotein SP_0198 from Streptococcus pneumoniae
Authors: Kim, Y. / Zhang, R. / Joachimiak, G. / Gornicki, P. / Joachimiak, A.
History
DepositionFeb 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 17, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lipoprotein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5577
Polymers14,1141
Non-polymers4436
Water1,47782
1
A: Lipoprotein, putative
hetero molecules

A: Lipoprotein, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,11314
Polymers28,2282
Non-polymers88612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z+2/31
Buried area1010 Å2
ΔGint-7.5 kcal/mol
Surface area9400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.007, 106.007, 64.613
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-201-

K

21A-202-

CL

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Components

#1: Protein Lipoprotein, putative


Mass: 14113.791 Da / Num. of mol.: 1 / Fragment: UNP residues 26-152
Source method: isolated from a genetically manipulated source
Details: N-terminal MBP-fusion with TVMV protease cut-site which is cleaved in vivo and a 6-His tag with TEV protease cut site
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21magic / References: UniProt: A5M522, UniProt: A0A0H2UNA1*PLUS
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE PROTEIN SEQUENCE PROVIDED BY AUTHORS IS THE SEQUENCE OF THE PROTEIN USED FOR CRYSTALLIZATION. ...THE PROTEIN SEQUENCE PROVIDED BY AUTHORS IS THE SEQUENCE OF THE PROTEIN USED FOR CRYSTALLIZATION. CHYMOTRYPSIN HAS BEEN INCLUDED AT 1:100 RATIO IN THE CRYSTALLIZATION.

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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: 3.71 Å3/Da / Density % sol: 66.87 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1 M Sodium acetate trihydrate pH 4.5, 2.0 M Ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 7, 2009 / Details: mirrors
RadiationMonochromator: double crystal / Protocol: SAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.2→40.9 Å / Num. all: 11211 / Num. obs: 11211 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.9 % / Biso Wilson estimate: 43.59 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 12.8
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 3 / Num. unique all: 537 / % possible all: 98.7

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Processing

Software
NameClassification
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
SHELXCDphasing
SHELXDphasing
MLPHAREphasing
DMmodel building
SOLVEphasing
RESOLVEmodel building
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
DMphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.203→37.421 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.224 527 4.72 %random
Rwork0.189 ---
all0.191 11161 --
obs0.191 11161 98.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 74.727 Å2 / ksol: 0.399 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.0853 Å20 Å20 Å2
2--1.0853 Å20 Å2
3----2.1706 Å2
Refinement stepCycle: LAST / Resolution: 2.203→37.421 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms683 0 26 82 791
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.019
X-RAY DIFFRACTIONf_angle_deg1.61
X-RAY DIFFRACTIONf_dihedral_angle_d19.8
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.203-2.42440.23891190.20092578269799
2.4244-2.77520.22011340.180626282762100
2.7752-3.4960.19891460.165126512797100
3.496-37.4260.22341280.19022777290998
Refinement TLS params.Method: refined / Origin x: 25.2015 Å / Origin y: 31.4046 Å / Origin z: 32.0837 Å
111213212223313233
T0.2683 Å20.0408 Å20.0158 Å2-0.3028 Å20.008 Å2--0.2592 Å2
L0.8036 °2-0.193 °20.0008 °2-1.6087 °2-0.1458 °2--1.6605 °2
S-0.0249 Å °-0.1256 Å °-0.061 Å °0.0796 Å °0.0193 Å °0.1684 Å °0.1673 Å °-0.0522 Å °0.0019 Å °
Refinement TLS groupSelection details: chain A

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