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- PDB-2hng: The Crystal Structure of Protein of Unknown Function SP1558 from ... -

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Basic information

Entry
Database: PDB / ID: 2hng
TitleThe Crystal Structure of Protein of Unknown Function SP1558 from Streptococcus pneumoniae
ComponentsHypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / alpha-beta / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyProtein of unknown function DUF1149 / Protein of unknown function (DUF1149) / Bacterial Protein-export protein SecB / SecB-like / SecB-like superfamily / Roll / Alpha Beta / Transposase / Uncharacterized protein
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.63 Å
AuthorsKim, Y. / Zhang, D. / Zhou, M. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published / Year: 2006
Title: The Crystal Structure of Hypothetical Protein SP_1558 from Streptococcus pneumoniae
Authors: Kim, Y. / Zhang, D. / Zhou, M. / Clancy, S. / Joachimiak, A.
History
DepositionJul 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 20, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)14,8371
Polymers14,8371
Non-polymers00
Water3,063170
1
A: Hypothetical protein

A: Hypothetical protein


Theoretical massNumber of molelcules
Total (without water)29,6742
Polymers29,6742
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Unit cell
Length a, b, c (Å)43.030, 42.581, 72.379
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number17
Space group name H-MP2221
Components on special symmetry positions
IDModelComponents
11A-160-

HOH

21A-210-

HOH

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Components

#1: Protein Hypothetical protein


Mass: 14837.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP_1558 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21DE3 / References: UniProt: Q97PP5, UniProt: A0A0H2UQV3*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 2.23 Å3/Da / Density % sol: 44.94 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2M Calcium chloride, 0.1M Bis-Tris pH 6.5, 45% MPD, 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: 0.97931 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 12, 2006 / Details: mirrors
RadiationMonochromator: double crystal monochromator, Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 1.63→43.03 Å / Num. all: 17399 / Num. obs: 16724 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.2
Reflection shellResolution: 1.63→1.69 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1283 / % possible all: 75

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.63→43.03 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.217 / SU ML: 0.078 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.122 / ESU R Free: 0.119
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflectionSelection details
Rfree0.23122 1682 10.1 %RANDOM
Rwork0.18887 ---
all0.19312 14910 --
obs0.19312 14910 96.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.122 Å2
Baniso -1Baniso -2Baniso -3
1-2.28 Å20 Å20 Å2
2---0.9 Å20 Å2
3----1.38 Å2
Refinement stepCycle: LAST / Resolution: 1.63→43.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1020 0 0 170 1190
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221217
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5471.9441677
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1485161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.86126.2572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.82315218
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.117156
X-RAY DIFFRACTIONr_chiral_restr0.1190.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021009
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2120.2547
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.2861
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1960.2149
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1860.242
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2030.233
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9751.5761
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.5421227
X-RAY DIFFRACTIONr_scbond_it2.6533503
X-RAY DIFFRACTIONr_scangle_it3.8794.5450
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.63→1.672 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 88 -
Rwork0.221 842 -
obs-842 74.4 %

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