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- PDB-2hiy: The structure of conserved bacterial protein SP0830 from Streptoc... -

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Basic information

Entry
Database: PDB / ID: 2hiy
TitleThe structure of conserved bacterial protein SP0830 from Streptococcus pneumoniae.
ComponentsHypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Streptococcus pneumoniae / COG3797 / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologybacterial protein sp0830 like / SP0830-like domains / Protein of unknown function DUF1697 / Protein of unknown function (DUF1697) / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta / Phosphopentomutase / Uncharacterized protein
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.4 Å
AuthorsCuff, M.E. / Zhou, M. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The structure of conserved bacterial protein SP0830 from Streptococcus pneumoniae. (CASP Target)
Authors: Cuff, M.E. / Zhou, M. / Abdullah, J. / Joachimiak, A.
History
DepositionJun 29, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 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 1.3Oct 16, 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 / pdbx_struct_conn_angle / struct / 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_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct.title / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300Author states that biological unit for the protein is not yet known and is most likely a monomer

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein
B: Hypothetical protein
C: Hypothetical protein
D: Hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,85912
Polymers85,4844
Non-polymers3758
Water29,8511657
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.252, 108.845, 65.527
Angle α, β, γ (deg.)90.00, 97.15, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Hypothetical protein


Mass: 21371.035 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP_0830 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q97RI5, UniProt: A0A0H2UPL4*PLUS
#2: Chemical
ChemComp-CL / CHLORIDE ION


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1657 / 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: 2.62 Å3/Da / Density % sol: 53.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris pH8.5, 0.2M MgCl2, 25% PEG 3000, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97906, 0.97923
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 21, 2005
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979061
20.979231
ReflectionResolution: 1.4→48.28 Å / Num. all: 160902 / Num. obs: 160902 / % possible obs: 98.23 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3
Reflection shellResolution: 1.4→1.45 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 2 / % possible all: 94.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
Omodel building
Cootmodel building
ARP/wARPmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.4→48.28 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 1.711 / SU ML: 0.036 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.058 / ESU R Free: 0.062
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19439 8487 5 %RANDOM
Rwork0.16269 ---
all0.16427 160902 --
obs0.16427 160902 98.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.701 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20.05 Å2
2---0.49 Å20 Å2
3---0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.4→48.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5950 0 18 1657 7625
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0226458
X-RAY DIFFRACTIONr_angle_refined_deg1.421.968748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4365793
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.70924.295305
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.158151200
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.191529
X-RAY DIFFRACTIONr_chiral_restr0.1060.2949
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024881
X-RAY DIFFRACTIONr_nbd_refined0.2020.23110
X-RAY DIFFRACTIONr_nbtor_refined0.3140.24649
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.21285
X-RAY DIFFRACTIONr_metal_ion_refined0.0540.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1470.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1680.2102
X-RAY DIFFRACTIONr_mcbond_it1.011.53924
X-RAY DIFFRACTIONr_mcangle_it1.50626203
X-RAY DIFFRACTIONr_scbond_it2.53532897
X-RAY DIFFRACTIONr_scangle_it3.5874.52545
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.272 581 -
Rwork0.258 11297 -
obs--93.58 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9252-0.78480.13710.8668-0.04820.3804-0.066-0.0543-0.04880.05520.04480.0773-0.0259-0.05770.0212-0.02280.00830.0019-0.02770.0045-0.036532.882926.58145.402
20.9305-0.77450.3171.1298-0.24380.27810.0416-0.0091-0.0155-0.03260.0030.1175-0.005-0.0021-0.0445-0.02460.00790.0047-0.03850.0051-0.033529.212537.297135.76
31.13240.8418-0.26570.8592-0.13770.1670.01280.00630.034-0.01060.01170.04260.0007-0.0091-0.0245-0.0148-0.0083-0.0057-0.0337-0.0071-0.04491.412649.8526-2.4577
40.81850.8652-0.30461.0172-0.22570.3007-0.04520.04880.0565-0.06250.06990.10170.0218-0.0401-0.0248-0.0195-0.0062-0.0104-0.02520.0155-0.0311-2.741960.102127.0118
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1804 - 183
2X-RAY DIFFRACTION2BB1 - 1784 - 181
3X-RAY DIFFRACTION3CC1 - 1794 - 182
4X-RAY DIFFRACTION4DD0 - 1803 - 183

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