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- PDB-2iaz: Crystal structure of a Conserved Protein of Unknown Function SP13... -

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Basic information

Entry
Database: PDB / ID: 2iaz
TitleCrystal structure of a Conserved Protein of Unknown Function SP1372 from Streptococcus pneumoniae
ComponentsHypothetical protein SP1372
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Streptococcus pneumoniae / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyYheA/YmcA-like / Control of competence regulator ComK, YlbF/YmcA / YheA/YmcA-like domain superfamily / Control of competence regulator ComK, YlbF/YmcA / YheA-like fold / Up-down Bundle / Mainly Alpha / UPF0342 protein SP_1372
Function and homology information
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsZhang, R. / Bigelow, L. / Abdullah, J. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: The crystal structure of a conserved hypothetical protein SP1372 from Streptococcus pneumoniae
Authors: Zhang, R. / Bigelow, L. / Abdullah, J. / Joachimiak, A.
History
DepositionSep 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein SP1372
B: Hypothetical protein SP1372
C: Hypothetical protein SP1372
D: Hypothetical protein SP1372


Theoretical massNumber of molelcules
Total (without water)50,6674
Polymers50,6674
Non-polymers00
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12080 Å2
ΔGint-105 kcal/mol
Surface area21370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.808, 86.715, 93.881
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsIt seems this protein exists as tetramer. The deposited coords. of molecules A,B,C,D represent the tetramer in the asymmetric unit.

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Components

#1: Protein
Hypothetical protein SP1372


Mass: 12666.843 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP1372 / Plasmid: PDM68 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q97Q59
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.6 Å3/Da / Density % sol: 52.74 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 60% Tacsimate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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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: Dec 5, 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: 2.4→33.63 Å / Num. all: 20205 / Num. obs: 20102 / % possible obs: 99.49 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 40.6 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 20.2
Reflection shellResolution: 2.4→2.462 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.366 / Mean I/σ(I) obs: 3 / Num. unique all: 1480 / % possible all: 99.48

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-2000data reduction
HKL-2000data scaling
HKL-3000phasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.4→33.63 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.893 / SU B: 20.906 / SU ML: 0.246 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.433 / ESU R Free: 0.297
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28902 1088 5.1 %RANDOM
Rwork0.22872 ---
all0.23188 20102 --
obs0.23188 20102 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.591 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20 Å20 Å2
2--2.83 Å20 Å2
3----0.86 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.04 Å0.032 Å
Luzzati d res low-6 Å
Luzzati sigma a0.5 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.4→33.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3438 0 0 105 3543
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0223489
X-RAY DIFFRACTIONr_bond_other_d0.0010.022389
X-RAY DIFFRACTIONr_angle_refined_deg1.6461.9764683
X-RAY DIFFRACTIONr_angle_other_deg1.02735877
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9355436
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.62226.364165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.61615650
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.326158
X-RAY DIFFRACTIONr_chiral_restr0.0860.2512
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023888
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02660
X-RAY DIFFRACTIONr_nbd_refined0.230.2937
X-RAY DIFFRACTIONr_nbd_other0.1810.22284
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21714
X-RAY DIFFRACTIONr_nbtor_other0.0950.21791
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2020.2112
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3630.25
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3030.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0650.25
X-RAY DIFFRACTIONr_mcbond_it1.1831.52712
X-RAY DIFFRACTIONr_mcbond_other0.1881.5892
X-RAY DIFFRACTIONr_mcangle_it1.3623474
X-RAY DIFFRACTIONr_scbond_it2.231490
X-RAY DIFFRACTIONr_scangle_it3.2124.51209
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.358 69 -
Rwork0.258 1472 -
obs-1472 99.48 %
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)
10.6816-0.19790.10293.3638-0.74580.65220.0921-0.14110.0262-0.10290.04120.22820.1404-0.1654-0.1333-0.1034-0.08190.0263-0.03590.0307-0.088836.201427.31315.6519
21.0009-0.7468-0.18092.18840.08980.0340.00620.03010.0205-0.10530.04350.0070.0080.0536-0.0496-0.03960.002-0.0446-0.0087-0.0022-0.056839.34128.927339.3024
30.70360.1591-0.87970.4094-0.33184.3995-0.1894-0.0172-0.06360.0354-0.024-0.20840.14280.07730.2133-0.13410.05180.016-0.0454-0.0019-0.044146.570746.289419.4139
40.5845-0.58160.39110.9493-0.17893.289-0.2590.08980.1844-0.08080.02080.0047-0.11510.52810.2382-0.1122-0.12-0.03510.01590.0422-0.069747.095210.54725.6588
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 502 - 51
2X-RAY DIFFRACTION1AA51 - 11152 - 112
3X-RAY DIFFRACTION2BB1 - 502 - 51
4X-RAY DIFFRACTION2BB51 - 11252 - 113
5X-RAY DIFFRACTION3CC2 - 513 - 52
6X-RAY DIFFRACTION3CC52 - 10853 - 109
7X-RAY DIFFRACTION4DD1 - 502 - 51
8X-RAY DIFFRACTION4DD51 - 11252 - 113

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