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- PDB-2ewc: Structure of hypothetical protein from Streptococcus pyogenes M1 ... -

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Entry
Database: PDB / ID: 2ewc
TitleStructure of hypothetical protein from Streptococcus pyogenes M1 GAS, member of highly conserved yjgF family of proteins
Componentsconserved hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / yjgF proteins family / conserved hypothetical protein / COG0251 / Putative translation initiation inhibitor / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyRutC-like / RutC-like superfamily / 60s Ribosomal Protein L30; Chain: A; / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesStreptococcus pyogenes (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsNocek, B. / Li, H. / Clancy, S. / Collart, F. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Structure of hypothetical protein from Streptococcus pyogenes M1 GAS, member of highly conserved yjgF family of proteins
Authors: Nocek, B. / Li, H. / Clancy, S. / Collart, F. / Joachimiak, A.
History
DepositionNov 2, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations ...Advisory / Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 12CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 12CHAIN(S). THE BIOLOGICAL MOLECULE FOR THE PROTEIN IS UNKNOWN.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: conserved hypothetical protein
B: conserved hypothetical protein
C: conserved hypothetical protein
D: conserved hypothetical protein
E: conserved hypothetical protein
F: conserved hypothetical protein
G: conserved hypothetical protein
H: conserved hypothetical protein
I: conserved hypothetical protein
J: conserved hypothetical protein
K: conserved hypothetical protein
L: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)176,91817
Polymers176,45712
Non-polymers4605
Water19,0601058
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: conserved hypothetical protein
B: conserved hypothetical protein
C: conserved hypothetical protein
G: conserved hypothetical protein
K: conserved hypothetical protein
L: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5059
Polymers88,2296
Non-polymers2763
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16830 Å2
ΔGint-75 kcal/mol
Surface area24840 Å2
MethodPISA, PQS
3
D: conserved hypothetical protein
E: conserved hypothetical protein
F: conserved hypothetical protein
H: conserved hypothetical protein
I: conserved hypothetical protein
J: conserved hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,4138
Polymers88,2296
Non-polymers1842
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16730 Å2
ΔGint-74 kcal/mol
Surface area24810 Å2
MethodPISA, PQS
4
A: conserved hypothetical protein
B: conserved hypothetical protein
C: conserved hypothetical protein
hetero molecules

D: conserved hypothetical protein
E: conserved hypothetical protein
F: conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)88,4138
Polymers88,2296
Non-polymers1842
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1/2,-y,z-1/21
Buried area14400 Å2
ΔGint-60 kcal/mol
Surface area27340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.120, 131.994, 135.640
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
conserved hypothetical protein


Mass: 14704.770 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pyogenes (bacteria) / Strain: M1 GAS / Gene: gi|13623057 / Plasmid: peT15b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99XS4
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 1058 / 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: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Peg 4k, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 15, 2005 / Details: mirrors
RadiationMonochromator: Si 111 channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 102417 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.1 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 17
Reflection shellResolution: 2.15→2.23 Å / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
SBC-Collectdata collection
HKL-2000data scaling
HKL-3000phasing
SHELXCDphasing
SOLVEphasing
RESOLVEphasing
ARPmodel building
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 7.896 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / ESU R: 0.192 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20439 5061 5 %RANDOM
Rwork0.16217 ---
obs0.1643 95976 98.62 %-
all-101037 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 29.625 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å20 Å20 Å2
2---0.51 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11596 0 30 1058 12684
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.02112050
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4151.93516267
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.33551468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.0523.557672
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.396152019
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1515111
X-RAY DIFFRACTIONr_chiral_restr0.1110.21680
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.029501
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.25633
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.28161
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2210.2974
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8781.57425
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.509211559
X-RAY DIFFRACTIONr_scbond_it2.56935222
X-RAY DIFFRACTIONr_scangle_it4.0664.54708
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.21 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.251 321 -
Rwork0.18 5796 -
obs--81.79 %
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)
10.81190.2549-0.41221.2379-0.57031.27580.0086-0.1338-0.0260.15-0.1079-0.3153-0.07330.18690.0992-0.07930.0022-0.0306-0.03920.04760.0202-66.99717.5903-24.1272
21.00580.5369-0.63430.9497-0.34411.1055-0.14430.0902-0.2011-0.4340.056-0.19360.24740.05640.08830.079-0.0110.0648-0.072-0.0194-0.0484-75.1674-1.1872-41.8045
30.76650.7672-0.4222.4625-0.90890.84620.00350.11880.1651-0.18610.10440.2261-0.062-0.1285-0.1078-0.02730.0164-0.0138-0.05970.0148-0.0443-83.518916.8817-33.9685
40.48970.27180.22720.64260.24591.14250.0539-0.0610.01020.1228-0.04910.05210.0595-0.031-0.0048-0.0348-0.0015-0.0028-0.0417-0.0034-0.0538-25.34997.72833.9298
50.89730.20670.14760.85920.2641.1938-0.01140.0479-0.1051-0.04460.0541-0.1780.08490.2329-0.0427-0.09650.0213-0.00430.0076-0.0301-0.0292-10.00586.372519.1885
60.86140.03440.15411.22640.57890.9541-0.0570.08150.0926-0.13090.0514-0.0158-0.18810.06620.0055-0.022-0.0137-0.0202-0.06770.0196-0.0413-23.729222.781618.806
70.71740.7158-0.6252.6663-1.14170.9797-0.10660.0546-0.0746-0.14640.13830.12520.1694-0.0168-0.0318-0.04230.01710.0334-0.07060.0161-0.0297-94.592-22.9245-16.8834
80.8970.59840.55851.02930.41251.06970.04230.0583-0.133-0.01580.0508-0.13780.16090.1056-0.0931-0.04450.0139-0.0139-0.0466-0.0153-0.023-34.9692-17.16151.9383
90.97310.2060.51660.78860.5431.41720.0324-0.14320.01060.1204-0.06360.10740.0668-0.22590.0312-0.0702-0.00950.0221-0.0138-0.0016-0.054-51.8446-7.172810.2992
100.95930.37140.41310.42220.3131.2467-0.08380.09190.0795-0.10650.05250.0264-0.1668-0.03990.0314-0.0182-0.0139-0.0151-0.04530.0185-0.0673-42.15450.8661-6.9238
110.76530.1117-0.90780.8822-0.1891.1307-0.0478-0.1947-0.00430.24220.0117-0.048-0.04210.15180.03620.0380.02380.0126-0.03730.0029-0.0758-94.4885-7.6516-1.9954
121.14270.4752-0.10260.4592-0.170.919-0.0483-0.01940.131-0.05010.03140.2596-0.1033-0.14940.0169-0.07240.03560.0069-0.0380.04620.0269-108.9428-7.1061-17.7132
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA3 - 1223 - 122
2X-RAY DIFFRACTION2BB3 - 1223 - 122
3X-RAY DIFFRACTION3CC3 - 1223 - 122
4X-RAY DIFFRACTION4DD3 - 1213 - 121
5X-RAY DIFFRACTION5EE3 - 1223 - 122
6X-RAY DIFFRACTION6FF3 - 1223 - 122
7X-RAY DIFFRACTION7GG3 - 1223 - 122
8X-RAY DIFFRACTION8HH3 - 1223 - 122
9X-RAY DIFFRACTION9II3 - 1223 - 122
10X-RAY DIFFRACTION10JJ3 - 1223 - 122
11X-RAY DIFFRACTION11KK3 - 1223 - 122
12X-RAY DIFFRACTION12LL3 - 1223 - 122

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