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- PDB-2ra2: X-Ray structure of the Q7CPV8 protein from Salmonella typhimurium... -

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Basic information

Entry
Database: PDB / ID: 2ra2
TitleX-Ray structure of the Q7CPV8 protein from Salmonella typhimurium at the resolution 1.9 A. Northeast Structural Genomics Consortium target StR88A
ComponentsPutative lipoprotein
KeywordsLIPOPROTEIN / NESG / StR88A / Q7CPV8 / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / UNKNOWN FUNCTION
Function / homologyProtein of unknown function DUF903 / Bacterial protein of unknown function (DUF903) / SH3 type barrels. - #100 / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta / plasma membrane / Putative lipoprotein
Function and homology information
Biological speciesSalmonella typhimurium LT2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsKuzin, A.P. / Su, M. / Seetharaman, J. / Vorobiev, S.M. / Wang, H. / Mao, L. / Cunningham, K. / Xiao, R. / Liu, J. / Baran, M.C. ...Kuzin, A.P. / Su, M. / Seetharaman, J. / Vorobiev, S.M. / Wang, H. / Mao, L. / Cunningham, K. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-Ray structure of the Q7CPV8 protein from Salmonella typhimurium at the resolution 1.9 A.
Authors: Kuzin, A.P. / Su, M. / Seetharaman, J. / Vorobiev, S.M. / Wang, H. / Mao, L. / Cunningham, K. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionSep 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative lipoprotein
B: Putative lipoprotein
C: Putative lipoprotein
D: Putative lipoprotein
E: Putative lipoprotein
F: Putative lipoprotein


Theoretical massNumber of molelcules
Total (without water)44,7996
Polymers44,7996
Non-polymers00
Water4,252236
1
A: Putative lipoprotein


Theoretical massNumber of molelcules
Total (without water)7,4671
Polymers7,4671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Putative lipoprotein


Theoretical massNumber of molelcules
Total (without water)7,4671
Polymers7,4671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Putative lipoprotein


Theoretical massNumber of molelcules
Total (without water)7,4671
Polymers7,4671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Putative lipoprotein


Theoretical massNumber of molelcules
Total (without water)7,4671
Polymers7,4671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Putative lipoprotein


Theoretical massNumber of molelcules
Total (without water)7,4671
Polymers7,4671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Putative lipoprotein


Theoretical massNumber of molelcules
Total (without water)7,4671
Polymers7,4671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
A: Putative lipoprotein
B: Putative lipoprotein
F: Putative lipoprotein

A: Putative lipoprotein
B: Putative lipoprotein
F: Putative lipoprotein


Theoretical massNumber of molelcules
Total (without water)44,7996
Polymers44,7996
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area6650 Å2
MethodPISA
8
C: Putative lipoprotein
D: Putative lipoprotein
E: Putative lipoprotein

C: Putative lipoprotein
D: Putative lipoprotein
E: Putative lipoprotein


Theoretical massNumber of molelcules
Total (without water)44,7996
Polymers44,7996
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
Buried area6460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.292, 110.426, 109.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Putative lipoprotein /


Mass: 7466.542 Da / Num. of mol.: 6 / Fragment: Residues 21-75
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium LT2 (bacteria)
Species: Salmonella typhimuriumSalmonella enterica subsp. enterica
Strain: SGSC1412 / Gene: ygdI, STM2983 / Production host: Escherichia coli (E. coli) / References: UniProt: Q7CPV8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 2.29 Å3/Da / Density % sol: 46.38 %
Description: The structure factor file contains Friedel pairs
Crystal growMethod: vapor diffusion, hanging drop / pH: 9
Details: 32% PEG 4000, 100mM NH4Cl, 100mM Tris-HCl, pH 9.0, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Details: Mirrors
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 62778 / Num. obs: 62778 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 24 % / Biso Wilson estimate: 9.4 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 25.6
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 6 / Num. unique all: 6285 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→30.81 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 104229.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
Details: The Friedel pairs were used for phasing. Bulk solvent model has been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2931 5 %RANDOM
Rwork0.228 ---
obs0.228 58453 92.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.038 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 23.1 Å2
Baniso -1Baniso -2Baniso -3
1-4.64 Å20 Å20 Å2
2---1 Å20 Å2
3----3.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å-0.02 Å
Refinement stepCycle: LAST / Resolution: 1.9→30.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2552 0 0 236 2788
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_improper_angle_d0.73
LS refinement shellResolution: 1.9→2.01 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.214 39 4.3 %
Rwork0.226 877 -
obs--7.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.paramwater.top

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