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- PDB-3hvz: Crystal Structure of the TGS domain of the CLOLEP_03100 protein f... -

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Basic information

Entry
Database: PDB / ID: 3hvz
TitleCrystal Structure of the TGS domain of the CLOLEP_03100 protein from Clostridium leptum, Northeast Structural Genomics Consortium Target QlR13A
ComponentsUncharacterized protein
KeywordsStructural Genomics / Unknown function / alpha-beta protein / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG
Function / homology
Function and homology information


GTP diphosphokinase activity / guanosine tetraphosphate biosynthetic process / GTP diphosphokinase
Similarity search - Function
RelA/SpoT family / RelA/SpoT, TGS domain / ACT domain / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / TGS domain / ACT domain profile. / ACT domain / HD domain profile. ...RelA/SpoT family / RelA/SpoT, TGS domain / ACT domain / Region found in RelA / SpoT proteins / RelA/SpoT / Region found in RelA / SpoT proteins / TGS domain / ACT domain profile. / ACT domain / HD domain profile. / TGS / TGS-like / Beta-grasp domain / Beta-grasp domain superfamily / Metal dependent phosphohydrolases with conserved 'HD' motif. / HD/PDEase domain / Nucleotidyltransferase superfamily / Ubiquitin-like (UB roll) / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesClostridium leptum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsForouhar, F. / Lew, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. ...Forouhar, F. / Lew, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target QlR13A
Authors: Forouhar, F. / Lew, S. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Lee, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionJun 16, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uncharacterized protein
B: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
E: Uncharacterized protein
F: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)52,4146
Polymers52,4146
Non-polymers00
Water2,360131
1
A: Uncharacterized protein
B: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)17,4712
Polymers17,4712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Uncharacterized protein
D: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)17,4712
Polymers17,4712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Uncharacterized protein
F: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)17,4712
Polymers17,4712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)107.765, 110.396, 107.957
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Uncharacterized protein


Mass: 8735.718 Da / Num. of mol.: 6 / Fragment: TGS domain residues 392-460
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium leptum (bacteria) / Strain: DSM 753 / Gene: CLOLEP_03100 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: A7VWX7
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 3.06 Å3/Da / Density % sol: 59.84 %
Crystal growTemperature: 277 K / pH: 7.5
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5), Reservoir solution: 100mM HEPES (pH 7.5) and 500mM magnesium Formate dihydrate, microbatch, under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 28, 2009 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. all: 63196 / Num. obs: 62970 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.058 / Net I/σ(I): 25.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.483 / Mean I/σ(I) obs: 2.9 / Num. unique all: 6275 / Rsym value: 0.392 / % possible all: 98.9

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Processing

Software
NameVersionClassificationNB
CNS1.2 & XtalViewrefinement
PDB_EXTRACT3data extraction
MAR345dtbdata collection
DENZOdata reduction
SCALEPACKdata scaling
SHELXthen SOLVE/RESOLVEphasing
REFMACrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.2→19.7 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 234070.531 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2722 5 %RANDOM
Rwork0.224 ---
all0.226 63116 --
obs0.225 54091 85.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.875 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 41.1 Å2
Baniso -1Baniso -2Baniso -3
1--7.99 Å20 Å20 Å2
2--5.89 Å20 Å2
3---2.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2898 0 0 131 3029
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.9
X-RAY DIFFRACTIONc_improper_angle_d0.79
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.262 194 5.4 %
Rwork0.231 3418 -
obs-3612 57.7 %

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