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- PDB-3q63: X-ray crystal structure of protein MLL2253 from Mesorhizobium lot... -

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Basic information

Entry
Database: PDB / ID: 3q63
TitleX-ray crystal structure of protein MLL2253 from Mesorhizobium loti, Northeast Structural Genomics Consortium Target MlR404.
ComponentsMll2253 protein
KeywordsStructural Genomics / unknown function / PSI-Biology / Protein Structure Initiative / alpha-beta protein / Unknown / Structure Genomics / Northeast Structural Genomics Consortium / NESG
Function / homologyActivator of Hsp90 ATPase homologue 1-like / Activator of Hsp90 ATPase homolog 1-like protein / START domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / START-like domain superfamily / 2-Layer Sandwich / Alpha Beta / Mll2253 protein
Function and homology information
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsForouhar, F. / Lew, S. / Seetharaman, J. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. ...Forouhar, F. / Lew, S. / Seetharaman, J. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: X-ray crystal structure of protein MLL2253 from Mesorhizobium loti, Northeast Structural Genomics Consortium Target MlR404.
Authors: Forouhar, F. / Lew, S. / Seetharaman, J. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Nair, R. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Hunt, J.F. / Tong, L.
History
DepositionDec 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mll2253 protein
B: Mll2253 protein
C: Mll2253 protein
D: Mll2253 protein
E: Mll2253 protein
F: Mll2253 protein


Theoretical massNumber of molelcules
Total (without water)106,5446
Polymers106,5446
Non-polymers00
Water12,448691
1
A: Mll2253 protein
B: Mll2253 protein


Theoretical massNumber of molelcules
Total (without water)35,5152
Polymers35,5152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-11 kcal/mol
Surface area13060 Å2
MethodPISA
2
C: Mll2253 protein
D: Mll2253 protein


Theoretical massNumber of molelcules
Total (without water)35,5152
Polymers35,5152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-10 kcal/mol
Surface area13410 Å2
MethodPISA
3
E: Mll2253 protein
F: Mll2253 protein


Theoretical massNumber of molelcules
Total (without water)35,5152
Polymers35,5152
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-10 kcal/mol
Surface area13580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.116, 148.122, 87.391
Angle α, β, γ (deg.)90.00, 98.33, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Mll2253 protein


Mass: 17757.326 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Tissue: MAFF303099 / Production host: Escherichia coli (E. coli) / References: UniProt: Q98IT8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 691 / 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: 2.4 Å3/Da / Density % sol: 48.7 %
Crystal growTemperature: 277 K / pH: 5.5
Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 100mM BIS-TRIS pH 5.5, 25% PEG 3350, and 200mM Lithium sulfate monohydrate, Microbatch, under ...Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 100mM BIS-TRIS pH 5.5, 25% PEG 3350, and 200mM Lithium sulfate monohydrate, Microbatch, under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 21, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 136539 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.147 / Rsym value: 0.145 / Net I/σ(I): 14.82
Reflection shellResolution: 2→2.07 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 3.9 / Num. unique all: 6853 / Rsym value: 0.315 / % possible all: 96.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXthen SOLVE/RESOLVEmodel building
CNS1.2 & XtalViewrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXthen SOLVE/RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2→19.99 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 482644.42 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.244 10889 9.9 %RANDOM
Rwork0.202 ---
all0.205 134465 --
obs0.202 110396 82.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.6816 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 25.2 Å2
Baniso -1Baniso -2Baniso -3
1-13.79 Å20 Å2-0.38 Å2
2---9.47 Å20 Å2
3----4.31 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 2→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6666 0 0 691 7357
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.07 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.258 770 9.4 %
Rwork0.21 7398 -
obs-7398 61 %

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