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- PDB-3rd6: Crystal structure of Mll3558 protein from Rhizobium loti. Northea... -

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Basic information

Entry
Database: PDB / ID: 3rd6
TitleCrystal structure of Mll3558 protein from Rhizobium loti. Northeast Structural Genomics Consortium target id MlR403
ComponentsMll3558 protein
KeywordsStructural Genomics / Unknown function / PSI-Biology / 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 / Mll3558 protein
Function and homology information
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å
AuthorsSeetharaman, J. / Chen, Y. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. ...Seetharaman, J. / Chen, Y. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of Mll3558 protein from Rhizobium loti. Northeast Structural Genomics Consortium target id MlR403
Authors: Seetharaman, J. / Chen, Y. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural ...Authors: Seetharaman, J. / Chen, Y. / Wang, D. / Ciccosanti, C. / Sahdev, S. / Rost, B. / Acton, T.B. / Xiao, R. / Everett, J.K. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
History
DepositionApr 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 25, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mll3558 protein
B: Mll3558 protein


Theoretical massNumber of molelcules
Total (without water)36,2182
Polymers36,2182
Non-polymers00
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-4 kcal/mol
Surface area13380 Å2
MethodPISA
2
A: Mll3558 protein

B: Mll3558 protein


Theoretical massNumber of molelcules
Total (without water)36,2182
Polymers36,2182
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y+1/2,-z+1/21
Buried area1320 Å2
ΔGint-14 kcal/mol
Surface area14250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.837, 84.071, 108.932
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 Mll3558 protein


Mass: 18109.049 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Gene: mll3558 / Production host: Escherichia coli (E. coli) / References: UniProt: Q98FZ2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.27 Å3/Da / Density % sol: 45.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M HEPES (pH 7.5), 20% PEG4000, Na Citrate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Mar 7, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 35914 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 38.5 Å2 / Rmerge(I) obs: 0.051
Reflection shellResolution: 2.8→2.86 Å / Num. unique all: 3274 / % possible all: 98

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SOLVEphasing
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 2.8→25.51 Å / Rfactor Rfree error: 0.012 / Data cutoff high absF: 127326.05 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.31 705 4.6 %RANDOM
Rwork0.245 ---
obs0.245 15270 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.6943 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 49.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20 Å2
2---1.04 Å20 Å2
3---0.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.68 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.8→25.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2138 0 0 167 2305
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d26.1
X-RAY DIFFRACTIONc_improper_angle_d1.03
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.426 129 5.2 %
Rwork0.33 2362 -
obs--95.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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