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- PDB-3q64: X-ray crystal structure of protein mll3774 from Mesorhizobium lot... -

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Basic information

Entry
Database: PDB / ID: 3q64
TitleX-ray crystal structure of protein mll3774 from Mesorhizobium loti, Northeast Structural Genomics Consortium Target MlR405.
ComponentsMll3774 protein
KeywordsStructure Genomics / unknown function / Structural Genomics / PSI-Biology / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / alpha-beta protein
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 / Mll3774 protein
Function and homology information
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 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 mll3774 from Mesorhizobium loti, Northeast Structural Genomics Consortium Target MlR405.
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
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 6, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: Mll3774 protein


Theoretical massNumber of molelcules
Total (without water)18,4181
Polymers18,4181
Non-polymers00
Water4,810267
1
A: Mll3774 protein

A: Mll3774 protein


Theoretical massNumber of molelcules
Total (without water)36,8362
Polymers36,8362
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area2150 Å2
ΔGint-5 kcal/mol
Surface area14860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.378, 86.378, 57.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-426-

HOH

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Components

#1: Protein Mll3774 protein


Mass: 18418.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Strain: MAFF303099 / Gene: mll3774 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q98FH6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 3.37 Å3/Da / Density % sol: 63.54 %
Crystal growTemperature: 277 K / pH: 6
Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 100 mM MES (pH 6), PEG 4000 20% (w/v),100 mM Magnesium sulfate heptahydrate, Microbatch, ...Details: Protein solution: 10 mM Tris (pH 7.5), 100 mM sodium chloride, and 5 mM DTT. Reservoir solution: 100 mM MES (pH 6), PEG 4000 20% (w/v),100 mM Magnesium sulfate heptahydrate, Microbatch, under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97897 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 4, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97897 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 77329 / Num. obs: 76634 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Biso Wilson estimate: 17.7 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.04 / Net I/σ(I): 50.2
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 5.6 / Num. unique all: 7716 / Rsym value: 0.338 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SHELXthen SOLVE/RESOLVEmodel building
CNS1.2refinement
ADSCQuantumdata collection
CNSrefinement
XTALVIEWrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXthen SOLVE/RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.958 / SU ML: 0.034 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19486 3993 10 %RANDOM
Rwork0.17684 ---
all0.179 35963 --
obs0.17864 35963 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.8 Å20.4 Å20 Å2
2--0.8 Å20 Å2
3----1.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1221 0 0 267 1488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221252
X-RAY DIFFRACTIONr_angle_refined_deg1.1841.961701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.635154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98723.27961
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.38215197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9131510
X-RAY DIFFRACTIONr_chiral_restr0.0770.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02976
X-RAY DIFFRACTIONr_nbd_refined0.2040.2555
X-RAY DIFFRACTIONr_nbtor_refined0.3120.2850
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2206
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.223
X-RAY DIFFRACTIONr_mcbond_it1.0141.5785
X-RAY DIFFRACTIONr_mcangle_it1.39721246
X-RAY DIFFRACTIONr_scbond_it2.2733514
X-RAY DIFFRACTIONr_scangle_it3.214.5455
X-RAY DIFFRACTIONr_rigid_bond_restr1.3831299
X-RAY DIFFRACTIONr_sphericity_free3.433267
X-RAY DIFFRACTIONr_sphericity_bonded2.04631221
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 296 -
Rwork0.19 2609 -
obs-5232 100 %

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