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- PDB-3otl: Three-dimensional Structure of the putative uncharacterized prote... -

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Basic information

Entry
Database: PDB / ID: 3otl
TitleThree-dimensional Structure of the putative uncharacterized protein from Rhizobium leguminosarum at the resolution 1.9A, Northeast Structural Genomics Consortium Target RlR261
ComponentsPutative uncharacterized protein
Keywordsstructural genomics / unknown function / PSI-Biology / Protein Structure Initiative / 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 / DI(HYDROXYETHYL)ETHER / Activator of Hsp90 ATPase homologue 1/2-like C-terminal domain-containing protein
Function and homology information
Biological speciesRhizobium leguminosarum bv. viciae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.901 Å
AuthorsKuzin, A. / Lew, S. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Lew, S. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target RlR261
Authors: Kuzin, A. / Lew, S. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / ...Authors: Kuzin, A. / Lew, S. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
History
DepositionSep 13, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Oct 6, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2534
Polymers35,9512
Non-polymers3012
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint2 kcal/mol
Surface area14590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.350, 82.350, 116.460
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Detailsdimer,43.24 kD,92.8%

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Components

#1: Protein Putative uncharacterized protein


Mass: 17975.709 Da / Num. of mol.: 2 / Mutation: S22A, T30A, S33A, V45Q, P46A, D83N, S97T, A111E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium leguminosarum bv. viciae (bacteria)
Strain: 3841 / Gene: RL2761 / References: UniProt: Q1MFM4
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / 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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 277 K / Method: microbatch under oil / pH: 6
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 0.1M NH4Cl, 0.1M MES, 12% PEG 20000, microbatch under oil, 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 4 / Detector: CCD / Date: Sep 2, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / 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. obs: 60275 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 13.8 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 40.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.484 / Mean I/σ(I) obs: 5.2 / Num. unique all: 5954 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.901→47.545 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.907 / SU ML: 0.23 / σ(F): 0.2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.203 2000 6.7 %
Rwork0.166 --
obs0.168 29839 92.61 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.008 Å2 / ksol: 0.323 e/Å3
Displacement parametersBiso max: 119.85 Å2 / Biso mean: 24.788 Å2 / Biso min: 4.54 Å2
Baniso -1Baniso -2Baniso -3
1--0.232 Å20 Å20 Å2
2---0.232 Å2-0 Å2
3---0.464 Å2
Refinement stepCycle: LAST / Resolution: 1.901→47.545 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2429 0 19 357 2805
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072510
X-RAY DIFFRACTIONf_angle_d1.113406
X-RAY DIFFRACTIONf_chiral_restr0.082366
X-RAY DIFFRACTIONf_plane_restr0.004443
X-RAY DIFFRACTIONf_dihedral_angle_d13.72905
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.901-1.9480.2351160.1731602171877
1.948-2.0010.1951260.1531772189884
2.001-2.060.1981370.1471905204290
2.06-2.1260.21390.151934207392
2.126-2.2020.211400.1571955209593
2.202-2.290.1861400.151939207991
2.29-2.3950.1961430.1551989213293
2.395-2.5210.2111400.1681948208892
2.521-2.6790.2231450.1712018216394
2.679-2.8860.2021470.1762051219896
2.886-3.1760.2181510.1742107225897
3.176-3.6360.1891540.1662131228599
3.636-4.580.1941560.1512188234499
4.58-47.560.2081660.192300246698
Refinement TLS params.Method: refined / Origin x: 41.125 Å / Origin y: 70.3702 Å / Origin z: 44.4942 Å
111213212223313233
T0.085 Å20.007 Å20.0078 Å2-0.0223 Å20.0006 Å2--0.0347 Å2
L1.0219 °20.4062 °2-0.2059 °2-0.7149 °20.0225 °2--0.8047 °2
S0.0642 Å °-0.0918 Å °0.0608 Å °0.025 Å °-0.0684 Å °0.0166 Å °0.0633 Å °-0.0193 Å °0.0154 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 154
2X-RAY DIFFRACTION1allB2 - 153
3X-RAY DIFFRACTION1allA1 - 159
4X-RAY DIFFRACTION1allB1 - 159
5X-RAY DIFFRACTION1allB1 - 359

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