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- PDB-3put: Crystal Structure of the CERT START domain (mutant V151E) from Rh... -

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Basic information

Entry
Database: PDB / ID: 3put
TitleCrystal Structure of the CERT START domain (mutant V151E) from Rhizobium etli at the resolution 1.8A, Northeast Structural Genomics Consortium Target ReR239.
ComponentsHypothetical conserved protein
KeywordsStructure Genomics / unknown function / Structural Genomics / 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 / HEXANE-1,6-DIOL / Hypothetical conserved protein
Function and homology information
Biological speciesRhizobium etli CFN 42 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.828 Å
AuthorsKuzin, A. / Chen, Y. / Seetharaman, J. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, D. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Chen, Y. / 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: Crystal Structure of the CERT START domain (mutant V151E) from Rhizobium etli at the resolution 1.8A, Northeast Structural Genomics Consortium Target ReR239.
Authors: Kuzin, A. / Chen, Y. / 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.
History
DepositionDec 6, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 1.4Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hypothetical conserved protein
B: Hypothetical conserved protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6284
Polymers38,3922
Non-polymers2362
Water3,477193
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2410 Å2
ΔGint-2 kcal/mol
Surface area15110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.515, 76.931, 55.742
Angle α, β, γ (deg.)90.000, 97.640, 90.000
Int Tables number4
Space group name H-MP1211
Detailsdimer,44.48 kD,99.8%

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Components

#1: Protein Hypothetical conserved protein


Mass: 19196.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizobium etli CFN 42 (bacteria) / Gene: RHE_CH02426 / References: UniProt: Q2K7I2
#2: Chemical ChemComp-HEZ / HEXANE-1,6-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 193 / 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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 277 K
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution:sodium bromide 0.1 M CAPS (pH 10) 0.1 M PEG 8000, 40% 1,6-hexanediol 3%, macrobatch under oil, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.979 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 28, 2010
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: 1.828→30 Å / Num. obs: 46994 / % possible obs: 83.7 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Biso Wilson estimate: 25.34 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.7
Reflection shellResolution: 1.83→1.9 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.265 / Mean I/σ(I) obs: 2 / % possible all: 41.5

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Processing

Software
NameVersionClassificationNB
PHENIX1.6.4_486refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3OTL

3otl


Resolution: 1.828→25.998 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.852 / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1342 5.06 %RANDOM, 5%
Rwork0.177 ---
obs0.179 26546 93.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 35.563 Å2 / ksol: 0.344 e/Å3
Displacement parametersBiso max: 171.81 Å2 / Biso mean: 32.329 Å2 / Biso min: 12.79 Å2
Baniso -1Baniso -2Baniso -3
1-1.679 Å2-0 Å24.372 Å2
2---2.099 Å2-0 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.828→25.998 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2445 0 16 193 2654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072546
X-RAY DIFFRACTIONf_angle_d1.1513460
X-RAY DIFFRACTIONf_chiral_restr0.083382
X-RAY DIFFRACTIONf_plane_restr0.004448
X-RAY DIFFRACTIONf_dihedral_angle_d13.161922
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.828-1.8930.351750.2731584165959
1.893-1.9690.2521190.2152456257591
1.969-2.0590.2521480.1822601274995
2.059-2.1670.2491480.1772601274997
2.167-2.3030.2661390.1752649278898
2.303-2.4810.2351420.1822662280499
2.481-2.730.2231470.1822674282198
2.73-3.1250.2261420.1812656279898
3.125-3.9350.1971400.1682672281298
3.935-26.0010.2021420.1662649279196
Refinement TLS params.Method: refined / Origin x: 6.5571 Å / Origin y: 9.8853 Å / Origin z: 13.0173 Å
111213212223313233
T0.1374 Å20.0022 Å2-0.0111 Å2-0.1207 Å20.0078 Å2--0.1336 Å2
L0.5472 °2-0.2612 °2-0.4151 °2-1.4667 °20.396 °2--0.8019 °2
S-0.0255 Å °-0.0151 Å °0.0347 Å °0.172 Å °0.0174 Å °0.0047 Å °0.0617 Å °0.004 Å °0.0086 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 154
2X-RAY DIFFRACTION1allB3 - 157
3X-RAY DIFFRACTION1allA - B1 - 218
4X-RAY DIFFRACTION1allA - B1 - 167

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