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- PDB-1xfs: X-Ray Crystal Structure of Protein NE0264 from Nitrosomonas europ... -

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Basic information

Entry
Database: PDB / ID: 1xfs
TitleX-Ray Crystal Structure of Protein NE0264 from Nitrosomonas europaea. Northeast Structural Genomics Consortium Target NeR5.
Componentsconserved hypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein Structure Initiative / NESG / alpha-beta protein / PSI / Northeast Structural Genomics Consortium
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 / Activator of Hsp90 ATPase homologue 1/2-like C-terminal domain-containing protein
Function and homology information
Biological speciesNitrosomonas europaea (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsForouhar, F. / Abashidze, M. / Vorobiev, S.M. / Ciano, M. / Ma, L.-C. / Shastry, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal Structure of the hypothetical Protein from Nitrosomonas europaea, NESG Target NeR5
Authors: Forouhar, F. / Abashidze, M. / Vorobiev, S.M. / Ciano, M. / Ma, L.-C. / Shastry, R. / Acton, T.B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionSep 15, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: conserved hypothetical protein
B: conserved hypothetical protein


Theoretical massNumber of molelcules
Total (without water)41,2212
Polymers41,2212
Non-polymers00
Water6,161342
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1760 Å2
ΔGint-13 kcal/mol
Surface area15950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.390, 63.197, 65.514
Angle α, β, γ (deg.)90.00, 97.87, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein conserved hypothetical protein / NC_840354


Mass: 20610.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Nitrosomonas europaea (bacteria) / Strain: ATCC 19718 / Plasmid: BL21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q82XK1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 2.55 Å3/Da / Density % sol: 50 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100mM Cacodylate Acid (pH 6.5), 20%PEG3350, 200mM ammonium Citrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97902 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 5, 2004 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97902 Å / Relative weight: 1
ReflectionResolution: 1.7→27.79 Å / Num. all: 287876 / Num. obs: 71306 / % possible obs: 93.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4 % / Biso Wilson estimate: 16 Å2 / Rmerge(I) obs: 0.033 / Rsym value: 0.036 / Net I/σ(I): 41.6
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.078 / Mean I/σ(I) obs: 14.8 / Num. unique all: 7100 / Rsym value: 0.074 / % possible all: 92.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SnBphasing
SOLVEphasing
RESOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→27.79 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1041734.09 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.255 6715 9.7 %RANDOM
Rwork0.221 ---
all0.223 71306 --
obs0.221 69290 91.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.1999 Å2 / ksol: 0.387838 e/Å3
Displacement parametersBiso mean: 21.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.65 Å20 Å2-1.62 Å2
2--1.68 Å20 Å2
3----3.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 1.7→27.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2470 0 0 342 2812
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d24.4
X-RAY DIFFRACTIONc_improper_angle_d0.77
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.286 1051 9.5 %
Rwork0.242 9997 -
obs-6715 87.2 %

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