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- PDB-2emq: Hypothetical Conserved Protein (GK1048) from Geobacillus Kaustophilus -

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Basic information

Entry
Database: PDB / ID: 2emq
TitleHypothetical Conserved Protein (GK1048) from Geobacillus Kaustophilus
ComponentsHypothetical conserved protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / CBS DOMAINS / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


: / : / CBS-domain / CBS-domain / CBS domain superfamily / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
Hypothetical conserved protein
Similarity search - Component
Biological speciesGeobacillus kaustophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsRehse, P.H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Hypothetical Conserved Protein (GK1048) from Geobacillus Kaustophilus
Authors: Rehse, P.H. / Yokoyama, S.
History
DepositionMar 28, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.2Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)36,1842
Polymers36,1842
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-29 kcal/mol
Surface area13440 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)56.194, 56.194, 211.224
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Hypothetical conserved protein


Mass: 18092.135 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus kaustophilus (bacteria) / Strain: HTA426 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: Q5L147
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.66 Å3/Da / Density % sol: 53.75 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2M Li2SO4, 0.1 M Tris, 1M Na tartrate, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 0.9794 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Dec 16, 2006 / Details: mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 12987 / Num. obs: 12961 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 16.4 % / Rmerge(I) obs: 0.088 / Χ2: 3.246 / Net I/σ(I): 18
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 16.9 % / Rmerge(I) obs: 0.526 / Mean I/σ(I) obs: 12.77 / Num. unique all: 1288 / Χ2: 2.671 / % possible all: 100

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Phasing

Phasing MRRfactor: 0.531 / Cor.coef. Fo:Fc: 0.43
Highest resolutionLowest resolution
Rotation3 Å47.42 Å
Translation3 Å47.42 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YAV

1yav


Resolution: 2.5→50 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.293 629 4.8 %random
Rwork0.231 ---
all0.231 13023 --
obs0.231 12372 95 %-
Solvent computationBsol: 39.661 Å2
Displacement parametersBiso mean: 51.914 Å2
Baniso -1Baniso -2Baniso -3
1--3.706 Å2-9.756 Å20 Å2
2---3.706 Å20 Å2
3---7.412 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.45 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2123 0 0 57 2180
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.0103211.5
X-RAY DIFFRACTIONc_angle_deg1.321562
X-RAY DIFFRACTIONc_dihedral_angle_d22.898572
X-RAY DIFFRACTIONc_improper_angle_d0.963722.5
LS refinement shellResolution: 2.5→2.59 Å
RfactorNum. reflection% reflection
Rfree0.3638 54 -
Rwork0.3666 --
obs-883 68.08 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param

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