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- PDB-2b4w: Hypothetical protein from leishmania major -

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Basic information

Entry
Database: PDB / ID: 2b4w
TitleHypothetical protein from leishmania major
Componentshypothetical protein, conserved
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Structural Genomics of Pathogenic Protozoa Consortium / SGPP
Function / homologyMannosyltransferase/phosphorylase 1-like, Leishmania / Protein of unknown function (DUF1861) / Glycosyl hydrolase domain; family 43 / 5 Propeller / Tachylectin-2; Chain A / Glycosyl hydrolase, five-bladed beta-propellor domain superfamily / Mainly Beta / Uncharacterized protein
Function and homology information
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.98 Å
AuthorsHolmes, M.A. / Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: TO BE PUBLISHED
Title: Hypothetical protein from leishmania major
Authors: Holmes, M.A. / Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
History
DepositionSep 26, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein, conserved


Theoretical massNumber of molelcules
Total (without water)35,2251
Polymers35,2251
Non-polymers00
Water3,333185
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)97.4, 97.4, 113.6
Angle α, β, γ (deg.)90.0, 90.0, 120.0
Int Tables number146
Space group name H-MH3

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Components

#1: Protein hypothetical protein, conserved


Mass: 35225.223 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote) / Gene: LmjF10.1260 / Plasmid: BG1861 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q4QH86
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 277 K / pH: 9
Details: 0.4 ul protein 10.7 mg/ml, 0.4 ul crystallization buffer 100mM KH2PO4, 18% PEG PEG 4000,100 mM TAPS, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 9.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.97941, 0.97962, 0.95372
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 22, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979411
20.979621
30.953721
ReflectionResolution: 1.93→50 Å / Num. obs: 28075 / % possible obs: 92.8 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 27.4
Reflection shellResolution: 1.93→2 Å / Rmerge(I) obs: 0.131 / Mean I/σ(I) obs: 10.3 / % possible all: 30.1

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.979417.2-16
13 wavelength20.97967.6-13.5
13 wavelength30.95373.2-3.2
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se15.3990.1010.4740.3330.186
2Se10.8640.0230.2610.0990.18
3Se26.8240.1260.0810.0180.175
4Se600.1580.2560.1360.328
5Se44.3230.0190.6470.3320.157
Phasing dmFOM : 0.62 / FOM acentric: 0.62 / FOM centric: 0 / Reflection: 30111 / Reflection acentric: 30111 / Reflection centric: 0
Phasing dm shell
Resolution (Å)FOM FOM acentricReflectionReflection acentric
5.5-30.6960.960.9613001300
3.4-5.50.960.9640414041
2.7-3.40.90.950925092
2.4-2.70.790.7951475147
2.1-2.40.430.4391389138
1.9-2.10.180.1853935393

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Processing

Software
NameVersionClassificationNB
SOLVE2.08phasing
RESOLVE2.08phasing
PDB_EXTRACT1.6data extraction
DENZOdata reduction
SCALEPACKdata scaling
SHELXrefinement
SHELXL-97refinement
RefinementMethod to determine structure: MAD / Resolution: 1.98→50 Å / Num. parameters: 9752 / Num. restraintsaints: 9384 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: TWINNED CRYSTAL REFINED IN SHELXL WITH "TWIN 0 1 0 1 0 0 0 0 -1" REFINED TWIN FRACTION "BASF"=0.39426
RfactorNum. reflection% reflectionSelection details
Rfree0.2109 1423 5.3 %RANDOM
all0.1317 26652 --
obs0.135 -94.5 %-
Solvent computationSolvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 2166 / Occupancy sum non hydrogen: 2437
Refinement stepCycle: LAST / Resolution: 1.98→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2250 0 0 185 2435
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.008
X-RAY DIFFRACTIONs_angle_d0.026
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0289
X-RAY DIFFRACTIONs_zero_chiral_vol0.038
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.043
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.018
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.087
X-RAY DIFFRACTIONs_approx_iso_adps0

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