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- PDB-1r75: Leishmania major hypothetical protein -

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Basic information

Entry
Database: PDB / ID: 1r75
TitleLeishmania major hypothetical protein
Componentshypothetical protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PSI / Protein Structure Initiative / Structural Genomics of Pathogenic Protozoa Consortium / SGPP
Function / homologyDomain of unknown function DUF1935 / Smp-1-like superfamily / Domain of unknown function (DUF1935) / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Immunoglobulin-like / Sandwich / Mainly Beta / Unknown protein
Function and homology information
Biological speciesLeishmania major (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.86 Å
AuthorsHan, G.W. / Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: To be Published
Title: LEISHMANIA MAJOR HYPOTHETICAL PROTEIN
Authors: Han, G.W. / Merritt, E.A.
History
DepositionOct 17, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3222
Polymers16,2301
Non-polymers921
Water1,892105
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.629, 57.629, 84.546
Angle α, β, γ (deg.)90.0, 90.0, 90.0
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein hypothetical protein


Mass: 16230.126 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania major (eukaryote)
Plasmid details: Cloned with MAHHHHHH appended to N-terminus
Plasmid: pET14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21 Star, T7 System / References: UniProt: P84150
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Details: GOL
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 298 K / pH: 7.6
Details: pH 7.6, sitting drop vapor diffusion, temperature 298K, pH 7.60
Components of the solutions
IDNameCrystal-IDSol-ID
1Lmaj002144AAA11
2Na/K Phosphate11
3Hepes Buffer11

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.1
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 12293 / % possible obs: 97.3 % / Redundancy: 6.23 % / Rsym value: 0.11 / Net I/σ(I): 16.5
Reflection shellResolution: 1.86→1.93 Å / Mean I/σ(I) obs: 2.5 / Rsym value: 0.11 / % possible all: 80.8

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Processing

Software
NameVersionClassificationNB
REFMACrefmac_5.1.24 24/04/2001refinement
HKL-2000data scaling
CNSphasing
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.86→18.77 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.94 / SU B: 2.973 / SU ML: 0.09 / ESU R: 0.139 / ESU R Free: 0.128 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.228 589 4.811 %
Rwork0.201 --
obs-12244 -
Displacement parametersBiso mean: 28.82 Å2
Baniso -1Baniso -2Baniso -3
1--0.001 Å20 Å20 Å2
2---0.001 Å20 Å2
3---0.002 Å2
Refinement stepCycle: LAST / Resolution: 1.86→18.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms895 0 6 105 1006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.022919
X-RAY DIFFRACTIONr_bond_other_d0.0020.02833
X-RAY DIFFRACTIONr_angle_refined_deg2.0961.9451242
X-RAY DIFFRACTIONr_angle_other_deg0.97131926
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0285108
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1290.2137
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021005
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02206
X-RAY DIFFRACTIONr_nbd_refined0.2020.2151
X-RAY DIFFRACTIONr_nbd_other0.260.21005
X-RAY DIFFRACTIONr_nbtor_refined0.1870.2440
X-RAY DIFFRACTIONr_nbtor_other0.0970.2618
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.275
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3150.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3070.278
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1970.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.611.5545
X-RAY DIFFRACTIONr_mcangle_it2.962885
X-RAY DIFFRACTIONr_scbond_it4.3253374
X-RAY DIFFRACTIONr_scangle_it7.4424.5357
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.86→1.9 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.275 38
Rwork0.27 657

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