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- PDB-1q7s: Crystal structure of bit1 -

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Basic information

Entry
Database: PDB / ID: 1q7s
TitleCrystal structure of bit1
Componentsbit1
KeywordsAPOPTOSIS
Function / homology
Function and homology information


positive regulation of anoikis / peptidyl-tRNA hydrolase / peptidyl-tRNA hydrolase activity / negative regulation of anoikis / mitochondrial outer membrane / Ub-specific processing proteases / negative regulation of gene expression / apoptotic process / mitochondrion / membrane / cytosol
Similarity search - Function
Peptidyl-tRNA hydrolase, PTH2 / Peptidyl-tRNA hydrolase PTH2 / Bit1 / Bit1 / Peptidyl-tRNA hydrolase II domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptidyl-tRNA hydrolase 2, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MAD / Resolution: 2 Å
AuthorsDe Pereda, J.M. / Waas, W.F. / Jan, Y. / Ruoslahti, E. / Schimmel, P. / Pascual, J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: Crystal structure of a human peptidyl-tRNA hydrolase reveals a new fold and suggests basis for a bifunctional activity.
Authors: De Pereda, J.M. / Waas, W.F. / Jan, Y. / Ruoslahti, E. / Schimmel, P. / Pascual, J.
History
DepositionAug 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: bit1
B: bit1


Theoretical massNumber of molelcules
Total (without water)25,3962
Polymers25,3962
Non-polymers00
Water2,216123
1
A: bit1


Theoretical massNumber of molelcules
Total (without water)12,6981
Polymers12,6981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: bit1


Theoretical massNumber of molelcules
Total (without water)12,6981
Polymers12,6981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-12 kcal/mol
Surface area10650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.861, 61.861, 178.135
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein bit1 / protein CGI-147


Mass: 12697.911 Da / Num. of mol.: 2 / Fragment: residues 63-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET18b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Rosetta / References: UniProt: Q9Y3E5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 3.35 Å3/Da / Density % sol: 63.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Hepes, PEG-10000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
2100 mMHEPES1reservoirpH7.5
320 %(w/v)PEG100001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.008 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 28, 2003
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.0081
21.54181
ReflectionResolution: 2→50 Å / Num. all: 24257 / Num. obs: 24275 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 17.6 Å2 / Net I/σ(I): 27.7
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 4.7 / % possible all: 99.9
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 168771 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 99.9 % / Rmerge(I) obs: 0.457

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
CNS1.1phasing
RefinementMethod to determine structure: MAD / Resolution: 2→42.84 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 2006169.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1674 6.9 %RANDOM
Rwork0.211 ---
obs0.211 24254 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.6595 Å2 / ksol: 0.346304 e/Å3
Displacement parametersBiso mean: 29.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.41 Å20 Å20 Å2
2--3.41 Å20 Å2
3----6.81 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2→42.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1763 0 0 123 1886
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_improper_angle_d0.84
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.271 274 7 %
Rwork0.257 3667 -
obs-168771 99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 43 Å / Num. reflection obs: 22580 / Rfactor Rfree: 0.237
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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