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- PDB-1wnh: Crystal structure of mouse Latexin (tissue carboxypeptidase inhibitor) -

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Basic information

Entry
Database: PDB / ID: 1wnh
TitleCrystal structure of mouse Latexin (tissue carboxypeptidase inhibitor)
ComponentsLatexin
KeywordsHYDROLASE INHIBITOR / bi-cystatin fold / cis-proline
Function / homology
Function and homology information


metalloendopeptidase inhibitor activity / detection of temperature stimulus involved in sensory perception of pain / heparin binding / inflammatory response / cytoplasm
Similarity search - Function
Proteinase inhibitor I47, latexin / : / Latexin / Latexin (LXN)-type cystatin domain profile. / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.83 Å
AuthorsAagaard, A. / Listwan, P. / Cowieson, N. / Huber, T. / Ravasi, T. / Wells, C.A. / Flanagan, J.U. / Hume, D.A. / Kobe, B. / Martin, J.L.
CitationJournal: Structure / Year: 2005
Title: An Inflammatory Role for the Mammalian Carboxypeptidase Inhibitor Latexin: Relationship to Cystatins and the Tumor Suppressor TIG1
Authors: Aagaard, A. / Listwan, P. / Cowieson, N. / Huber, T. / Ravasi, T. / Wells, C.A. / Flanagan, J.U. / Kellie, S. / Hume, D.A. / Kobe, B. / Martin, J.L.
History
DepositionAug 4, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Latexin


Theoretical massNumber of molelcules
Total (without water)25,8381
Polymers25,8381
Non-polymers00
Water3,315184
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.900, 103.900, 60.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
DetailsThe molecule in the asymmetric unit is assumed to represent the biological unit

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Components

#1: Protein Latexin / carboxypeptidase inhibitor


Mass: 25838.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: LXN / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / References: UniProt: P70202
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 184 / 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: 2.9 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.8M ammonium sulfate, 0.1M cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0781, 0.9794, 0.9796, 0.9077
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 8, 2003
RadiationMonochromator: Double-crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.07811
20.97941
30.97961
40.90771
ReflectionResolution: 1.83→50 Å / Num. obs: 29633 / % possible obs: 99.7 % / Redundancy: 14 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 19.9
Reflection shellResolution: 1.83→1.9 Å / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 4.5 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.83→46.47 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 606163.56 / 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
Rfree0.237 2897 10 %RANDOM
Rwork0.211 ---
obs0.211 28971 98 %-
all-28971 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.986 Å2 / ksol: 0.370558 e/Å3
Displacement parametersBiso mean: 39.9 Å2
Baniso -1Baniso -2Baniso -3
1-0.35 Å20 Å20 Å2
2--0.35 Å20 Å2
3----0.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.83→46.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1873 0 0 186 2059
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_improper_angle_d0.98
X-RAY DIFFRACTIONc_mcbond_it1.661.5
X-RAY DIFFRACTIONc_mcangle_it2.592
X-RAY DIFFRACTIONc_scbond_it2.342
X-RAY DIFFRACTIONc_scangle_it3.512.5
LS refinement shellResolution: 1.83→1.94 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.268 439 9.6 %
Rwork0.259 4112 -
obs--94.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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