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- PDB-1rn7: Structure of human cystatin D -

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Basic information

Entry
Database: PDB / ID: 1rn7
TitleStructure of human cystatin D
ComponentsCystatin D
KeywordsPROTEIN BINDING / inhibitor of cysteine peptidases / cystatin D
Function / homology
Function and homology information


cysteine-type endopeptidase inhibitor activity / vesicle / extracellular space / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
Proteinase inhibitor I25, cystatin, conserved site / Cysteine proteases inhibitors signature. / Cystatin domain / Cystatin-like domain / Cystatin domain / Nuclear Transport Factor 2; Chain: A, - #10 / Cystatin superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsAlvarez-Fernandez, M. / Liang, Y.H. / Abrahamson, M. / Su, X.D.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal structure of human cystatin D, a cysteine peptidase inhibitor with restricted inhibition profile.
Authors: Alvarez-Fernandez, M. / Liang, Y.H. / Abrahamson, M. / Su, X.D.
History
DepositionNov 30, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 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.name
Revision 1.4Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cystatin D


Theoretical massNumber of molelcules
Total (without water)13,9281
Polymers13,9281
Non-polymers00
Water57632
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.900, 84.370, 47.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Cystatin D


Mass: 13927.619 Da / Num. of mol.: 1 / Mutation: C26R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: parotid gland / Plasmid: pHD389 / Production host: Escherichia coli (E. coli) / Strain (production host): MC1061 / References: UniProt: P28325
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.75 Å3/Da / Density % sol: 54.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Tris-HCl, PEG400, (NH4)2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 291 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 10, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 5243 / Num. obs: 4955 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 45.1 Å2 / Rmerge(I) obs: 0.076
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.252 / Num. unique all: 467 / % possible all: 96.8

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Processing

Software
NameVersionClassification
CNS1refinement
MAR345data collection
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CEW

1cew


Resolution: 2.5→28.16 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 560375.71 / 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
Rfree0.229 501 10.4 %RANDOM
Rwork0.191 ---
obs0.191 4835 92.6 %-
all-5220 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 62.6499 Å2 / ksol: 0.344637 e/Å3
Displacement parametersBiso mean: 44.6 Å2
Baniso -1Baniso -2Baniso -3
1--5.65 Å20 Å20 Å2
2---2.89 Å20 Å2
3---8.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.5→28.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms912 0 0 32 944
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.87
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.861.5
X-RAY DIFFRACTIONc_mcangle_it7.72
X-RAY DIFFRACTIONc_scbond_it11.382
X-RAY DIFFRACTIONc_scangle_it15.692.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.041 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.353 76 9.9 %
Rwork0.247 691 -
obs-691 91.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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