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- PDB-1i71: HIGH RESOLUTION CRYSTAL STRUCTURE OF APOLIPOPROTEIN(A) KRINGLE IV... -

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Basic information

Entry
Database: PDB / ID: 1i71
TitleHIGH RESOLUTION CRYSTAL STRUCTURE OF APOLIPOPROTEIN(A) KRINGLE IV TYPE 7: INSIGHTS INTO LIGAND BINDING
ComponentsAPOLIPOPROTEIN(A)
KeywordsHYDROLASE / alipoprotein(a) / kringle / protein-ligand interaction / lysine binding
Function / homology
Function and homology information


plasma lipoprotein particle / LDL remodeling / blood circulation / endopeptidase inhibitor activity / lipid transport / fibronectin binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / apolipoprotein binding / lipid metabolic process / heparin binding ...plasma lipoprotein particle / LDL remodeling / blood circulation / endopeptidase inhibitor activity / lipid transport / fibronectin binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / apolipoprotein binding / lipid metabolic process / heparin binding / serine-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Plasminogen Kringle 4 / Plasminogen Kringle 4 / : / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain ...Plasminogen Kringle 4 / Plasminogen Kringle 4 / : / Kringle domain / Kringle / Kringle, conserved site / Kringle superfamily / Kringle domain signature. / Kringle domain profile. / Kringle domain / Kringle-like fold / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 Å
AuthorsYe, Q. / Rahman, M.N. / Koschinsky, M.L. / Jia, Z.
CitationJournal: Protein Sci. / Year: 2001
Title: High-resolution crystal structure of apolipoprotein(a) kringle IV type 7: insights into ligand binding.
Authors: Ye, Q. / Rahman, M.N. / Koschinsky, M.L. / Jia, Z.
History
DepositionMar 7, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.4Nov 13, 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: APOLIPOPROTEIN(A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,8752
Polymers9,7791
Non-polymers961
Water2,090116
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.11, 40.49, 65.46
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein APOLIPOPROTEIN(A) / APO(A)


Mass: 9778.745 Da / Num. of mol.: 1
Fragment: RECOMBINANT KRINGLE IV TYPE 7 (RESIDUES 3781-3863)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PET16B / Production host: Escherichia coli (E. coli)
References: UniProt: P08519, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.38 Å3/Da / Density % sol: 48.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: Ammonium sulfate, 2-[N-morpholino]ethane sulfonic acid, , pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
PH range low: 6 / PH range high: 5.5
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
121-23 %ammonium sulfate1reservoir
20.1 MMES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.9479 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 20, 2000 / Details: synchrotron optics
RadiationMonochromator: CHESS A1 optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9479 Å / Relative weight: 1
ReflectionResolution: 1.45→25 Å / Num. all: 48859 / Num. obs: 48859 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Biso Wilson estimate: 15.9 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.069 / Net I/σ(I): 14.8
Reflection shellResolution: 1.45→1.5 Å / Redundancy: 1.1 % / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 2.6 / Num. unique all: 1070 / Rsym value: 0.239 / % possible all: 96.7
Reflection
*PLUS
Num. obs: 15774 / % possible obs: 91.8 % / Num. measured all: 48859 / Rmerge(I) obs: 0.069

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1PK4

1pk4


Resolution: 1.45→6 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1571 -Random
Rwork0.173 ---
all0.173 16857 --
obs0.173 15494 91.9 %-
Refinement stepCycle: LAST / Resolution: 1.45→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms683 0 5 116 804
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.16
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 6 Å / σ(F): 0 / Rfactor obs: 0.171 / Rfactor Rfree: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.044
X-RAY DIFFRACTIONc_angle_deg1.42

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