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- PDB-3kiv: RECOMBINANT KRINGLE IV-10/M66 VARIANT OF HUMAN APOLIPOPROTEIN(A) -

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Basic information

Entry
Database: PDB / ID: 3kiv
TitleRECOMBINANT KRINGLE IV-10/M66 VARIANT OF HUMAN APOLIPOPROTEIN(A)
ComponentsAPOLIPOPROTEIN
KeywordsKRINGLE / LYSINE BINDING SITE / APOLIPOPROTEIN(A)
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
6-AMINOHEXANOIC ACID / Apolipoprotein(a)
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMochalkin, I. / Tulinsky, A. / Scanu, A.
CitationJournal: Biochemistry / Year: 1999
Title: Recombinant kringle IV-10 modules of human apolipoprotein(a): structure, ligand binding modes, and biological relevance.
Authors: Mochalkin, I. / Cheng, B. / Klezovitch, O. / Scanu, A.M. / Tulinsky, A.
History
DepositionSep 8, 1998Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: APOLIPOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,3002
Polymers9,1691
Non-polymers1311
Water1,946108
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.300, 45.670, 63.360
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


Mass: 9169.012 Da / Num. of mol.: 1 / Fragment: KRINGLE IV-10
Source method: isolated from a genetically manipulated source
Details: KIV-10/T66 VARIANT OF HUMAN APOLIPOPROTEIN(A) / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P08519
#2: Chemical ChemComp-ACA / 6-AMINOHEXANOIC ACID / AMINOCAPROIC ACID


Type: peptide linking / Mass: 131.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O
Compound detailsN-TERMINAL (VR) AND C-TERMINAL (SDTEGTV) INTERKRINGULAR PARTS ARE DISORDERED. THE P30 RESIDUE IS IN ...N-TERMINAL (VR) AND C-TERMINAL (SDTEGTV) INTERKRINGULAR PARTS ARE DISORDERED. THE P30 RESIDUE IS IN CIS CONFORMATION. M66T POLYMORPHISM IS BIOLOGICALLY SILENT. EACA BOUND IN AN EMBEDDED WAY.
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: 1.76 Å3/Da / Density % sol: 30.6 %
Crystal growpH: 7 / Details: pH 7.0
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
124 mg/mlprotein1drop
320 %2-propanol1reservoir
420 %PEG40001reservoir
50.1 Msodium citrate1reservoir
2EACA1reservoir10-fold molar excess

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Oct 1, 1997 / Details: MSC-YALE MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→23 Å / Num. obs: 5656 / % possible obs: 81 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 12.8
Reflection shellResolution: 1.8→2 Å / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 4.7 / % possible all: 53
Reflection
*PLUS
Num. measured all: 12758 / Rmerge(I) obs: 0.06
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 2 Å / % possible obs: 53 % / Rmerge(I) obs: 0.101

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Processing

Software
NameVersionClassification
RIGAKUR-AXISdata collection
RIGAKUR-AXISdata reduction
PROFFTrefinement
R-AXIS(RIGAKU)data reduction
R-AXIS(RIGAKU)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→9 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.182 --
obs-5207 92 %
Displacement parametersBiso mean: 15.9 Å2
Refinement stepCycle: LAST / Resolution: 1.8→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms640 0 0 109 749
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.02
X-RAY DIFFRACTIONp_angle_d0.0390.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0470.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.1581.5
X-RAY DIFFRACTIONp_mcangle_it2.1712
X-RAY DIFFRACTIONp_scbond_it3.032.5
X-RAY DIFFRACTIONp_scangle_it3.5393
X-RAY DIFFRACTIONp_plane_restr0.0270.03
X-RAY DIFFRACTIONp_chiral_restr0.1690.15
X-RAY DIFFRACTIONp_singtor_nbd0.20.6
X-RAY DIFFRACTIONp_multtor_nbd0.280.6
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.320.6
X-RAY DIFFRACTIONp_planar_tor4.13
X-RAY DIFFRACTIONp_staggered_tor23.115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor25.420
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.182
Solvent computation
*PLUS
Displacement parameters
*PLUS

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