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- PDB-4kiv: RECOMBINANT KRINGLE IV-10/W72R MUTANT OF HUMAN APOLIPOPROTEIN(A) -

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Basic information

Entry
Database: PDB / ID: 4kiv
TitleRECOMBINANT KRINGLE IV-10/W72R MUTANT OF HUMAN APOLIPOPROTEIN(A)
ComponentsAPOLIPOPROTEIN
KeywordsLYSINE BINDING SITE / SITE MUTATION
Function / homology
Function and homology information


plasma lipoprotein particle / LDL remodeling / blood circulation / endopeptidase inhibitor activity / lipid transport / fibronectin binding / apolipoprotein binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / lipid metabolic process / heparin binding ...plasma lipoprotein particle / LDL remodeling / blood circulation / endopeptidase inhibitor activity / lipid transport / fibronectin binding / apolipoprotein binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / 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 / MOLECULAR REPLACEMENT / Resolution: 2.2 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
DepositionAug 26, 1998Processing site: BNL
Revision 1.0May 18, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 14, 2018Group: Database references / Category: struct_ref_seq_dif / Item: _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: APOLIPOPROTEIN


Theoretical massNumber of molelcules
Total (without water)9,1701
Polymers9,1701
Non-polymers00
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)24.300, 45.820, 56.230
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: 9170.088 Da / Num. of mol.: 1 / Fragment: KRINGLE IV-10 / Mutation: W72R
Source method: isolated from a genetically manipulated source
Details: KIV-10/W72R MUTANT OF HUMAN APOLIPOPROTEIN(A) / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P08519
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O
Compound detailsN-TERMINAL (VR) AND C-TERMINAL (SDTEGTV) INTERKRINGULAR PARTS ARE DISORDERED. SIDE CHAIN FOR ...N-TERMINAL (VR) AND C-TERMINAL (SDTEGTV) INTERKRINGULAR PARTS ARE DISORDERED. SIDE CHAIN FOR RESIDUE GLN0 IS MISSING. THE P30 RESIDUE IS IN CIS CONFORMATION.
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: 1.56 Å3/Da / Density % sol: 22 %
Crystal growpH: 6.5 / Details: pH 6.5
Crystal
*PLUS
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
220 %PEG80001reservoir
30.1 Msodium cacodylate1reservoir
40.1 M1reservoirLi2SO4

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / 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: 2.2→24.3 Å / Num. obs: 6494 / % possible obs: 64 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 7.2
Reflection shellResolution: 2.2→2.5 Å / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 2 / % possible all: 45
Reflection
*PLUS
Num. obs: 2241 / Num. measured all: 6494
Reflection shell
*PLUS
% possible obs: 45 % / Rmerge(I) obs: 0.089

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Processing

Software
NameVersionClassification
RIGAKUR-AXISdata collection
RIGAKUR-AXISdata reduction
AMoREphasing
PROFFTrefinement
R-AXIS(RIGAKU)data reduction
R-AXIS(RIGAKU)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→7 Å / σ(F): 1
RfactorNum. reflection% reflection
Rwork0.162 --
obs-2114 44 %
Displacement parametersBiso mean: 21.5 Å2
Refinement stepCycle: LAST / Resolution: 2.2→7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms632 0 0 41 673
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.02
X-RAY DIFFRACTIONp_angle_d0.0320.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0410.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.0461.5
X-RAY DIFFRACTIONp_mcangle_it1.6452
X-RAY DIFFRACTIONp_scbond_it1.7482.3
X-RAY DIFFRACTIONp_scangle_it2.4562.5
X-RAY DIFFRACTIONp_plane_restr0.0280.03
X-RAY DIFFRACTIONp_chiral_restr0.130.12
X-RAY DIFFRACTIONp_singtor_nbd0.220.6
X-RAY DIFFRACTIONp_multtor_nbd0.280.6
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.290.6
X-RAY DIFFRACTIONp_planar_tor43
X-RAY DIFFRACTIONp_staggered_tor1915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor22.320
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROFFT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.166
Solvent computation
*PLUS
Displacement parameters
*PLUS

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