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- PDB-3ldm: Crystal structure of aprotinin in complex with sucrose octasulfat... -

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Basic information

Entry
Database: PDB / ID: 3ldm
TitleCrystal structure of aprotinin in complex with sucrose octasulfate: unusual interactions and implication for heparin binding
ComponentsPancreatic trypsin inhibitor
KeywordsHYDROLASE INHIBITOR / aprotinin / sucrose octasulfate
Function / homology
Function and homology information


trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity ...trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / negative regulation of platelet aggregation / potassium channel inhibitor activity / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity / protease binding / calcium ion binding / extracellular space
Similarity search - Function
Pancreatic trypsin inhibitor Kunitz domain / Factor Xa Inhibitor / Proteinase inhibitor I2, Kunitz, conserved site / Pancreatic trypsin inhibitor (Kunitz) family signature. / BPTI/Kunitz family of serine protease inhibitors. / Pancreatic trypsin inhibitor Kunitz domain / Kunitz/Bovine pancreatic trypsin inhibitor domain / Pancreatic trypsin inhibitor (Kunitz) family profile. / Pancreatic trypsin inhibitor Kunitz domain superfamily / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsYang, I.S. / Kim, T.G. / Park, B.S. / Kim, K.H.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2010
Title: Crystal structures of aprotinin and its complex with sucrose octasulfate reveal multiple modes of interactions with implications for heparin binding.
Authors: Yang, I.S. / Kim, T.G. / Park, B.S. / Cho, K.J. / Lee, J.H. / Park, Y. / Kim, K.H.
History
DepositionJan 13, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pancreatic trypsin inhibitor
B: Pancreatic trypsin inhibitor
C: Pancreatic trypsin inhibitor
D: Pancreatic trypsin inhibitor
E: Pancreatic trypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)32,6385
Polymers32,6385
Non-polymers00
Water1,56787
1
A: Pancreatic trypsin inhibitor
B: Pancreatic trypsin inhibitor
C: Pancreatic trypsin inhibitor
D: Pancreatic trypsin inhibitor
E: Pancreatic trypsin inhibitor

A: Pancreatic trypsin inhibitor
B: Pancreatic trypsin inhibitor
C: Pancreatic trypsin inhibitor
D: Pancreatic trypsin inhibitor
E: Pancreatic trypsin inhibitor


Theoretical massNumber of molelcules
Total (without water)65,27610
Polymers65,27610
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_664-y+1,-x+1,-z-2/31
Buried area15440 Å2
ΔGint-68 kcal/mol
Surface area24230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.894, 92.894, 159.353
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein
Pancreatic trypsin inhibitor / Basic protease inhibitor / BPTI / BPI / Aprotinin


Mass: 6527.568 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00974
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 3.04 Å3/Da / Density % sol: 59.55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 100mM sodium acetate pH4.6, 2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. all: 23745 / Num. obs: 23698 / % possible obs: 99.8 % / Rsym value: 0.089 / Net I/σ(I): 10.7
Reflection shellResolution: 2.6→2.66 Å / Rsym value: 0.45 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0102refinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→50 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 1 / SU B: 22.657 / SU ML: 0.214 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.257 644 4.9 %RANDOM
Rwork0.203 ---
obs0.206 13118 99.7 %-
all-13157 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 112.78 Å2 / Biso mean: 41.093 Å2 / Biso min: 10.58 Å2
Baniso -1Baniso -2Baniso -3
1-1.79 Å20.89 Å20 Å2
2--1.79 Å20 Å2
3----2.68 Å2
Refinement stepCycle: LAST / Resolution: 2.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2220 0 0 87 2307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222295
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.9673090
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4255275
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.55320.909110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.82415375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.2741530
X-RAY DIFFRACTIONr_chiral_restr0.1110.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0211810
X-RAY DIFFRACTIONr_mcbond_it1.9191.51395
X-RAY DIFFRACTIONr_mcangle_it3.60222225
X-RAY DIFFRACTIONr_scbond_it4.3943900
X-RAY DIFFRACTIONr_scangle_it7.2444.5865
X-RAY DIFFRACTIONr_rigid_bond_restr2.39432295
LS refinement shellResolution: 2.598→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 44 -
Rwork0.278 891 -
all-935 -
obs--99.47 %

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