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- PDB-2fi3: Crystal structure of a BPTI variant (Cys14->Ser, Cys38->Ser) in c... -

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Basic information

Entry
Database: PDB / ID: 2fi3
TitleCrystal structure of a BPTI variant (Cys14->Ser, Cys38->Ser) in complex with trypsin
Components
  • Cationic trypsin
  • Pancreatic trypsin inhibitor
Keywordshydrolase/hydrolase inhibitor / PROTEASE-INHIBITOR COMPLEX / hydrolase-hydrolase inhibitor COMPLEX
Function / homology
Function and homology information


trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / trypsin / serpin family protein binding ...trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / trypsin / serpin family protein binding / digestion / serine protease inhibitor complex / serine-type endopeptidase inhibitor activity / endopeptidase activity / protease binding / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / metal ion binding
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 ...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 / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Serine protease 1 / Pancreatic trypsin inhibitor
Similarity search - Component
Biological speciesBos taurus (cattle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsZakharova, E. / Horvath, M.P. / Goldenberg, D.P.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Functional and structural roles of the Cys14-Cys38 disulfide of bovine pancreatic trypsin inhibitor.
Authors: Zakharova, E. / Horvath, M.P. / Goldenberg, D.P.
History
DepositionDec 27, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: Cationic trypsin
I: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,06419
Polymers29,8202
Non-polymers1,24417
Water4,486249
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4160 Å2
ΔGint-100 kcal/mol
Surface area11920 Å2
MethodPISA
2
E: Cationic trypsin
I: Pancreatic trypsin inhibitor
hetero molecules

E: Cationic trypsin
I: Pancreatic trypsin inhibitor
hetero molecules

E: Cationic trypsin
I: Pancreatic trypsin inhibitor
hetero molecules

E: Cationic trypsin
I: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,25576
Polymers119,2798
Non-polymers4,97668
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_575x,-y+2,-z1
Buried area25380 Å2
ΔGint-538 kcal/mol
Surface area39110 Å2
MethodPISA
3
E: Cationic trypsin
I: Pancreatic trypsin inhibitor
hetero molecules

E: Cationic trypsin
I: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,12838
Polymers59,6394
Non-polymers2,48834
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
Buried area10710 Å2
ΔGint-239 kcal/mol
Surface area21450 Å2
MethodPISA
4
E: Cationic trypsin
I: Pancreatic trypsin inhibitor
hetero molecules

E: Cationic trypsin
I: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,12838
Polymers59,6394
Non-polymers2,48834
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_575x,-y+2,-z1
Buried area9890 Å2
ΔGint-225 kcal/mol
Surface area22350 Å2
MethodPISA
5
E: Cationic trypsin
hetero molecules

E: Cationic trypsin
hetero molecules

I: Pancreatic trypsin inhibitor
hetero molecules

I: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,12838
Polymers59,6394
Non-polymers2,48834
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_575x,-y+2,-z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_555-x,y,-z1
Buried area8220 Å2
ΔGint-243 kcal/mol
Surface area24030 Å2
MethodPISA
6
E: Cationic trypsin
hetero molecules

E: Cationic trypsin
hetero molecules

I: Pancreatic trypsin inhibitor
hetero molecules

I: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,12838
Polymers59,6394
Non-polymers2,48834
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_566x,-y+1,-z+11
crystal symmetry operation6_565-x+1/2,-y+3/2,z+1/21
crystal symmetry operation7_545-x+1/2,y-1/2,-z+1/21
Buried area6100 Å2
ΔGint-219 kcal/mol
Surface area26150 Å2
MethodPISA
7
E: Cationic trypsin
hetero molecules

I: Pancreatic trypsin inhibitor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,06419
Polymers29,8202
Non-polymers1,24417
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
Buried area3670 Å2
ΔGint-110 kcal/mol
Surface area12410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.744, 81.748, 124.274
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11I-2003-

CA

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Components

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Protein , 2 types, 2 molecules EI

#1: Protein Cationic trypsin / Beta-trypsin


Mass: 23324.287 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00760, trypsin
#2: Protein Pancreatic trypsin inhibitor / Basic protease inhibitor / BPI / BPTI / Aprotinin


Mass: 6495.438 Da / Num. of mol.: 1 / Mutation: C14S, C38S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle)
Plasmid details: as described in Biochemistry 1988, 27, 2481-2489
Plasmid: pTI103 / Production host: Escherichia coli (E. coli) / Strain (production host): HB101 / References: UniProt: P00974

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Non-polymers , 5 types, 266 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 249 / 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: 3.18 Å3/Da / Density % sol: 61.34 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.75 M ammonium sulfate, 0.1 M HEPES, 0.02% sodium azide, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å
DetectorType: NONIUS KAPPA CCD2000 / Detector: CCD / Date: Oct 23, 2004 / Details: OSMIC CONFOCAL MAX-FLUX (GREEN)
RadiationMonochromator: OSMIC CONFOCAL MAX-FLUX (GREEN) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.56→20 Å / Num. all: 54071 / Num. obs: 53322 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 20.4
Reflection shellResolution: 1.56→1.62 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 3.8 / Num. unique all: 4633 / % possible all: 86.7

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2PTC
Resolution: 1.58→20 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber
Details: Maximum-likelihood using measured intensities (mli) target implemented with CNS SOLVE 1.1
RfactorNum. reflection% reflectionSelection details
Rfree0.2177 4237 -RANDOM
Rwork0.2032 ---
all0.2044 52391 --
obs0.2044 51979 99.2 %-
Solvent computationBsol: 18.5858 Å2 / ksol: 0.360625 e/Å3
Displacement parametersBiso mean: 14.4 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.16 Å0.14 Å
Refinement stepCycle: LAST / Resolution: 1.58→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2219 0 71 261 2551
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.32
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.9361.5
X-RAY DIFFRACTIONc_mcangle_it1.5582
X-RAY DIFFRACTIONc_scbond_it1.5142
X-RAY DIFFRACTIONc_scangle_it2.1382.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection obs% reflection obs (%)
1.58-1.680.2677010.249821995.3
1.68-1.810.266960.228652100
1.81-1.990.2396810.2148657100
1.99-2.280.2227040.2078695100
2.28-2.870.2226940.2048777100
2.87-200.1897610.186897999.9

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