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- PDB-1bjr: COMPLEX FORMED BETWEEN PROTEOLYTICALLY GENERATED LACTOFERRIN FRAG... -

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Basic information

Entry
Database: PDB / ID: 1bjr
TitleCOMPLEX FORMED BETWEEN PROTEOLYTICALLY GENERATED LACTOFERRIN FRAGMENT AND PROTEINASE K
Components
  • LACTOFERRIN
  • PROTEINASE K
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PROTEINASE K / LACTOFERRIN / IRON TRANSPORT / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


peptidase K / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8/S53 domain / : / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site ...Proteinase K-like catalytic domain / Peptidase S8 propeptide/proteinase inhibitor I9 / Peptidase inhibitor I9 / Peptidase S8 propeptide/proteinase inhibitor I9 superfamily / Peptidase S8/S53 domain / : / Peptidase S8, subtilisin, His-active site / Serine proteases, subtilase family, histidine active site. / Serine proteases, subtilase family, aspartic acid active site. / Peptidase S8, subtilisin, Asp-active site / Serine proteases, subtilase family, serine active site. / Peptidase S8, subtilisin, Ser-active site / Peptidase S8, subtilisin-related / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesEngyodontium album (fungus)
Bubalus bubalis (water buffalo)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.44 Å
AuthorsSingh, T.P. / Sharma, S. / Karthikeyan, S. / Betzel, C. / Bhatia, K.L.
Citation
Journal: Proteins / Year: 1998
Title: Crystal structure of a complex formed between proteolytically-generated lactoferrin fragment and proteinase K.
Authors: Singh, T.P. / Sharma, S. / Karthikeyan, S. / Betzel, C. / Bhatia, K.L.
#1: Journal: J.Biol.Chem. / Year: 1991
Title: Inhibition of Proteinase K by Methoxysuccinyl-Ala-Ala-Pro-Ala-Chloromethyl Ketone. An X-Ray Study at 2.2-A Resolution
Authors: Wolf, W.M. / Bajorath, J. / Muller, A. / Raghunathan, S. / Singh, T.P. / Hinrichs, W. / Saenger, W.
#2: Journal: Acta Crystallogr.,Sect.B / Year: 1988
Title: Synchrotron X-Ray Data Collection and Restrained Least-Squares Refinement of the Crystal Structure of Proteinase K at 1.5 A Resolution
Authors: Betzel, C. / Pal, G.P. / Saenger, W.
History
DepositionJun 27, 1998Processing site: BNL
Revision 1.0Nov 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations / Refinement description
Category: database_2 / pdbx_initial_refinement_model ...database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / 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_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.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.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.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_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: PROTEINASE K
I: LACTOFERRIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8254
Polymers29,7452
Non-polymers802
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.600, 38.581, 79.220
Angle α, β, γ (deg.)90.00, 105.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEINASE K


Mass: 28930.783 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Engyodontium album (fungus) / Strain: LIMBER / References: UniProt: P06873, peptidase K
#2: Protein/peptide LACTOFERRIN


Mass: 813.899 Da / Num. of mol.: 1 / Fragment: FRAGMENT / Source method: isolated from a natural source / Source: (natural) Bubalus bubalis (water buffalo)
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.19 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 279 K / Method: microdialysis / pH: 6
Details: 60 MG/ML PROTEIN IN 10MM TRIS.HCL, PH 6.0 WAS MICRODIALYZED AGAINST 10% ETHANOL AT 6 DEGREE CELSIUS, microdialysis, temperature 279K
Crystal
*PLUS
Crystal grow
*PLUS
Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
130 mg/mlprotein11
210 %ethanol12

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1997 / Details: PIN HOLE
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.44→12 Å / Num. obs: 9051 / % possible obs: 92.2 % / Observed criterion σ(I): 3 / Redundancy: 2.42 % / Biso Wilson estimate: 29.19 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 22.2
Reflection shellResolution: 2.44→2.57 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.168 / Mean I/σ(I) obs: 9.7 / Rsym value: 0.168 / % possible all: 80.9
Reflection
*PLUS
Num. measured all: 23005

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CCP4refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PRK

3prk


Resolution: 2.44→12 Å / Cross valid method: A POSTERIORI / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.225 903 10 %RANDOM
Rwork0.16 ---
obs0.167 9044 92.2 %-
all-9044 --
Displacement parametersBiso mean: 19.3 Å2
Refine analyzeLuzzati d res low obs: 12 Å / Luzzati sigma a obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 2.44→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2086 0 2 201 2289
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0080.01
X-RAY DIFFRACTIONp_angle_d0.0210.015
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0620.02
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.9051
X-RAY DIFFRACTIONp_mcangle_it1.5031.5
X-RAY DIFFRACTIONp_scbond_it1.9411.5
X-RAY DIFFRACTIONp_scangle_it2.862
X-RAY DIFFRACTIONp_plane_restr0.024
X-RAY DIFFRACTIONp_chiral_restr0.1640.12
X-RAY DIFFRACTIONp_singtor_nbd0.1960.3
X-RAY DIFFRACTIONp_multtor_nbd0.320.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor95
X-RAY DIFFRACTIONp_staggered_tor20.84615
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor26.9215
X-RAY DIFFRACTIONp_special_tor05
Software
*PLUS
Name: CCP4 / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.167 / Rfactor Rwork: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.9 Å / Rfactor obs: 0.214

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