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- PDB-4auc: Bovine chymosin in complex with Pepstatin A -

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Basic information

Entry
Database: PDB / ID: 4auc
TitleBovine chymosin in complex with Pepstatin A
Components
  • CHYMOSIN
  • PEPSTATIN A
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / HYDROLASE / HYDROLASE INHIBITOR / PEPTIDASE / INHIBITION
Function / homology
Function and homology information


chymosin / digestion / aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Pepsin catalytic domain / Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site ...Pepsin catalytic domain / Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesBOS TAURUS (cattle)
ACTINOMYCES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLangholm Jensen, J. / Navarro Poulsen, J.C. / Jacobsen, J. / van den Brink, J.M. / Qvist, K.B. / Larsen, S.
CitationJournal: To be Published
Title: The Structure of Bovine Chymosin in Complex with Pepstatin A
Authors: Langholm Jensen, J. / Navarro Poulsen, J.C. / Jacobsen, J. / van den Brink, J.M. / Qvist, K.B. / Larsen, S.
History
DepositionMay 16, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 29, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 2.0Dec 20, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_initial_refinement_model / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conf / struct_conn / struct_conn_type / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.ndb_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_nonpoly_scheme.pdb_strand_id / _pdbx_struct_special_symmetry.auth_seq_id / _struct_conf.pdbx_PDB_helix_id / _struct_conn_type.id / _struct_sheet.id / _struct_sheet.number_strands

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CHYMOSIN
B: PEPSTATIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,7428
Polymers36,3592
Non-polymers3846
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2040 Å2
ΔGint-5.4 kcal/mol
Surface area13970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.500, 93.500, 89.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-401-

NA

21A-546-

HOH

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

#1: Protein CHYMOSIN / PREPRORENNIN


Mass: 35672.695 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) BOS TAURUS (cattle) / Tissue: MUCOSA / Cell: GASTRIC CHIEF CELL / Organ: ABOMASUM / Production host: ASPERGILLUS NIGER (mold) / References: UniProt: P00794, chymosin
#2: Protein/peptide PEPSTATIN A


Mass: 685.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ACTINOMYCES (bacteria)

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Non-polymers , 4 types, 332 molecules

#3: Chemical ChemComp-NA / SODIUM ION


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


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsSTATINE (STA): PART OF PEPSTATIN A ISOVALERIC ACID (IVA): PART OF PEPSTATIN A

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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: 3.1 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 5.5
Details: RESERVOIR: 75 MM BIS-TRIS PH 5.5, 0.15 M NACL, 19% (W/V) PEG3350, 7.5 MM CDCL2. SAMPLE: 7.2 MG/ML OF PROTEIN COMPLEX IN 10 MM NAH2PO4 PH 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.89993
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 24, 2012 / Details: TOROIDAL MIRROR WITH RH COATING
RadiationMonochromator: CHANNEL-CUT SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89993 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 59710 / % possible obs: 99.9 % / Observed criterion σ(I): 5.5 / Redundancy: 8.7 % / Biso Wilson estimate: 18.85 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 27
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 5.5 / % possible all: 99.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1CMS

1cms


Resolution: 1.6→41.388 Å / SU ML: 0.36 / σ(F): 2.01 / Phase error: 17.44 / Stereochemistry target values: ML
Details: DISORDERED LOOP 159-160 WAS MODELED STEREOCHEMICALLY. VM CALCULATED USING A TOTAL MASS OF 36.3 KDA CORRESPONDING CHYMOSIN INHIBITED BY PEPSTATIN
RfactorNum. reflection% reflection
Rfree0.1971 3009 5.1 %
Rwork0.1743 --
obs0.1754 59607 99.94 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.504 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 24.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.0212 Å20 Å20 Å2
2---1.0212 Å20 Å2
3---2.0424 Å2
Refinement stepCycle: LAST / Resolution: 1.6→41.388 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2559 0 18 326 2903
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192689
X-RAY DIFFRACTIONf_angle_d1.2493651
X-RAY DIFFRACTIONf_dihedral_angle_d14.365957
X-RAY DIFFRACTIONf_chiral_restr0.095406
X-RAY DIFFRACTIONf_plane_restr0.006473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62620.22161340.21732675X-RAY DIFFRACTION100
1.6262-1.65430.24321360.22292700X-RAY DIFFRACTION100
1.6543-1.68440.23651560.21832641X-RAY DIFFRACTION100
1.6844-1.71680.26351440.21032653X-RAY DIFFRACTION100
1.7168-1.75180.21681350.20092669X-RAY DIFFRACTION100
1.7518-1.78990.20661310.20162683X-RAY DIFFRACTION100
1.7899-1.83150.21741580.19162646X-RAY DIFFRACTION100
1.8315-1.87730.21151540.1822670X-RAY DIFFRACTION100
1.8773-1.92810.21231260.17792707X-RAY DIFFRACTION100
1.9281-1.98480.18711510.17812657X-RAY DIFFRACTION100
1.9848-2.04890.19091430.17792684X-RAY DIFFRACTION100
2.0489-2.12210.20381390.18032694X-RAY DIFFRACTION100
2.1221-2.20710.22331440.17982669X-RAY DIFFRACTION100
2.2071-2.30750.21571640.18022680X-RAY DIFFRACTION100
2.3075-2.42920.2021480.17922690X-RAY DIFFRACTION100
2.4292-2.58130.19061220.18322717X-RAY DIFFRACTION100
2.5813-2.78060.21611520.18032685X-RAY DIFFRACTION100
2.7806-3.06030.21221420.17292725X-RAY DIFFRACTION100
3.0603-3.5030.18311450.16282730X-RAY DIFFRACTION100
3.503-4.41260.14841530.14442745X-RAY DIFFRACTION100
4.4126-41.40140.20061320.16942878X-RAY DIFFRACTION100

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