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- PDB-4aa9: Camel chymosin at 1.6A resolution -

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Basic information

Entry
Database: PDB / ID: 4aa9
TitleCamel chymosin at 1.6A resolution
ComponentsCHYMOSIN
KeywordsHYDROLASE / ASPARTIC PEPTIDASE / RENNET
Function / homology
Function and homology information


chymosin / digestion / proteolysis involved in protein catabolic process / aspartic-type endopeptidase activity
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 speciesCAMELUS DROMEDARIUS (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLangholm Jensen, J. / Molgaard, A. / Navarro Poulsen, J.C. / van den Brink, J.M. / Harboe, M. / Simonsen, J.B. / Qvist, K.B. / Larsen, S.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Camel and Bovine Chymosin: The Relationship between Their Structures and Cheese-Making Properties.
Authors: Langholm Jensen, J. / Molgaard, A. / Navarro Poulsen, J.C. / Harboe, M.K. / Simonsen, J.B. / Lorentzen, A.M. / Hjerno, K. / van den Brink, J.M. / Qvist, K.B. / Larsen, S.
History
DepositionNov 30, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2May 15, 2013Group: Database references
Revision 1.3Jan 17, 2018Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.page_last / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_sheet
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_sheet.number_strands
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHYMOSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,64413
Polymers35,3701
Non-polymers1,27412
Water7,963442
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.310, 66.110, 133.740
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 CHYMOSIN


Mass: 35370.461 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAMELUS DROMEDARIUS (Arabian camel) / Production host: ASPERGILLUS NIGER (mold) / References: UniProt: Q9GK11, chymosin
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / 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 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growpH: 5.5
Details: RESERVOIR: 2 M (NH4)2SO4, 100 MM BIS-TRIS, PH 5.5. SAMPLE: 30 MG/ML PROTEIN IN 50 MM BIS-TRIS, PH 6.0.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04
DetectorType: MARRESEARCH MAR165 / Detector: CCD / Date: Dec 3, 2011
Details: MULTILAYER MIRROR, CURVED TO FOCUS IN THE VERTICAL (R 400 M).
RadiationMonochromator: BENT SI (111) CRYSTAL, HORIZONTALLY FOCUSING.
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 62765 / % possible obs: 99 % / Observed criterion σ(I): 15 / Redundancy: 8.6 % / Biso Wilson estimate: 19.66 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 31
Reflection shellResolution: 1.6→1.7 Å / Redundancy: 9.6 % / Rmerge(I) obs: 0.14 / Mean I/σ(I) obs: 6 / % possible all: 23

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Processing

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

1cms


Resolution: 1.6→24.795 Å / SU ML: 0.2 / σ(F): 2 / Phase error: 18.7 / Stereochemistry target values: ML
Details: DISORDERED LOOP 159-162 WAS MODELLED STEREOCHEMICALLY. VM CALCULATED USING A TOTAL MASS OF 40 KDA (DETERMINED USING MASS SPECTROMETRY) DUE TO TWO GLYCOSYLATIONS).
RfactorNum. reflection% reflection
Rfree0.2084 3182 5.1 %
Rwork0.1862 --
obs0.1874 62748 99.32 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.012 Å2 / ksol: 0.424 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.5168 Å20 Å20 Å2
2--1.1275 Å20 Å2
3----3.6443 Å2
Refinement stepCycle: LAST / Resolution: 1.6→24.795 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2438 0 70 442 2950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072587
X-RAY DIFFRACTIONf_angle_d1.0613528
X-RAY DIFFRACTIONf_dihedral_angle_d11.984909
X-RAY DIFFRACTIONf_chiral_restr0.075381
X-RAY DIFFRACTIONf_plane_restr0.005451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.62390.32371210.29322411X-RAY DIFFRACTION94
1.6239-1.64930.33551390.2722573X-RAY DIFFRACTION100
1.6493-1.67630.28551390.24582557X-RAY DIFFRACTION99
1.6763-1.70520.2731250.22562552X-RAY DIFFRACTION100
1.7052-1.73620.24621510.22552582X-RAY DIFFRACTION100
1.7362-1.76960.25831270.21062571X-RAY DIFFRACTION100
1.7696-1.80570.21541390.19522562X-RAY DIFFRACTION100
1.8057-1.84490.24691300.18982638X-RAY DIFFRACTION100
1.8449-1.88780.20571440.18312551X-RAY DIFFRACTION100
1.8878-1.9350.21431400.17512562X-RAY DIFFRACTION100
1.935-1.98730.21341360.17692581X-RAY DIFFRACTION100
1.9873-2.04580.21351540.17942568X-RAY DIFFRACTION100
2.0458-2.11180.19141340.1732601X-RAY DIFFRACTION100
2.1118-2.18720.20031420.17372600X-RAY DIFFRACTION100
2.1872-2.27470.19771280.18012601X-RAY DIFFRACTION100
2.2747-2.37820.20411370.1782603X-RAY DIFFRACTION100
2.3782-2.50340.20811120.18172646X-RAY DIFFRACTION100
2.5034-2.66010.18671260.18842638X-RAY DIFFRACTION100
2.6601-2.86520.25011460.19672603X-RAY DIFFRACTION100
2.8652-3.15310.22091530.19552643X-RAY DIFFRACTION100
3.1531-3.60810.19271670.1692611X-RAY DIFFRACTION100
3.6081-4.54130.16511450.15362659X-RAY DIFFRACTION99
4.5413-24.79830.2071470.2082653X-RAY DIFFRACTION94

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