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- PDB-2apr: STRUCTURE AND REFINEMENT AT 1.8 ANGSTROMS RESOLUTION OF THE ASPAR... -

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Basic information

Entry
Database: PDB / ID: 2apr
TitleSTRUCTURE AND REFINEMENT AT 1.8 ANGSTROMS RESOLUTION OF THE ASPARTIC PROTEINASE FROM RHIZOPUS CHINENSIS
ComponentsRHIZOPUSPEPSIN
KeywordsHYDROLASE (ASPARTIC PROTEINASE)
Function / homology
Function and homology information


rhizopuspepsin / aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Aspergillopepsin-like catalytic domain / 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 ...Aspergillopepsin-like catalytic domain / 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 speciesRhizopus microsporus var. chinensis (fungus)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsSuguna, K. / Davies, D.R.
Citation
Journal: J.Mol.Biol. / Year: 1987
Title: Structure and refinement at 1.8 A resolution of the aspartic proteinase from Rhizopus chinensis.
Authors: Suguna, K. / Bott, R.R. / Padlan, E.A. / Subramanian, E. / Sheriff, S. / Cohen, G.H. / Davies, D.R.
#1: Journal: Biochemistry / Year: 1982
Title: Three-Dimensional Structure of the Complex of the Rhizopus Chinensis Carboxyl Proteinase and Pepstatin at 2.5 Angstroms Resolution
Authors: Bott, R.R. / Subramanian, E. / Davies, D.R.
#2: Journal: Adv.Exp.Med.Biol. / Year: 1977
Title: The Crystal Structure of an Acid Protease from Rhizopus Chinensis at 2.5 Angstroms Resolution
Authors: Subramanian, E. / Liu, M. / Swan, I.D.A. / Davies, D.R.
#3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1977
Title: Homology Among Acid Proteases. Comparison of Crystal Structures at 3 Angstroms Resolution of Acid Proteases from Rhizopus Chinensis and Endothia Parasitica
Authors: Subramanian, E. / Swan, I.D.A. / Liu, M. / Davies, D.R. / Jenkins, J.A. / Tickle, I.J. / Blundell, T.L.
History
DepositionMar 19, 1987Processing site: BNL
SupersessionJul 16, 1987ID: 1APR
Revision 1.0Jul 16, 1987Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. THESE ARE REPRESENTED BY TWO SHEETS ...SHEET THERE ARE SEVERAL BIFURCATED SHEETS IN THIS STRUCTURE. THESE ARE REPRESENTED BY TWO SHEETS WHICH HAVE ONE OR MORE IDENTICAL STRANDS. SHEETS *S2A* AND *S2B* REPRESENT ONE BIFURCATED SHEET. SHEETS *S3A* AND *S3B* REPRESENT ONE BIFURCATED SHEET. SHEETS *S4A* AND *S4B* REPRESENT ONE BIFURCATED SHEET.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RHIZOPUSPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1092
Polymers34,0691
Non-polymers401
Water6,720373
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.310, 60.600, 106.970
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: RESIDUES 26 AND 316 ARE CIS PROLINES.

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Components

#1: Protein RHIZOPUSPEPSIN


Mass: 34068.629 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhizopus microsporus var. chinensis (fungus)
Species: Rhizopus microsporus / Strain: var. chinensis / References: UniProt: P06026, EC: 3.4.23.6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.11 %
Crystal grow
*PLUS
pH: 6 / Method: other
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
120 mMcalcium acetate solution11
250 mg/mlprotein11

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Data collection

Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 38090 / Num. measured all: 129693 / Rmerge(I) obs: 0.043

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementHighest resolution: 1.8 Å
Details: THERE IS DISORDER AT SER 116, ARG 151, ARG 192, SER 211.
RfactorNum. reflection
obs0.143 31917
Refine analyzeLuzzati coordinate error obs: 0.16 Å
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2417 0 1 373 2791
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.01
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
σ(F): 3 / Highest resolution: 1.8 Å / Num. reflection obs: 31917 / Rfactor obs: 0.143
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d0.030.034
X-RAY DIFFRACTIONp_plane_restr0.020.01
X-RAY DIFFRACTIONp_chiral_restr0.10.11

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