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- PDB-2rmp: RMP-pepstatin A complex -

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Basic information

Entry
Database: PDB / ID: 2rmp
TitleRMP-pepstatin A complex
Components
  • MUCOROPEPSIN
  • PEPSTATIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ASPARTIC PROTEINASE / PEPSTATIN A / ASPARTYL PROTEASE-PEPTIDE complex / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


mucorpepsin / aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Pepsin-like 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 ...Pepsin-like 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
Pepstatin / Mucorpepsin
Similarity search - Component
Biological speciesRhizomucor miehei (fungus)
Streptomyces (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT ELECTRON DENSITY DIFFERENCE MAP / Resolution: 2.7 Å
AuthorsYang, J. / Quail, J.W.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 1999
Title: Structure of the Rhizomucor miehei aspartic proteinase complexed with the inhibitor pepstatin A at 2.7 A resolution.
Authors: Yang, J. / Quail, J.W.
History
DepositionMay 30, 1997Processing site: BNL
Revision 1.0Sep 17, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 25, 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 1.3Feb 27, 2013Group: Other
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / 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_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 2023Group: Database references / Refinement description / Structure summary
Category: chem_comp / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Remark 650 HELIX DETERMINATION METHOD: AUTHOR-DETERMINED
Remark 700 SHEET DETERMINATION METHOD: TAKEN FROM RELEASED PDB ENTRY 2ASI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MUCOROPEPSIN
B: PEPSTATIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0264
Polymers39,4222
Non-polymers6052
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-1 kcal/mol
Surface area14300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.520, 50.820, 172.710
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 MUCOROPEPSIN / MUCOR RENIN / RHIOMUCOR MIEHEI ASPARTIC PROTEINASE


Mass: 38735.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rhizomucor miehei (fungus) / References: UniProt: P00799, mucorpepsin
#2: Protein/peptide PEPSTATIN


Type: Oligopeptide / Class: Enzyme inhibitor / Mass: 685.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: STREPTOMYCES (PEPSTATIN A WAS ISOLATED FROM STREPTOMYCES)
Source: (natural) Streptomyces (bacteria) / Genus: Streptomyces / References: Pepstatin
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: 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
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: 2.31 Å3/Da / Density % sol: 49 %
Crystal growpH: 3.6 / Details: pH 3.6
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
126 %PEG80001reservoir
220 mMcitrate1reservoir
325 mg/mlRMP1drop
40.45 mg/mlpepstain A1drop
52 mMcitrate1drop

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 1.15
DetectorType: ENRAF-NONIUS FAST / Detector: DIFFRACTOMETER / Date: Nov 1, 1996 / Details: MIRROR
RadiationMonochromator: SINGLE FLAT CRYSTALS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.15 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 9360 / % possible obs: 84.9 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 45.4 Å2 / Rsym value: 0.092 / Net I/σ(I): 15
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2 / Rsym value: 0.159 / % possible all: 48
Reflection
*PLUS
Highest resolution: 2.7 Å / Num. measured all: 43156 / Rmerge(I) obs: 0.092
Reflection shell
*PLUS
Highest resolution: 2.7 Å / Lowest resolution: 2.8 Å / % possible obs: 47.9 % / Rmerge(I) obs: 0.159

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8model building
X-PLOR3.8refinement
X-PLOR3.8phasing
RefinementMethod to determine structure: DIRECT ELECTRON DENSITY DIFFERENCE MAP
Starting model: PDB ENTRY 2ASI

2asi


Resolution: 2.7→8 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.28 432 5 %RANDOM
Rwork0.193 ---
obs0.193 8599 84.5 %-
Displacement parametersBiso mean: 25.1 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.7→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2713 0 39 0 2752
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.2
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.8
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it4.3
X-RAY DIFFRACTIONx_mcangle_it6.8
X-RAY DIFFRACTIONx_scbond_it5.9
X-RAY DIFFRACTIONx_scangle_it8.6
LS refinement shellResolution: 2.7→2.82 Å / Rfactor Rfree error: 0.06 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.314 24 4.6 %
Rwork0.298 516 -
obs--43.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2PARAM3.CHOTOPH3.CHO
X-RAY DIFFRACTION3TOPOLOGY.PEPSTATIN
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.2
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.8

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