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- PDB-3rp2: THE STRUCTURE OF RAT MAST CELL PROTEASE II AT 1.9-ANGSTROMS RESOLUTION -

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Basic information

Entry
Database: PDB / ID: 3rp2
TitleTHE STRUCTURE OF RAT MAST CELL PROTEASE II AT 1.9-ANGSTROMS RESOLUTION
ComponentsRAT MAST CELL PROTEASE II
KeywordsSERINE PROTEINASE
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / protein maturation / serine-type endopeptidase activity / proteolysis / extracellular space
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Mast cell protease 2
Similarity search - Component
Biological speciesRattus rattus (black rat)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsReynolds, R. / Remington, S. / Weaver, L. / Fischer, R. / Anderson, W. / Ammon, H. / Matthews, B.
Citation
Journal: Biochemistry / Year: 1988
Title: The structure of rat mast cell protease II at 1.9-A resolution.
Authors: Remington, S.J. / Woodbury, R.G. / Reynolds, R.A. / Matthews, B.W. / Neurath, H.
#1: Journal: Acta Crystallogr.,Sect.B / Year: 1985
Title: Structure of a Serine Protease from Rat Mast Cells Determined from Twinned Crystals by Isomorphous and Molecular Replacement
Authors: Reynolds, R.A. / Remington, S.J. / Weaver, L.H. / Fisher, R.G. / Anderson, W.F. / Ammon, H.L. / Matthews, B.W.
#2: Journal: Biochemistry / Year: 1978
Title: Covalent Structure of a Group-Specific Protease from Rat Small Intestine
Authors: Woodbury, R.G. / Katunuma, N. / Kobayashi, K. / Titani, K. / Neurath, H.
#3: Journal: Biochemistry / Year: 1978
Title: Covalent Structure of a Group-Specific Protease from Rat Small Intestine. Appendix. Crystallographic Data for a Group Specific Protease from Rat Intestine
Authors: Anderson, W.F. / Matthews, B.W. / Woodbury, R.G.
#4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1978
Title: Immunofluorescent Localization of a Serine Protease in Rat Small Intestine
Authors: Woodbury, R.G. / Gruzenski, G.M. / Lagunoff, D.
History
DepositionSep 10, 1984Processing site: BNL
Revision 1.0Oct 29, 1984Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Oct 23, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RAT MAST CELL PROTEASE II
B: RAT MAST CELL PROTEASE II


Theoretical massNumber of molelcules
Total (without water)49,6062
Polymers49,6062
Non-polymers00
Water2,216123
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.200, 78.200, 96.800
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Atom site foot note1: RESIDUES PRO A 225 AND PRO B 225 ARE CIS-PROLINES.
2: AN OCCUPANCY OF 0.0 INDICATES THAT THE COORDINATES WERE GENERATED USING STEREOCHEMICAL CRITERIA.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9955, 0.0465, -0.08263), (0.0465, -0.99892, -0.00193), (-0.08263, -0.00193, -0.99658)
Vector: 2.791, -2.688, 65.984)
DetailsTHE TRANSFORMATION GIVEN ON THE *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR THE B CHAIN WHEN APPLIED TO THE A CHAIN.

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Components

#1: Protein RAT MAST CELL PROTEASE II


Mass: 24802.816 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus rattus (black rat) / References: UniProt: P00770
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRMCPII HAS ALSO BEEN REFERRED TO AS GSP (GROUP SPECIFIC PROTEASE) IN OLDER LITERATURE.
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: 3.44 Å3/Da / Density % sol: 64.27 %
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
Conc.: 23 %sat / Common name: ammonium sulfate

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Data collection

Reflection
*PLUS

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Processing

SoftwareName: EREF / Classification: refinement
RefinementResolution: 1.9→5 Å
Details: RESIDUE 237 OF EACH CHAIN IS TRP. IN THE PAPER CITED AS REFERENCE 2 ABOVE RESIDUE 237 WAS IDENTIFIED AS THR BUT THIS WAS A TYPOGRAPHICAL ERROR IN THE PAPER.
RfactorNum. reflection
Rwork0.191 -
obs-28782
Refinement stepCycle: LAST / Resolution: 1.9→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3452 0 0 123 3575
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONo_bond_d0.016
X-RAY DIFFRACTIONo_bond_d_na
X-RAY DIFFRACTIONo_bond_d_prot
X-RAY DIFFRACTIONo_angle_d
X-RAY DIFFRACTIONo_angle_d_na
X-RAY DIFFRACTIONo_angle_d_prot
X-RAY DIFFRACTIONo_angle_deg2.7
X-RAY DIFFRACTIONo_angle_deg_na
X-RAY DIFFRACTIONo_angle_deg_prot
X-RAY DIFFRACTIONo_dihedral_angle_d
X-RAY DIFFRACTIONo_dihedral_angle_d_na
X-RAY DIFFRACTIONo_dihedral_angle_d_prot
X-RAY DIFFRACTIONo_improper_angle_d
X-RAY DIFFRACTIONo_improper_angle_d_na
X-RAY DIFFRACTIONo_improper_angle_d_prot
X-RAY DIFFRACTIONo_mcbond_it
X-RAY DIFFRACTIONo_mcangle_it
X-RAY DIFFRACTIONo_scbond_it
X-RAY DIFFRACTIONo_scangle_it
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 5 Å / Num. reflection obs: 28782 / Rfactor obs: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: o_angle_d

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