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- PDB-1mvp: STRUCTURAL STUDIES OF THE RETROVIRAL PROTEINASE FROM AVIAN MYELOB... -

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Basic information

Entry
Database: PDB / ID: 1mvp
TitleSTRUCTURAL STUDIES OF THE RETROVIRAL PROTEINASE FROM AVIAN MYELOBLASTOSIS ASSOCIATED VIRUS
ComponentsMYELOBLASTOSIS ASSOCIATED VIRAL PROTEASE
KeywordsHYDROLASE(ASPARTIC PROTEINASE)
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / aspartic-type endopeptidase activity
Similarity search - Function
Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / 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 speciesAvian myeloblastosis-associated virus
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsOhlendorf, D.H. / Foundling, S.I. / Salemme, F.R.
CitationJournal: Proteins / Year: 1992
Title: Structural studies of the retroviral proteinase from avian myeloblastosis associated virus.
Authors: Ohlendorf, D.H. / Foundling, S.I. / Wendoloski, J.J. / Sedlacek, J. / Strop, P. / Salemme, F.R.
History
DepositionSep 7, 1990Processing site: BNL
Revision 1.0Jan 15, 1992Provider: 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 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MYELOBLASTOSIS ASSOCIATED VIRAL PROTEASE
B: MYELOBLASTOSIS ASSOCIATED VIRAL PROTEASE


Theoretical massNumber of molelcules
Total (without water)27,2242
Polymers27,2242
Non-polymers00
Water2,396133
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2890 Å2
ΔGint-7 kcal/mol
Surface area11990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.920, 88.920, 78.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11B-142-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.06347, 0.57288, -0.81718), (0.57291, -0.64955, -0.49986), (-0.81716, -0.4999, -0.28698)
Vector: 37.94168, 86.01433, 103.7883)
DetailsTHE TRANSFORMATION PRESENTED IN THE *MTRIX1* RECORDS BELOW WILL YIELD THE COORDINATES OF CHAIN *B* WHEN APPLIED TO THE COORDINATES OF CHAIN *A*.

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Components

#1: Protein MYELOBLASTOSIS ASSOCIATED VIRAL PROTEASE


Mass: 13611.836 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Avian myeloblastosis-associated virus / Genus: Alpharetrovirus
References: UniProt: P26315, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 133 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.74 %
Crystal grow
*PLUS
pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 mMMAV proteinase1drop
20.05 Mcitrate1dropcan be replaced with phosphate
38-12 %satammonium sulfate1drop
45 %(v/v)dimethyl formamide1drop
50.05 %beta-mercaptoethanol1drop
60.05 Mcitrate1reservoircan be replaced with phosphate
78-12 %satammonium sulfate1reservoir
85 %(v/v)dimethyl formamide1reservoir
90.05 %beta-mercaptoethanol1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 16968 / Num. measured all: 196542

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 2.2→5 Å
Details: THE SG ATOMS OF CYS A 113 AND CYS B 113 HAVE BEEN REFINED IN TWO ALTERNATE POSITIONS WITH AN OCCUPANCY OF 0.5 FOR EACH POSITION.
RfactorNum. reflection
obs0.172 17283
Refinement stepCycle: LAST / Resolution: 2.2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1741 0 0 133 1874
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0180.03
X-RAY DIFFRACTIONp_angle_d0.0340.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0340.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.8281
X-RAY DIFFRACTIONp_mcangle_it1.4912
X-RAY DIFFRACTIONp_scbond_it1.5731.5
X-RAY DIFFRACTIONp_scangle_it2.6273
X-RAY DIFFRACTIONp_plane_restr0.0150.03
X-RAY DIFFRACTIONp_chiral_restr0.2060.3
X-RAY DIFFRACTIONp_singtor_nbd0.1990.5
X-RAY DIFFRACTIONp_multtor_nbd0.210.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.190.5
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
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.172
Solvent computation
*PLUS
Displacement parameters
*PLUS

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