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- PDB-2o40: Crystal Structure of a Chemically Synthesized 203 Amino Acid 'Cov... -

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Basic information

Entry
Database: PDB / ID: 2o40
TitleCrystal Structure of a Chemically Synthesized 203 Amino Acid 'Covalent Dimer' HIV-1 Protease Molecule
Componentscovalent dimer HIV-1 protease
KeywordsHydrolase/Hydrolase inhibitor / beta-turn / Hydrolase-Hydrolase inhibitor complex
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis
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
N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide / Chem-2NC / Protease
Similarity search - Component
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsTorbeev, V.Y. / Kent, S.B.H.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2007
Title: Convergent chemical synthesis and crystal structure of a 203 amino acid "covalent dimer" HIV-1 protease enzyme molecule.
Authors: Torbeev, V.Y. / Kent, S.B.
History
DepositionDec 2, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 19, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Feb 27, 2013Group: Other
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: covalent dimer HIV-1 protease
A: N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6632
Polymers21,8921
Non-polymers7711
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.326, 58.306, 61.699
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 covalent dimer HIV-1 protease


Mass: 21891.650 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: total protein synthesis / References: UniProt: O38716*PLUS, HIV-1 retropepsin
#2: Chemical ChemComp-2NC / N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide / p2/NC


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 770.983 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H68N11O8
References: N-{(2S)-2-[(N-acetyl-L-threonyl-L-isoleucyl)amino]hexyl}-L-norleucyl-L-glutaminyl-N~5~-[amino(iminio)methyl]-L-ornithinamide
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE INHIBITOR HAS A REDUCED PEPTIDE BOND ISOSTERE [CH2-NH] IN PLACE OF THE SCISSILE AMIDE

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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: 2.04 Å3/Da / Density % sol: 39.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M citrate, 0.2M sodium phophate, 30% (w/v) ammonium sulfate, 10% (v/v) DMSO, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97932 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 22, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97932 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 22728 / Num. obs: 22342 / % possible obs: 98.3 % / Observed criterion σ(F): 1672 / Observed criterion σ(I): 1672 / Redundancy: 4.8 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 14.6
Reflection shellResolution: 1.651→1.694 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 2.67 / Num. unique all: 1583 / % possible all: 88.68

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPVRSION 8.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.65→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.923 / SU B: 4.116 / SU ML: 0.068 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.108 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23748 1163 5.2 %RANDOM
Rwork0.19106 ---
obs0.19335 21383 98.7 %-
all-21665 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.973 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2---0.15 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.65→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1543 0 54 57 1654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0221625
X-RAY DIFFRACTIONr_bond_other_d0.0040.021116
X-RAY DIFFRACTIONr_angle_refined_deg1.5991.9862200
X-RAY DIFFRACTIONr_angle_other_deg0.8932749
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2145207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.37624.91559
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44915294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.352159
X-RAY DIFFRACTIONr_chiral_restr0.1050.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021756
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02282
X-RAY DIFFRACTIONr_nbd_refined0.2050.2201
X-RAY DIFFRACTIONr_nbd_other0.1940.21063
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2779
X-RAY DIFFRACTIONr_nbtor_other0.0910.2902
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.237
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1880.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1670.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2970.23
X-RAY DIFFRACTIONr_mcbond_it1.1681.51060
X-RAY DIFFRACTIONr_mcbond_other0.3391.5437
X-RAY DIFFRACTIONr_mcangle_it1.81121674
X-RAY DIFFRACTIONr_scbond_it2.6263635
X-RAY DIFFRACTIONr_scangle_it4.0054.5526
LS refinement shellResolution: 1.651→1.694 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 61 -
Rwork0.241 1404 -
obs--88.68 %
Refinement TLS params.Method: refined / Origin x: 5.177 Å / Origin y: 1.1035 Å / Origin z: 18.1827 Å
111213212223313233
T-0.067 Å20.0002 Å20.0043 Å2--0.0994 Å20.0126 Å2---0.1013 Å2
L2.3868 °2-0.6434 °20.408 °2-1.5769 °20.3313 °2--1.1569 °2
S0.0006 Å °0.0774 Å °-0.0465 Å °0.0598 Å °0.0316 Å °-0.0219 Å °0.0234 Å °0.0854 Å °-0.0322 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 2031 - 203
2X-RAY DIFFRACTION1AB0 - 61 - 6

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