PDB Short entry for 2R8N HEADER HYDROLASE 11-SEP-07 2R8N TITLE STRUCTURAL ANALYSIS OF THE UNBOUND FORM OF HIV-1 SUBTYPE C PROTEASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: POL PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HIV-1 PROTEASE SUBTYPE C, UNP RESIDUES 1-99; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN IMMUNODEFICIENCY VIRUS 1; SOURCE 3 STRAIN: SUBTYPE C; SOURCE 4 GENE: POL; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)STAR PLYSS; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET23A KEYWDS HIV-1 SUBTYPE C, ASPARTYL PROTEASE, HYDROLASE, MULTIFUNCTIONAL KEYWDS 2 ENZYME, NUCLEOTIDYLTRANSFERASE, PROTEASE, RNA-DIRECTED DNA KEYWDS 3 POLYMERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.M.COMAN,A.H.ROBBINS,R.MCKENNA,B.M.DUNN REVDAT 7 20-OCT-21 2R8N 1 SEQADV REVDAT 6 28-JUL-21 2R8N 1 REMARK REVDAT 5 24-JUL-19 2R8N 1 REMARK REVDAT 4 25-OCT-17 2R8N 1 REMARK REVDAT 3 13-JUL-11 2R8N 1 VERSN REVDAT 2 24-FEB-09 2R8N 1 VERSN REVDAT 1 29-JUL-08 2R8N 0 JRNL AUTH R.M.COMAN,A.H.ROBBINS,M.M.GOODENOW,B.M.DUNN,R.MCKENNA JRNL TITL HIGH-RESOLUTION STRUCTURE OF UNBOUND HUMAN IMMUNODEFICIENCY JRNL TITL 2 VIRUS 1 SUBTYPE C PROTEASE: IMPLICATIONS OF FLAP DYNAMICS JRNL TITL 3 AND DRUG RESISTANCE. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 64 754 2008 JRNL REFN ISSN 0907-4449 JRNL PMID 18566511 JRNL DOI 10.1107/S090744490801278X REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 CROSS-VALIDATION METHOD : R-FREE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.141 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.178 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 1667 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 35611 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 754 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 166 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 ANGLE DISTANCES (A) : 0.030 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.030 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.076 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.040 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2R8N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-SEP-07. REMARK 100 THE DEPOSITION ID IS D_1000044562. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-FEB-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000, DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33850 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : 0.07600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.24 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.27300 REMARK 200 R SYM FOR SHELL (I) : 0.27300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30 MM CITRIC ACID, 1 M NACL, TRITONX REMARK 280 -100, PH 5.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.35400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 23.35550 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 23.35550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 25.17700 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 23.35550 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 23.35550 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 75.53100 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 23.35550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 23.35550 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 25.17700 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 23.35550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 23.35550 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 75.53100 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 50.35400 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: THE BIOLOGICAL UNIT IS A HOMODIMER. THERE IS ONE HALF OF THE REMARK 300 BIOLOGICAL UNIT IN THE ASYMMETRIC UNIT (CHAIN A). REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3720 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 302 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 303 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 304 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 436 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 8 NE - CZ - NH2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ARG A 41 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG A 57 CD - NE - CZ ANGL. DEV. = 9.5 DEGREES REMARK 500 ARG A 57 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 301 REMARK 999 REMARK 999 THE AUTHORS STATE THAT THE PR CLONE USED IN THIS REMARK 999 STUDY DOES NOT HARBOR A FREQUENT POLYMORPHISM REMARK 999 FOUND IN SUBTYPE C PRS:R41K. IT IS ONE OF THE REMARK 999 RESIDUES THAT APPEAR TO BE INVOLVED IN PRESERVING REMARK 999 OR AUGMENTING THE CATALYTIC EFFICIENCY OF THE REMARK 999 SUBTYPE C PR AND ENHANCING THE VIRAL FITNESS REMARK 999 WHEN COMPARED TO SUBTYPE B VIRUSES. DBREF 2R8N A 1 99 UNP Q8ALR4 Q8ALR4_9HIV1 1 99 SEQADV 2R8N LYS A 7 UNP Q8ALR4 GLN 7 ENGINEERED MUTATION SEQADV 2R8N ILE A 33 UNP Q8ALR4 LEU 33 ENGINEERED MUTATION SEQADV 2R8N ARG A 41 UNP Q8ALR4 LYS 41 SEE REMARK 999 SEQADV 2R8N ILE A 63 UNP Q8ALR4 LEU 63 ENGINEERED MUTATION SEQRES 1 A 99 PRO GLN ILE THR LEU TRP LYS ARG PRO LEU VAL SER ILE SEQRES 2 A 99 LYS VAL GLY GLY GLN ILE LYS GLU ALA LEU LEU ASP THR SEQRES 3 A 99 GLY ALA ASP ASP THR VAL ILE GLU GLU ILE ALA LEU PRO SEQRES 4 A 99 GLY ARG TRP LYS PRO LYS MET ILE GLY GLY ILE GLY GLY SEQRES 5 A 99 PHE ILE LYS VAL ARG GLN TYR ASP GLN ILE ILE ILE GLU SEQRES 6 A 99 ILE CYS GLY LYS LYS ALA ILE GLY THR VAL LEU VAL GLY SEQRES 7 A 99 PRO THR PRO VAL ASN ILE ILE GLY ARG ASN MET LEU THR SEQRES 8 A 99 GLN LEU GLY CYS THR LEU ASN PHE HET GOL A 300 6 HET GOL A 301 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 2(C3 H8 O3) FORMUL 4 HOH *166(H2 O) HELIX 1 1 GLY A 86 LEU A 93 1 8 SHEET 1 A 8 LYS A 43 GLY A 48 0 SHEET 2 A 8 PHE A 53 ILE A 66 -1 O GLN A 58 N LYS A 43 SHEET 3 A 8 LYS A 69 VAL A 77 -1 O VAL A 77 N ARG A 57 SHEET 4 A 8 VAL A 32 ILE A 33 1 N ILE A 33 O LEU A 76 SHEET 5 A 8 ILE A 84 ILE A 85 -1 O ILE A 84 N VAL A 32 SHEET 6 A 8 GLN A 18 LEU A 24 1 N LEU A 23 O ILE A 85 SHEET 7 A 8 LEU A 10 VAL A 15 -1 N ILE A 13 O LYS A 20 SHEET 8 A 8 PHE A 53 ILE A 66 -1 O GLU A 65 N LYS A 14 SITE 1 AC1 5 GLY A 16 PRO A 39 ILE A 62 ILE A 63 SITE 2 AC1 5 HOH A 313 SITE 1 AC2 6 LYS A 14 GLY A 17 ILE A 63 ILE A 64 SITE 2 AC2 6 GLU A 65 HOH A 384 CRYST1 46.711 46.711 100.708 90.00 90.00 90.00 P 41 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.021408 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021408 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009930 0.00000