HEADER VIRAL PROTEIN 28-MAY-02 1LVB TITLE CATALYTICALLY INACTIVE TOBACCO ETCH VIRUS PROTEASE COMPLEXED WITH TITLE 2 SUBSTRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA); COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE; COMPND 8 CHAIN: C, D; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TOBACCO ETCH VIRUS; SOURCE 3 ORGANISM_TAXID: 12227; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PRK529; SOURCE 9 MOL_ID: 2 KEYWDS BETA BARREL, PROTEIN-PEPTIDE COMPLEX, CHYMOTRYPSIN-LIKE CYSTEIN KEYWDS 2 PROTEASE, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.PHAN,A.ZDANOV,A.G.EVDOKIMOV,J.E.TROPEA,H.K.PETERS III,R.B.KAPUST, AUTHOR 2 M.LI,A.WLODAWER,D.S.WAUGH REVDAT 5 27-OCT-21 1LVB 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 1LVB 1 VERSN REVDAT 3 24-FEB-09 1LVB 1 VERSN REVDAT 2 09-MAR-04 1LVB 1 JRNL REVDAT 1 27-NOV-02 1LVB 0 JRNL AUTH J.PHAN,A.ZDANOV,A.G.EVDOKIMOV,J.E.TROPEA,H.K.PETERS III, JRNL AUTH 2 R.B.KAPUST,M.LI,A.WLODAWER,D.S.WAUGH JRNL TITL STRUCTURAL BASIS FOR THE SUBSTRATE SPECIFICITY OF TOBACCO JRNL TITL 2 ETCH VIRUS PROTEASE. JRNL REF J.BIOL.CHEM. V. 277 50564 2002 JRNL REFN ISSN 0021-9258 JRNL PMID 12377789 JRNL DOI 10.1074/JBC.M207224200 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.69 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 272840.060 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 38759 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.236 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2411 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 83.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6703 REMARK 3 BIN R VALUE (WORKING SET) : 0.3940 REMARK 3 BIN FREE R VALUE : 0.4350 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 400 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.022 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3590 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 181 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.47000 REMARK 3 B22 (A**2) : -7.47000 REMARK 3 B33 (A**2) : 14.93000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.39 REMARK 3 ESD FROM SIGMAA (A) : 0.43 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.42 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.47 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.015 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.800 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.050 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.580 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.180 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.150 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 65.61 REMARK 3 REMARK 3 NCS MODEL : CONSTR REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : TOPP REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1LVB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAY-02. REMARK 100 THE DEPOSITION ID IS D_1000016310. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-DEC-01 REMARK 200 TEMPERATURE (KELVIN) : 112 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9755,0.9794,0.9796 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38759 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 6000, TRIS, PH 8, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z 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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 62.65850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 62.65850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 63.96650 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 62.65850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 62.65850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 63.96650 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 62.65850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 62.65850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 63.96650 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 62.65850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 62.65850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 63.96650 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 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4, 5 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 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: 1980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C 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 REMARK 350 BIOMOLECULE: 2 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: 1980 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10550 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -9.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D 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 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXADECAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 26620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 73700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -135.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, B, D 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 -1.000000 0.000000 0.000000 125.31700 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 125.31700 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 0.000000 -1.000000 0.000000 125.31700 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 125.31700 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, B, D 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 -1.000000 0.000000 0.000000 125.31700 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 125.31700 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 5 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, B, D 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 SER A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 GLY A 1 REMARK 465 GLU A 2 REMARK 465 SER A 3 REMARK 465 LEU A 4 REMARK 465 PHE A 5 REMARK 465 LYS A 6 REMARK 465 GLY A 7 REMARK 465 GLU A 222 REMARK 465 GLU A 223 REMARK 465 PRO A 224 REMARK 465 PHE A 225 REMARK 465 GLN A 226 REMARK 465 PRO A 227 REMARK 465 VAL A 228 REMARK 465 LYS A 229 REMARK 465 GLU A 230 REMARK 465 ALA A 231 REMARK 465 THR A 232 REMARK 465 GLN A 233 REMARK 465 LEU A 234 REMARK 465 MET A 235 REMARK 465 ASN A 236 REMARK 465 SER B -7 REMARK 465 HIS B -6 REMARK 465 HIS B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 HIS B -1 REMARK 465 GLY B 1 REMARK 465 GLU B 2 REMARK 465 SER B 3 REMARK 465 LEU B 4 REMARK 465 PHE B 5 REMARK 465 LYS B 6 REMARK 465 GLY B 7 REMARK 465 GLU B 222 REMARK 465 GLU B 223 REMARK 465 PRO B 224 REMARK 465 PHE B 225 REMARK 465 GLN B 226 REMARK 465 PRO B 227 REMARK 465 VAL B 228 REMARK 465 LYS B 229 REMARK 465 GLU B 230 REMARK 465 ALA B 231 REMARK 465 THR B 232 REMARK 465 GLN B 233 REMARK 465 LEU B 234 REMARK 465 MET B 235 REMARK 465 ASN B 236 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 67 CG CD CE NZ REMARK 480 LYS A 89 CG CD CE NZ REMARK 480 ASP A 136 OD1 OD2 REMARK 480 LYS A 147 CG CD CE NZ REMARK 480 LYS A 184 CG CD CE NZ REMARK 480 GLN A 193 CD OE1 NE2 REMARK 480 ASP A 207 CB CG OD1 OD2 REMARK 480 GLU B 24 CD OE1 OE2 REMARK 480 LYS B 67 CG CD CE NZ REMARK 480 LYS B 89 CG CD CE NZ REMARK 480 ASP B 136 OD1 OD2 REMARK 480 LYS B 141 CG CD CE NZ REMARK 480 GLN B 145 CG CD OE1 NE2 REMARK 480 LYS B 147 CD CE NZ REMARK 480 GLN B 193 CD OE1 NE2 REMARK 480 GLU B 194 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 SG CYS B 130 SG CYS B 130 7555 1.43 REMARK 500 REMARK 500 REMARK: NULL 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 LEU A 155 CA - CB - CG ANGL. DEV. = -14.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 HIS A 46 3.31 -68.46 REMARK 500 ASN A 51 74.13 -154.49 REMARK 500 ASN A 52 54.52 -161.37 REMARK 500 PRO A 88 151.46 -49.11 REMARK 500 SER A 135 -115.79 40.16 REMARK 500 SER A 168 -57.46 -126.36 REMARK 500 GLN A 197 74.95 -118.35 REMARK 500 GLN C 307 47.55 -89.02 REMARK 500 HIS B 46 4.34 -66.23 REMARK 500 PHE B 48 44.01 -100.45 REMARK 500 ASN B 51 77.14 -158.02 REMARK 500 ASN B 52 50.79 -164.95 REMARK 500 PRO B 88 152.59 -48.91 REMARK 500 PRO B 95 -172.25 -69.24 REMARK 500 GLN B 96 42.54 -142.33 REMARK 500 SER B 135 -110.02 44.53 REMARK 500 SER B 168 -57.47 -130.59 REMARK 500 ASN B 205 57.72 -140.82 REMARK 500 GLN D 307 46.18 -87.78 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LVM RELATED DB: PDB REMARK 900 CATALYTICALLY ACTIVE TOBACCO ETCH VIRUS PROTEASE COMPLEXED WITH REMARK 900 PRODUCT DBREF 1LVB A 1 236 UNP P04517 POLG_TEV 2038 2273 DBREF 1LVB C 301 310 UNP P04517 POLG_TEV 2785 2794 DBREF 1LVB B 1 236 UNP P04517 POLG_TEV 2038 2273 DBREF 1LVB D 301 310 UNP P04517 POLG_TEV 2785 2794 SEQADV 1LVB SER A -7 UNP P04517 EXPRESSION TAG SEQADV 1LVB HIS A -6 UNP P04517 EXPRESSION TAG SEQADV 1LVB HIS A -5 UNP P04517 EXPRESSION TAG SEQADV 1LVB HIS A -4 UNP P04517 EXPRESSION TAG SEQADV 1LVB HIS A -3 UNP P04517 EXPRESSION TAG SEQADV 1LVB HIS A -2 UNP P04517 EXPRESSION TAG SEQADV 1LVB HIS A -1 UNP P04517 EXPRESSION TAG SEQADV 1LVB MSE A 82 UNP P04517 MET 2119 MODIFIED RESIDUE SEQADV 1LVB MSE A 87 UNP P04517 MET 2124 MODIFIED RESIDUE SEQADV 1LVB MSE A 121 UNP P04517 MET 2158 MODIFIED RESIDUE SEQADV 1LVB MSE A 124 UNP P04517 MET 2161 MODIFIED RESIDUE SEQADV 1LVB ALA A 151 UNP P04517 CYS 2188 ENGINEERED MUTATION SEQADV 1LVB MSE A 187 UNP P04517 MET 2224 MODIFIED RESIDUE SEQADV 1LVB MSE A 218 UNP P04517 MET 2255 MODIFIED RESIDUE SEQADV 1LVB SER B -7 UNP P04517 EXPRESSION TAG SEQADV 1LVB HIS B -6 UNP P04517 EXPRESSION TAG SEQADV 1LVB HIS B -5 UNP P04517 EXPRESSION TAG SEQADV 1LVB HIS B -4 UNP P04517 EXPRESSION TAG SEQADV 1LVB HIS B -3 UNP P04517 EXPRESSION TAG SEQADV 1LVB HIS B -2 UNP P04517 EXPRESSION TAG SEQADV 1LVB HIS B -1 UNP P04517 EXPRESSION TAG SEQADV 1LVB MSE B 82 UNP P04517 MET 2119 MODIFIED RESIDUE SEQADV 1LVB MSE B 87 UNP P04517 MET 2124 MODIFIED RESIDUE SEQADV 1LVB MSE B 121 UNP P04517 MET 2158 MODIFIED RESIDUE SEQADV 1LVB MSE B 124 UNP P04517 MET 2161 MODIFIED RESIDUE SEQADV 1LVB ALA B 151 UNP P04517 CYS 2188 ENGINEERED MUTATION SEQADV 1LVB MSE B 187 UNP P04517 MET 2224 MODIFIED RESIDUE SEQADV 1LVB MSE B 218 UNP P04517 MET 2255 MODIFIED RESIDUE SEQRES 1 A 243 SER HIS HIS HIS HIS HIS HIS GLY GLU SER LEU PHE LYS SEQRES 2 A 243 GLY PRO ARG ASP TYR ASN PRO ILE SER SER THR ILE CYS SEQRES 3 A 243 HIS LEU THR ASN GLU SER ASP GLY HIS THR THR SER LEU SEQRES 4 A 243 TYR GLY ILE GLY PHE GLY PRO PHE ILE ILE THR ASN LYS SEQRES 5 A 243 HIS LEU PHE ARG ARG ASN ASN GLY THR LEU LEU VAL GLN SEQRES 6 A 243 SER LEU HIS GLY VAL PHE LYS VAL LYS ASN THR THR THR SEQRES 7 A 243 LEU GLN GLN HIS LEU ILE ASP GLY ARG ASP MSE ILE ILE SEQRES 8 A 243 ILE ARG MSE PRO LYS ASP PHE PRO PRO PHE PRO GLN LYS SEQRES 9 A 243 LEU LYS PHE ARG GLU PRO GLN ARG GLU GLU ARG ILE CYS SEQRES 10 A 243 LEU VAL THR THR ASN PHE GLN THR LYS SER MSE SER SER SEQRES 11 A 243 MSE VAL SER ASP THR SER CYS THR PHE PRO SER SER ASP SEQRES 12 A 243 GLY ILE PHE TRP LYS HIS TRP ILE GLN THR LYS ASP GLY SEQRES 13 A 243 GLN ALA GLY SER PRO LEU VAL SER THR ARG ASP GLY PHE SEQRES 14 A 243 ILE VAL GLY ILE HIS SER ALA SER ASN PHE THR ASN THR SEQRES 15 A 243 ASN ASN TYR PHE THR SER VAL PRO LYS ASN PHE MSE GLU SEQRES 16 A 243 LEU LEU THR ASN GLN GLU ALA GLN GLN TRP VAL SER GLY SEQRES 17 A 243 TRP ARG LEU ASN ALA ASP SER VAL LEU TRP GLY GLY HIS SEQRES 18 A 243 LYS VAL PHE MSE SER LYS PRO GLU GLU PRO PHE GLN PRO SEQRES 19 A 243 VAL LYS GLU ALA THR GLN LEU MET ASN SEQRES 1 C 10 THR GLU ASN LEU TYR PHE GLN SER GLY THR SEQRES 1 B 243 SER HIS HIS HIS HIS HIS HIS GLY GLU SER LEU PHE LYS SEQRES 2 B 243 GLY PRO ARG ASP TYR ASN PRO ILE SER SER THR ILE CYS SEQRES 3 B 243 HIS LEU THR ASN GLU SER ASP GLY HIS THR THR SER LEU SEQRES 4 B 243 TYR GLY ILE GLY PHE GLY PRO PHE ILE ILE THR ASN LYS SEQRES 5 B 243 HIS LEU PHE ARG ARG ASN ASN GLY THR LEU LEU VAL GLN SEQRES 6 B 243 SER LEU HIS GLY VAL PHE LYS VAL LYS ASN THR THR THR SEQRES 7 B 243 LEU GLN GLN HIS LEU ILE ASP GLY ARG ASP MSE ILE ILE SEQRES 8 B 243 ILE ARG MSE PRO LYS ASP PHE PRO PRO PHE PRO GLN LYS SEQRES 9 B 243 LEU LYS PHE ARG GLU PRO GLN ARG GLU GLU ARG ILE CYS SEQRES 10 B 243 LEU VAL THR THR ASN PHE GLN THR LYS SER MSE SER SER SEQRES 11 B 243 MSE VAL SER ASP THR SER CYS THR PHE PRO SER SER ASP SEQRES 12 B 243 GLY ILE PHE TRP LYS HIS TRP ILE GLN THR LYS ASP GLY SEQRES 13 B 243 GLN ALA GLY SER PRO LEU VAL SER THR ARG ASP GLY PHE SEQRES 14 B 243 ILE VAL GLY ILE HIS SER ALA SER ASN PHE THR ASN THR SEQRES 15 B 243 ASN ASN TYR PHE THR SER VAL PRO LYS ASN PHE MSE GLU SEQRES 16 B 243 LEU LEU THR ASN GLN GLU ALA GLN GLN TRP VAL SER GLY SEQRES 17 B 243 TRP ARG LEU ASN ALA ASP SER VAL LEU TRP GLY GLY HIS SEQRES 18 B 243 LYS VAL PHE MSE SER LYS PRO GLU GLU PRO PHE GLN PRO SEQRES 19 B 243 VAL LYS GLU ALA THR GLN LEU MET ASN SEQRES 1 D 10 THR GLU ASN LEU TYR PHE GLN SER GLY THR MODRES 1LVB MSE A 82 MET SELENOMETHIONINE MODRES 1LVB MSE A 87 MET SELENOMETHIONINE MODRES 1LVB MSE A 121 MET SELENOMETHIONINE MODRES 1LVB MSE A 124 MET SELENOMETHIONINE MODRES 1LVB MSE A 187 MET SELENOMETHIONINE MODRES 1LVB MSE A 218 MET SELENOMETHIONINE MODRES 1LVB MSE B 82 MET SELENOMETHIONINE MODRES 1LVB MSE B 87 MET SELENOMETHIONINE MODRES 1LVB MSE B 121 MET SELENOMETHIONINE MODRES 1LVB MSE B 124 MET SELENOMETHIONINE MODRES 1LVB MSE B 187 MET SELENOMETHIONINE MODRES 1LVB MSE B 218 MET SELENOMETHIONINE HET MSE A 82 8 HET MSE A 87 8 HET MSE A 121 8 HET MSE A 124 8 HET MSE A 187 8 HET MSE A 218 8 HET MSE B 82 8 HET MSE B 87 8 HET MSE B 121 8 HET MSE B 124 8 HET MSE B 187 8 HET MSE B 218 8 HET GOL A 401 6 HET GOL B 402 6 HETNAM MSE SELENOMETHIONINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 MSE 12(C5 H11 N O2 SE) FORMUL 5 GOL 2(C3 H8 O3) FORMUL 7 HOH *181(H2 O) HELIX 1 1 TYR A 11 SER A 16 1 6 HELIX 2 2 ASN A 44 ARG A 49 5 6 HELIX 3 3 ASN A 68 LEU A 72 5 5 HELIX 4 4 ASN A 185 ASN A 192 1 8 HELIX 5 5 GLN A 193 GLN A 196 5 4 HELIX 6 6 TYR B 11 SER B 16 1 6 HELIX 7 7 ASN B 44 ARG B 49 5 6 HELIX 8 8 ASN B 68 LEU B 72 5 5 HELIX 9 9 ASN B 185 ASN B 192 1 8 HELIX 10 10 GLN B 193 GLN B 196 5 4 SHEET 1 A 7 GLY A 62 VAL A 66 0 SHEET 2 A 7 GLY A 53 SER A 59 -1 O LEU A 55 N VAL A 66 SHEET 3 A 7 ILE A 18 SER A 25 -1 N HIS A 20 O GLN A 58 SHEET 4 A 7 HIS A 28 PHE A 37 -1 O HIS A 28 N SER A 25 SHEET 5 A 7 PHE A 40 THR A 43 -1 O PHE A 40 N PHE A 37 SHEET 6 A 7 ILE A 83 ARG A 86 -1 N ILE A 83 O THR A 43 SHEET 7 A 7 GLN A 73 LEU A 76 -1 O GLN A 73 N ARG A 86 SHEET 1 B24 PHE A 132 SER A 134 0 SHEET 2 B24 PHE A 139 HIS A 142 -1 O PHE A 139 N SER A 134 SHEET 3 B24 ASN A 177 SER A 181 -1 O ASN A 177 N HIS A 142 SHEET 4 B24 ILE A 163 ASN A 171 -1 O ILE A 166 N THR A 180 SHEET 5 B24 LEU C 304 PHE C 306 -1 N TYR C 305 O SER A 170 SHEET 6 B24 HIS A 214 PHE A 217 1 O LYS A 215 N LEU C 304 SHEET 7 B24 SER A 208 TRP A 211 -1 O VAL A 209 N VAL A 216 SHEET 8 B24 HIS A 214 PHE A 217 -1 N HIS A 214 O TRP A 211 SHEET 9 B24 LEU C 304 PHE C 306 1 O LEU C 304 N PHE A 217 SHEET 10 B24 ILE A 163 ASN A 171 -1 O SER A 170 N TYR C 305 SHEET 11 B24 PRO A 154 SER A 157 -1 N LEU A 155 O GLY A 165 SHEET 12 B24 ILE A 109 PHE A 116 -1 O CYS A 110 N VAL A 156 SHEET 13 B24 SER A 120 VAL A 125 -1 O SER A 122 N ASN A 115 SHEET 14 B24 SER B 120 VAL B 125 -1 O MSE B 121 N SER A 123 SHEET 15 B24 ARG B 108 PHE B 116 -1 N THR B 113 O MSE B 124 SHEET 16 B24 SER B 129 PRO B 133 -1 O SER B 129 N ILE B 109 SHEET 17 B24 PHE B 139 HIS B 142 -1 N LYS B 141 O PHE B 132 SHEET 18 B24 ASN B 177 SER B 181 -1 O ASN B 177 N HIS B 142 SHEET 19 B24 ILE B 163 ASN B 171 -1 O ILE B 166 N THR B 180 SHEET 20 B24 PRO B 154 SER B 157 -1 O LEU B 155 N VAL B 164 SHEET 21 B24 ILE B 163 ASN B 171 -1 N VAL B 164 O LEU B 155 SHEET 22 B24 LEU D 304 PHE D 306 -1 N TYR D 305 O SER B 170 SHEET 23 B24 HIS B 214 PHE B 217 1 O LYS B 215 N LEU D 304 SHEET 24 B24 SER B 208 TRP B 211 -1 O VAL B 209 N VAL B 216 SHEET 1 C 7 GLY B 62 VAL B 66 0 SHEET 2 C 7 GLY B 53 SER B 59 -1 O LEU B 55 N VAL B 66 SHEET 3 C 7 ILE B 18 SER B 25 -1 N HIS B 20 O GLN B 58 SHEET 4 C 7 HIS B 28 PHE B 37 -1 O HIS B 28 N SER B 25 SHEET 5 C 7 PHE B 40 THR B 43 -1 O PHE B 40 N PHE B 37 SHEET 6 C 7 ILE B 83 ARG B 86 -1 N ILE B 83 O THR B 43 SHEET 7 C 7 GLN B 73 LEU B 76 -1 O GLN B 73 N ARG B 86 SSBOND 1 CYS A 130 CYS A 130 1555 2665 2.06 LINK C ASP A 81 N MSE A 82 1555 1555 1.33 LINK C MSE A 82 N ILE A 83 1555 1555 1.33 LINK C ARG A 86 N MSE A 87 1555 1555 1.33 LINK C MSE A 87 N PRO A 88 1555 1555 1.34 LINK C SER A 120 N MSE A 121 1555 1555 1.32 LINK C MSE A 121 N SER A 122 1555 1555 1.33 LINK C SER A 123 N MSE A 124 1555 1555 1.33 LINK C MSE A 124 N VAL A 125 1555 1555 1.33 LINK C PHE A 186 N MSE A 187 1555 1555 1.33 LINK C MSE A 187 N GLU A 188 1555 1555 1.33 LINK C PHE A 217 N MSE A 218 1555 1555 1.33 LINK C MSE A 218 N SER A 219 1555 1555 1.33 LINK C ASP B 81 N MSE B 82 1555 1555 1.33 LINK C MSE B 82 N ILE B 83 1555 1555 1.33 LINK C ARG B 86 N MSE B 87 1555 1555 1.33 LINK C MSE B 87 N PRO B 88 1555 1555 1.35 LINK C SER B 120 N MSE B 121 1555 1555 1.32 LINK C MSE B 121 N SER B 122 1555 1555 1.33 LINK C SER B 123 N MSE B 124 1555 1555 1.33 LINK C MSE B 124 N VAL B 125 1555 1555 1.32 LINK C PHE B 186 N MSE B 187 1555 1555 1.33 LINK C MSE B 187 N GLU B 188 1555 1555 1.33 LINK C PHE B 217 N MSE B 218 1555 1555 1.33 LINK C MSE B 218 N SER B 219 1555 1555 1.33 SITE 1 AC1 8 ARG A 9 ASP A 10 TYR A 11 ASN A 12 SITE 2 AC1 8 SER A 15 SER B 120 MSE B 121 HOH B 460 SITE 1 AC2 9 SER A 120 MSE A 121 ARG B 9 ASP B 10 SITE 2 AC2 9 TYR B 11 ASN B 12 SER B 15 SER B 123 SITE 3 AC2 9 HOH B 408 CRYST1 125.317 125.317 127.933 90.00 90.00 90.00 P 42 21 2 16 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 0.007980 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007980 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007817 0.00000