HEADER VIRAL PROTEIN 28-MAY-02 1LVM TITLE CATALYTICALLY ACTIVE TOBACCO ETCH VIRUS PROTEASE COMPLEXED WITH TITLE 2 PRODUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA); COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 1-221; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASE; COMPND 9 CHAIN: C, D; COMPND 10 FRAGMENT: RESIDUES 302-310; COMPND 11 ENGINEERED: YES; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA); COMPND 14 CHAIN: E; COMPND 15 FRAGMENT: RESIDUES 230-236; COMPND 16 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TOBACCO ETCH VIRUS; SOURCE 3 ORGANISM_TAXID: 12227; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: PRK529; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: TOBACCO ETCH VIRUS; SOURCE 11 ORGANISM_TAXID: 12227; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 EXPRESSION_SYSTEM_STRAIN: PRK529; SOURCE 15 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 16 EXPRESSION_SYSTEM_PLASMID: BL21(DE3); SOURCE 17 MOL_ID: 3; SOURCE 18 ORGANISM_SCIENTIFIC: TOBACCO ETCH VIRUS; SOURCE 19 ORGANISM_TAXID: 12227; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 21 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 22 EXPRESSION_SYSTEM_STRAIN: PRK529; SOURCE 23 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 24 EXPRESSION_SYSTEM_PLASMID: BL21(DE3) KEYWDS BETA BARREL, CHYMOTRYPSIN-TYPE CYSTEIN PROTEASE, ENZYME-PEPTIDE KEYWDS 2 COMPLEX, 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 30-OCT-24 1LVM 1 REMARK REVDAT 4 27-OCT-21 1LVM 1 REMARK SEQADV LINK REVDAT 3 24-FEB-09 1LVM 1 VERSN REVDAT 2 09-MAR-04 1LVM 1 JRNL REVDAT 1 27-NOV-02 1LVM 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. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 140622.420 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 48452 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) : 0.171 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 4885 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.00 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 6658 REMARK 3 BIN R VALUE (WORKING SET) : 0.2430 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 759 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.011 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3750 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 574 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.28000 REMARK 3 B22 (A**2) : -1.28000 REMARK 3 B33 (A**2) : 2.56000 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) : 0.18 REMARK 3 ESD FROM SIGMAA (A) : 0.17 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) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.21 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.020 REMARK 3 BOND ANGLES (DEGREES) : 2.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.310 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) : 11.750; 3.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 11.560; 4.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 16.280; 4.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 15.910; 4.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 54.52 REMARK 3 REMARK 3 NCS MODEL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1LVM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JUN-02. REMARK 100 THE DEPOSITION ID IS D_1000016317. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JAN-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48452 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.0 REMARK 200 DATA REDUNDANCY : 6.200 REMARK 200 R MERGE (I) : 0.05800 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) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1LVB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, MAGNESIUM CHLORIDE, REMARK 280 TRIS-HCL, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 91.58350 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 37.75250 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 37.75250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 137.37525 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 37.75250 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 37.75250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 45.79175 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 37.75250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 37.75250 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 137.37525 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 37.75250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 37.75250 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 45.79175 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 91.58350 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12080 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, E 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: 1610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10670 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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: PENTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 GLY B -8 REMARK 465 HIS 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 C 308 REMARK 465 GLY C 309 REMARK 465 THR C 310 REMARK 465 SER D 308 REMARK 465 GLY D 309 REMARK 465 THR D 310 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 2 CG CD OE1 OE2 REMARK 470 THR A 118 OG1 CG2 REMARK 470 LYS A 119 CG CD CE NZ REMARK 470 SER A 120 OG REMARK 470 ASN A 205 CG OD1 ND2 REMARK 470 ASN B 205 CG OD1 ND2 REMARK 470 ASN E 236 CG OD1 ND2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 446 O HOH B 222 2.02 REMARK 500 CB THR A 113 O HOH A 405 2.11 REMARK 500 O HOH A 329 O HOH A 542 2.16 REMARK 500 O SER A 123 O HOH A 446 2.16 REMARK 500 O HOH B 360 O HOH B 402 2.19 REMARK 500 O HOH A 265 O HOH A 270 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLY A -8 N GLY A -8 CA 0.095 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 72 CA - CB - CG ANGL. DEV. = 14.1 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 LEU A 32 -176.29 -171.92 REMARK 500 PHE A 48 30.75 -97.29 REMARK 500 ASN A 51 78.62 -150.21 REMARK 500 ASN A 52 35.66 -162.12 REMARK 500 SER A 135 -129.58 72.29 REMARK 500 ASP B 26 71.93 32.63 REMARK 500 LEU B 32 -169.88 -168.65 REMARK 500 PHE B 48 41.34 -103.79 REMARK 500 ASN B 52 71.55 -170.20 REMARK 500 GLN B 117 -145.49 -92.30 REMARK 500 SER B 135 -113.52 45.93 REMARK 500 SER B 168 -37.39 -131.35 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 ACE C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACE D 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1LVB RELATED DB: PDB REMARK 900 CATALYTICALLY INACTIVE TOBACCO ETCH VIRUS PROTEASE COMPLEXED WITH REMARK 900 SUBSTRATE REMARK 999 REMARK 999 SEQUENCE AUTHOR STATES RESIDUES 308-310 ARE NOT IN THE CRYSTAL REMARK 999 OF CHAINS C AND D AND RESIDUES 309-310 ARE NOT IN THE PEPTIDE REMARK 999 SEQUENCE FOR THIS MUTANT. RESIDUE GLY 308 WAS CLEAVED OFF BY THE REMARK 999 ENZYME AND NOT PRESENT IN THE CRYSTAL. DBREF 1LVM A 1 221 UNP P04517 POLG_TEV 2038 2258 DBREF 1LVM B 1 221 UNP P04517 POLG_TEV 2038 2258 DBREF 1LVM C 302 310 UNP P04517 POLG_TEV 2786 2794 DBREF 1LVM D 302 310 UNP P04517 POLG_TEV 2786 2794 DBREF 1LVM E 230 236 UNP P04517 POLG_TEV 2267 2273 SEQADV 1LVM GLY A -8 UNP P04517 EXPRESSION TAG SEQADV 1LVM HIS A -7 UNP P04517 EXPRESSION TAG SEQADV 1LVM HIS A -6 UNP P04517 EXPRESSION TAG SEQADV 1LVM HIS A -5 UNP P04517 EXPRESSION TAG SEQADV 1LVM HIS A -4 UNP P04517 EXPRESSION TAG SEQADV 1LVM HIS A -3 UNP P04517 EXPRESSION TAG SEQADV 1LVM HIS A -2 UNP P04517 EXPRESSION TAG SEQADV 1LVM HIS A -1 UNP P04517 EXPRESSION TAG SEQADV 1LVM ASP A 219 UNP P04517 SER 2256 ENGINEERED MUTATION SEQADV 1LVM GLY B -8 UNP P04517 EXPRESSION TAG SEQADV 1LVM HIS B -7 UNP P04517 EXPRESSION TAG SEQADV 1LVM HIS B -6 UNP P04517 EXPRESSION TAG SEQADV 1LVM HIS B -5 UNP P04517 EXPRESSION TAG SEQADV 1LVM HIS B -4 UNP P04517 EXPRESSION TAG SEQADV 1LVM HIS B -3 UNP P04517 EXPRESSION TAG SEQADV 1LVM HIS B -2 UNP P04517 EXPRESSION TAG SEQADV 1LVM HIS B -1 UNP P04517 EXPRESSION TAG SEQADV 1LVM ASP B 219 UNP P04517 SER 2256 ENGINEERED MUTATION SEQRES 1 A 229 GLY HIS HIS HIS HIS HIS HIS HIS GLY GLU SER LEU PHE SEQRES 2 A 229 LYS GLY PRO ARG ASP TYR ASN PRO ILE SER SER THR ILE SEQRES 3 A 229 CYS HIS LEU THR ASN GLU SER ASP GLY HIS THR THR SER SEQRES 4 A 229 LEU TYR GLY ILE GLY PHE GLY PRO PHE ILE ILE THR ASN SEQRES 5 A 229 LYS HIS LEU PHE ARG ARG ASN ASN GLY THR LEU LEU VAL SEQRES 6 A 229 GLN SER LEU HIS GLY VAL PHE LYS VAL LYS ASN THR THR SEQRES 7 A 229 THR LEU GLN GLN HIS LEU ILE ASP GLY ARG ASP MET ILE SEQRES 8 A 229 ILE ILE ARG MET PRO LYS ASP PHE PRO PRO PHE PRO GLN SEQRES 9 A 229 LYS LEU LYS PHE ARG GLU PRO GLN ARG GLU GLU ARG ILE SEQRES 10 A 229 CYS LEU VAL THR THR ASN PHE GLN THR LYS SER MET SER SEQRES 11 A 229 SER MET VAL SER ASP THR SER CYS THR PHE PRO SER SER SEQRES 12 A 229 ASP GLY ILE PHE TRP LYS HIS TRP ILE GLN THR LYS ASP SEQRES 13 A 229 GLY GLN CYS GLY SER PRO LEU VAL SER THR ARG ASP GLY SEQRES 14 A 229 PHE ILE VAL GLY ILE HIS SER ALA SER ASN PHE THR ASN SEQRES 15 A 229 THR ASN ASN TYR PHE THR SER VAL PRO LYS ASN PHE MET SEQRES 16 A 229 GLU LEU LEU THR ASN GLN GLU ALA GLN GLN TRP VAL SER SEQRES 17 A 229 GLY TRP ARG LEU ASN ALA ASP SER VAL LEU TRP GLY GLY SEQRES 18 A 229 HIS LYS VAL PHE MET ASP LYS PRO SEQRES 1 B 229 GLY HIS HIS HIS HIS HIS HIS HIS GLY GLU SER LEU PHE SEQRES 2 B 229 LYS GLY PRO ARG ASP TYR ASN PRO ILE SER SER THR ILE SEQRES 3 B 229 CYS HIS LEU THR ASN GLU SER ASP GLY HIS THR THR SER SEQRES 4 B 229 LEU TYR GLY ILE GLY PHE GLY PRO PHE ILE ILE THR ASN SEQRES 5 B 229 LYS HIS LEU PHE ARG ARG ASN ASN GLY THR LEU LEU VAL SEQRES 6 B 229 GLN SER LEU HIS GLY VAL PHE LYS VAL LYS ASN THR THR SEQRES 7 B 229 THR LEU GLN GLN HIS LEU ILE ASP GLY ARG ASP MET ILE SEQRES 8 B 229 ILE ILE ARG MET PRO LYS ASP PHE PRO PRO PHE PRO GLN SEQRES 9 B 229 LYS LEU LYS PHE ARG GLU PRO GLN ARG GLU GLU ARG ILE SEQRES 10 B 229 CYS LEU VAL THR THR ASN PHE GLN THR LYS SER MET SER SEQRES 11 B 229 SER MET VAL SER ASP THR SER CYS THR PHE PRO SER SER SEQRES 12 B 229 ASP GLY ILE PHE TRP LYS HIS TRP ILE GLN THR LYS ASP SEQRES 13 B 229 GLY GLN CYS GLY SER PRO LEU VAL SER THR ARG ASP GLY SEQRES 14 B 229 PHE ILE VAL GLY ILE HIS SER ALA SER ASN PHE THR ASN SEQRES 15 B 229 THR ASN ASN TYR PHE THR SER VAL PRO LYS ASN PHE MET SEQRES 16 B 229 GLU LEU LEU THR ASN GLN GLU ALA GLN GLN TRP VAL SER SEQRES 17 B 229 GLY TRP ARG LEU ASN ALA ASP SER VAL LEU TRP GLY GLY SEQRES 18 B 229 HIS LYS VAL PHE MET ASP LYS PRO SEQRES 1 C 10 ACE GLU ASN LEU TYR PHE GLN SER GLY THR SEQRES 1 D 10 ACE GLU ASN LEU TYR PHE GLN SER GLY THR SEQRES 1 E 7 GLU ALA THR GLN LEU MET ASN HET ACE C 301 3 HET ACE D 301 3 HETNAM ACE ACETYL GROUP FORMUL 3 ACE 2(C2 H4 O) FORMUL 6 HOH *574(H2 O) HELIX 1 1 HIS A -1 LEU A 4 5 5 HELIX 2 2 TYR A 11 SER A 16 1 6 HELIX 3 3 ASN A 44 ARG A 50 5 7 HELIX 4 4 ASN A 68 THR A 71 5 4 HELIX 5 5 ASN A 185 ASN A 192 1 8 HELIX 6 6 GLN A 193 GLN A 196 5 4 HELIX 7 7 TYR B 11 SER B 16 1 6 HELIX 8 8 ASN B 44 ARG B 49 5 6 HELIX 9 9 ASN B 68 THR B 71 5 4 HELIX 10 10 THR B 118 MET B 121 5 4 HELIX 11 11 ASN B 185 ASN B 192 1 8 HELIX 12 12 GLN B 193 GLN B 196 5 4 SHEET 1 A 9 THR E 232 GLN E 233 0 SHEET 2 A 9 GLY A 62 VAL A 66 1 O VAL A 63 N THR E 232 SHEET 3 A 9 THR A 54 SER A 59 -1 O LEU A 55 N VAL A 66 SHEET 4 A 9 ILE A 18 SER A 25 -1 O HIS A 20 N GLN A 58 SHEET 5 A 9 HIS A 28 PHE A 37 -1 N HIS A 28 O SER A 25 SHEET 6 A 9 PHE A 40 THR A 43 -1 N PHE A 40 O PHE A 37 SHEET 7 A 9 ILE A 83 ARG A 86 -1 N ILE A 83 O THR A 43 SHEET 8 A 9 GLN A 73 LEU A 76 -1 O GLN A 73 N ARG A 86 SHEET 9 A 9 TRP A 198 SER A 200 -1 O VAL A 199 N GLN A 74 SHEET 1 B15 PHE A 132 SER A 134 0 SHEET 2 B15 PHE A 139 HIS A 142 -1 O PHE A 139 N SER A 134 SHEET 3 B15 ASN A 177 SER A 181 -1 O ASN A 177 N HIS A 142 SHEET 4 B15 ILE A 163 ASN A 171 -1 O ILE A 166 N THR A 180 SHEET 5 B15 LEU C 304 PHE C 306 -1 N TYR C 305 O SER A 170 SHEET 6 B15 HIS A 214 PHE A 217 1 O LYS A 215 N LEU C 304 SHEET 7 B15 SER A 208 TRP A 211 -1 O VAL A 209 N VAL A 216 SHEET 8 B15 HIS A 214 PHE A 217 -1 N HIS A 214 O TRP A 211 SHEET 9 B15 LEU C 304 PHE C 306 1 N LEU C 304 O LYS A 215 SHEET 10 B15 ILE A 163 ASN A 171 -1 O SER A 170 N TYR C 305 SHEET 11 B15 PRO A 154 SER A 157 -1 N LEU A 155 O GLY A 165 SHEET 12 B15 ARG A 108 ASN A 115 -1 O CYS A 110 N VAL A 156 SHEET 13 B15 SER A 129 CYS A 130 -1 O SER A 129 N ILE A 109 SHEET 14 B15 ARG A 108 ASN A 115 -1 N ILE A 109 O SER A 129 SHEET 15 B15 SER A 122 VAL A 125 -1 O SER A 122 N ASN A 115 SHEET 1 C 8 GLY B 62 VAL B 66 0 SHEET 2 C 8 GLY B 53 SER B 59 -1 O LEU B 55 N VAL B 66 SHEET 3 C 8 ILE B 18 SER B 25 -1 O HIS B 20 N GLN B 58 SHEET 4 C 8 HIS B 28 PHE B 37 -1 O HIS B 28 N SER B 25 SHEET 5 C 8 PHE B 40 THR B 43 -1 O PHE B 40 N PHE B 37 SHEET 6 C 8 ILE B 83 ARG B 86 -1 O ILE B 83 N THR B 43 SHEET 7 C 8 GLN B 73 LEU B 76 -1 O GLN B 73 N ARG B 86 SHEET 8 C 8 TRP B 198 SER B 200 -1 O VAL B 199 N GLN B 74 SHEET 1 D15 SER B 123 VAL B 125 0 SHEET 2 D15 ARG B 108 THR B 114 -1 N THR B 113 O MET B 124 SHEET 3 D15 SER B 129 CYS B 130 -1 N SER B 129 O ILE B 109 SHEET 4 D15 ARG B 108 THR B 114 -1 O ILE B 109 N SER B 129 SHEET 5 D15 PRO B 154 SER B 157 -1 O PRO B 154 N VAL B 112 SHEET 6 D15 ILE B 163 ASN B 171 -1 N VAL B 164 O LEU B 155 SHEET 7 D15 LEU D 304 PHE D 306 -1 N TYR D 305 O SER B 170 SHEET 8 D15 HIS B 214 PHE B 217 1 O LYS B 215 N LEU D 304 SHEET 9 D15 SER B 208 TRP B 211 -1 O VAL B 209 N VAL B 216 SHEET 10 D15 HIS B 214 PHE B 217 -1 N HIS B 214 O TRP B 211 SHEET 11 D15 LEU D 304 PHE D 306 1 O LEU D 304 N PHE B 217 SHEET 12 D15 ILE B 163 ASN B 171 -1 N SER B 170 O TYR D 305 SHEET 13 D15 ASN B 177 SER B 181 -1 N TYR B 178 O ALA B 169 SHEET 14 D15 PHE B 139 HIS B 142 -1 O TRP B 140 N PHE B 179 SHEET 15 D15 PHE B 132 SER B 134 -1 O PHE B 132 N LYS B 141 LINK C ACE C 301 N GLU C 302 1555 1555 1.32 LINK C ACE D 301 N GLU D 302 1555 1555 1.33 SITE 1 AC1 2 HIS A 214 HOH C 81 SITE 1 AC2 3 HOH D 133 HOH D 176 HOH D 421 CRYST1 75.505 75.505 183.167 90.00 90.00 90.00 P 43 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 0.013244 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013244 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005459 0.00000