HEADER HYDROLASE 05-OCT-06 2IN2 TITLE NMR STRUCTURE OF THE APO HUMAN RHINOVIRUS 3C PROTEASE (SEROTYPE 14) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PICORNAIN 3C; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HUMAN RHINOVIRUS 3C PROTEASE; COMPND 5 SYNONYM: PROTEASE 3C, P3C; COMPND 6 EC: 3.4.22.28; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HUMAN RHINOVIRUS 14; SOURCE 3 ORGANISM_TAXID: 12131; SOURCE 4 STRAIN: SEROTYPE 14; SOURCE 5 GENE: HRV-3ABC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PLYSS KEYWDS HYDROLASE, PROTEASE, BETA BARREL, RNA BINDING, RNA POLYMERASE BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR T.C.BJORNDAHL,V.SEMENCHENKO,D.S.WISHART REVDAT 4 14-JUN-23 2IN2 1 REMARK REVDAT 3 26-FEB-20 2IN2 1 REMARK REVDAT 2 13-MAY-08 2IN2 1 JRNL VERSN REVDAT 1 24-OCT-06 2IN2 0 JRNL AUTH T.C.BJORNDAHL,L.C.ANDREW,V.SEMENCHENKO,D.S.WISHART JRNL TITL NMR SOLUTION STRUCTURES OF THE APO AND PEPTIDE-INHIBITED JRNL TITL 2 HUMAN RHINOVIRUS 3C PROTEASE (SEROTYPE 14): STRUCTURAL AND JRNL TITL 3 DYNAMIC COMPARISON. JRNL REF BIOCHEMISTRY V. 46 12945 2007 JRNL REFN ISSN 0006-2960 JRNL PMID 17944485 JRNL DOI 10.1021/BI7010866 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 3.1C, CNS 1.1 REMARK 3 AUTHORS : GRAY, G. (VNMR), BRUNGER, A.T. (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES WERE CALCULATED WITH 1515 NOE, 129 PHI, 100 PSI, 3 REMARK 3 CHI AND 64 HYDROGEN BOND RESTRAINTS AND REMARK 3 29 STEREOSPECIFIC ASSIGNMENTS REMARK 4 REMARK 4 2IN2 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-OCT-06. REMARK 100 THE DEPOSITION ID IS D_1000039770. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 20 MM REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : U-13C/15N; 20MM PHOSPHATE REMARK 210 BUFFER; 0.5MM EDTA; 15MM DTT; REMARK 210 0.3% NAN3; 90% H2O, 10% D2O; U- REMARK 210 13C/15N; 20MM PHOSPHATE BUFFER; REMARK 210 0.5MM EDTA; 15MM DTT; NAN3; 99.6% REMARK 210 D2O; U-15N; 20MM PHOSPHATE REMARK 210 BUFFER; 0.5MM EDTA; 15MM DTT; 90% REMARK 210 H2O, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY; 3D_13C REMARK 210 -SEPARATED_NOESY; HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.3, NMRVIEW 5.2.2, REMARK 210 CYANA 2.1 REMARK 210 METHOD USED : NULL REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 300 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE REMARK 210 COVALENT GEOMETRY,STRUCTURES REMARK 210 WITH THE LEAST RESTRAINT REMARK 210 VIOLATIONS,STRUCTURES WITH THE REMARK 210 LOWEST ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: AMIDES INVOLVED IN HYDROGEN BONDS WERE IDENTIFIED THROUGH REMARK 210 H/D EXCHANGE REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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: MONOMERIC 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 OD1 ASP A 45 HZ1 LYS A 59 1.57 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 1 LYS A 13 -61.66 -90.23 REMARK 500 1 PHE A 25 -169.70 -114.02 REMARK 500 1 ASP A 32 -98.67 58.29 REMARK 500 1 GLN A 42 84.01 58.85 REMARK 500 1 ASP A 85 96.72 -61.47 REMARK 500 1 ASN A 110 70.20 58.97 REMARK 500 1 SER A 128 -12.69 80.81 REMARK 500 1 ARG A 133 47.97 74.63 REMARK 500 1 ALA A 140 99.70 -64.50 REMARK 500 1 GLN A 145 40.29 -90.30 REMARK 500 1 THR A 153 102.39 -59.53 REMARK 500 2 HIS A 31 147.33 -170.85 REMARK 500 2 ASP A 32 -81.09 60.53 REMARK 500 2 ARG A 33 13.19 -149.85 REMARK 500 2 GLN A 42 82.43 61.60 REMARK 500 2 PRO A 65 -3.22 -56.57 REMARK 500 2 ASP A 85 99.06 -67.66 REMARK 500 2 THR A 153 96.02 -62.79 REMARK 500 3 THR A 20 -157.54 -96.02 REMARK 500 3 ASP A 32 -79.98 67.18 REMARK 500 3 ARG A 33 11.88 -140.46 REMARK 500 3 GLN A 42 82.00 60.44 REMARK 500 3 ASN A 110 71.82 58.77 REMARK 500 3 SER A 127 77.03 55.88 REMARK 500 3 SER A 128 -19.68 67.72 REMARK 500 3 THR A 153 101.22 -57.41 REMARK 500 4 THR A 20 -157.75 -89.74 REMARK 500 4 ASP A 32 -135.57 52.06 REMARK 500 4 GLN A 42 76.60 57.22 REMARK 500 4 ASN A 50 -3.90 74.03 REMARK 500 4 LYS A 57 -71.34 -79.68 REMARK 500 4 LEU A 94 -29.76 -141.50 REMARK 500 4 ASN A 110 70.71 60.15 REMARK 500 4 TYR A 139 124.35 -171.34 REMARK 500 5 ASP A 32 -92.24 53.72 REMARK 500 5 GLN A 42 87.46 60.04 REMARK 500 5 PRO A 65 5.23 -62.98 REMARK 500 5 ASN A 67 40.06 70.66 REMARK 500 5 GLU A 71 -20.59 72.50 REMARK 500 5 ASN A 110 62.90 64.45 REMARK 500 5 ASN A 125 -77.56 -159.27 REMARK 500 5 SER A 128 60.59 60.53 REMARK 500 5 ASN A 132 97.18 -66.31 REMARK 500 5 ARG A 133 80.35 62.76 REMARK 500 6 LYS A 13 -65.63 -99.93 REMARK 500 6 ASP A 32 -92.62 61.21 REMARK 500 6 GLN A 42 84.89 53.35 REMARK 500 6 LYS A 57 -69.77 -97.87 REMARK 500 6 PRO A 65 -17.25 -47.31 REMARK 500 6 ASN A 110 70.60 68.48 REMARK 500 REMARK 500 THIS ENTRY HAS 168 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 1 ARG A 87 0.08 SIDE CHAIN REMARK 500 12 ARG A 55 0.09 SIDE CHAIN REMARK 500 14 ARG A 33 0.11 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2B0F RELATED DB: PDB REMARK 900 SAME PROTEIN WITH ACE-LEALFQ-ETHYLPROPIONATE INHIBITOR REMARK 900 RELATED ID: 5659 RELATED DB: BMRB REMARK 900 CHEMICAL SHIFTS FOR THIS PROTEIN REMARK 900 RELATED ID: 1CQQ RELATED DB: PDB REMARK 900 HOMOLOGOUS 3C PROTEIN FROM RHINOVIRUS SEROTYPE 2 (51% SEQUENCE REMARK 900 IDENTITY) REMARK 900 RELATED ID: 1L1N RELATED DB: PDB REMARK 900 HOMOLOGOUS 3C PROTEIN FROM POLIO VIRUS (49% SEQUENCE IDENTITY) DBREF 2IN2 A 1 182 UNP P03303 POLG_HRV14 1537 1718 SEQRES 1 A 182 GLY PRO ASN THR GLU PHE ALA LEU SER LEU LEU ARG LYS SEQRES 2 A 182 ASN ILE MET THR ILE THR THR SER LYS GLY GLU PHE THR SEQRES 3 A 182 GLY LEU GLY ILE HIS ASP ARG VAL CYS VAL ILE PRO THR SEQRES 4 A 182 HIS ALA GLN PRO GLY ASP ASP VAL LEU VAL ASN GLY GLN SEQRES 5 A 182 LYS ILE ARG VAL LYS ASP LYS TYR LYS LEU VAL ASP PRO SEQRES 6 A 182 GLU ASN ILE ASN LEU GLU LEU THR VAL LEU THR LEU ASP SEQRES 7 A 182 ARG ASN GLU LYS PHE ARG ASP ILE ARG GLY PHE ILE SER SEQRES 8 A 182 GLU ASP LEU GLU GLY VAL ASP ALA THR LEU VAL VAL HIS SEQRES 9 A 182 SER ASN ASN PHE THR ASN THR ILE LEU GLU VAL GLY PRO SEQRES 10 A 182 VAL THR MET ALA GLY LEU ILE ASN LEU SER SER THR PRO SEQRES 11 A 182 THR ASN ARG MET ILE ARG TYR ASP TYR ALA THR LYS THR SEQRES 12 A 182 GLY GLN CYS GLY GLY VAL LEU CYS ALA THR GLY LYS ILE SEQRES 13 A 182 PHE GLY ILE HIS VAL GLY GLY ASN GLY ARG GLN GLY PHE SEQRES 14 A 182 SER ALA GLN LEU LYS LYS GLN TYR PHE VAL GLU LYS GLN HELIX 1 1 GLY A 1 ASN A 14 1 14 HELIX 2 2 ASP A 85 ILE A 90 5 6 HELIX 3 3 LYS A 174 VAL A 179 5 6 SHEET 1 A 7 ILE A 15 THR A 19 0 SHEET 2 A 7 GLU A 24 HIS A 31 -1 O PHE A 25 N ILE A 18 SHEET 3 A 7 VAL A 34 PRO A 38 -1 O VAL A 34 N ILE A 30 SHEET 4 A 7 ILE A 68 LEU A 77 -1 O LEU A 75 N CYS A 35 SHEET 5 A 7 GLN A 52 ASP A 64 -1 N TYR A 60 O VAL A 74 SHEET 6 A 7 ASP A 46 VAL A 49 -1 N VAL A 49 O GLN A 52 SHEET 7 A 7 ILE A 15 THR A 19 -1 N THR A 19 O LEU A 48 SHEET 1 B 7 THR A 111 PRO A 117 0 SHEET 2 B 7 ASP A 98 VAL A 103 -1 N LEU A 101 O LEU A 113 SHEET 3 B 7 GLY A 148 ALA A 152 -1 O CYS A 151 N THR A 100 SHEET 4 B 7 LYS A 155 HIS A 160 -1 O HIS A 160 N GLY A 148 SHEET 5 B 7 GLY A 165 GLN A 172 -1 O ALA A 171 N ILE A 159 SHEET 6 B 7 THR A 129 THR A 141 -1 N THR A 141 O GLY A 165 SHEET 7 B 7 THR A 119 LEU A 126 -1 N ILE A 124 O THR A 131 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1