HEADER VIRAL PROTEIN, RNA BINDING PROTEIN 05-NOV-08 2KAF TITLE SOLUTION STRUCTURE OF THE SARS-UNIQUE DOMAIN-C FROM THE NONSTRUCTURAL TITLE 2 PROTEIN 3 (NSP3) OF THE SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NON-STRUCTURAL PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: SARS-UNIQUE DOMAIN-C, RESIDUES 1473-1532; COMPND 5 SYNONYM: REPLICASE POLYPROTEIN 1A, PP1A, ORF1A POLYPROTEIN, NSP3, COMPND 6 PAPAIN-LIKE PROTEINASE, PL-PRO, PL2-PRO; COMPND 7 EC: 3.4.22.-; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SARS CORONAVIRUS; SOURCE 3 ORGANISM_COMMON: SARS-COV; SOURCE 4 ORGANISM_TAXID: 227859; SOURCE 5 GENE: 1A; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-28B KEYWDS SARS CORONAVIRUS, NONSTRUCTURAL PROTEIN 3, SARS-UNIQUE DOMAIN-C, KEYWDS 2 AUTOMATION IN NMR STRUCTURE DETERMINATION, VIRAL PROTEIN, HYDROLASE. KEYWDS 3 JOINT CENTER FOR STRUCTURAL GENOMICS. JCSG. PSI, PROTEIN STRUCTURE KEYWDS 4 INITIATIVE, RNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.A.JOHNSON,B.MOHANTY,B.PEDRINI,P.SERRANO,A.CHATTERJEE,T.HERRMANN, AUTHOR 2 J.JOSEPH,K.SAIKATENDU,I.A.WILSON,M.J.BUCHMEIER,P.KUHN,K.WUTHRICH, AUTHOR 3 JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 3 10-OCT-12 2KAF 1 JRNL VERSN REVDAT 2 24-FEB-09 2KAF 1 VERSN REVDAT 1 25-NOV-08 2KAF 0 JRNL AUTH M.A.JOHNSON,A.CHATTERJEE,B.W.NEUMAN,K.WUTHRICH JRNL TITL SARS CORONAVIRUS UNIQUE DOMAIN: THREE-DOMAIN MOLECULAR JRNL TITL 2 ARCHITECTURE IN SOLUTION AND RNA BINDING. JRNL REF J.MOL.BIOL. V. 400 724 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20493876 JRNL DOI 10.1016/J.JMB.2010.05.027 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : OPAL REMARK 3 AUTHORS : LUGINBUHL, GUNTERT, BILLETER AND WUTHRICH REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2KAF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-NOV-08. REMARK 100 THE RCSB ID CODE IS RCSB100878. 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 : 0.0628 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.2 MM [U-98% 13C; U-98% 15N] REMARK 210 PROTEIN, 20 MM SODIUM CHLORIDE, REMARK 210 2.8 MM SODIUM AZIDE, 20 MM SODIUM REMARK 210 PHOSPHATE, 93% H2O/7% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D 1H-15N NOESY; 3D 1H-13C NOESY; REMARK 210 5D APSY-CBCACONH; 5D APSY- REMARK 210 HACACONH; 4D APSY-HACANH REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, ENERGY REMARK 210 MINIMIZATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 80 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL 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: 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 9 LEU A 62 CB - CG - CD2 ANGL. DEV. = 10.8 DEGREES REMARK 500 16 ARG A 35 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 16 LEU A 59 CB - CG - CD2 ANGL. DEV. = 10.4 DEGREES REMARK 500 20 LEU A 59 CB - CG - CD2 ANGL. DEV. = 10.3 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 1 ARG A 17 -82.00 51.23 REMARK 500 1 SER A 22 -111.03 -140.61 REMARK 500 1 PHE A 32 -112.97 -98.50 REMARK 500 1 ASP A 53 -22.57 68.24 REMARK 500 2 ARG A 17 -81.11 53.83 REMARK 500 2 SER A 22 -111.00 -137.94 REMARK 500 2 PHE A 32 -112.81 -81.76 REMARK 500 3 ARG A 17 -78.30 57.81 REMARK 500 3 SER A 22 -111.26 -112.11 REMARK 500 3 PHE A 32 -112.58 -95.33 REMARK 500 4 SER A 15 165.32 177.23 REMARK 500 4 ARG A 17 -85.80 50.82 REMARK 500 4 SER A 22 -111.54 -136.57 REMARK 500 4 PHE A 32 -112.98 -89.79 REMARK 500 4 ASP A 37 -1.12 74.95 REMARK 500 4 ASP A 53 -57.47 72.97 REMARK 500 5 ARG A 17 -86.99 45.94 REMARK 500 5 SER A 22 -110.87 -138.70 REMARK 500 5 PHE A 32 -113.96 -100.86 REMARK 500 6 ARG A 17 -85.38 54.72 REMARK 500 6 SER A 22 -111.35 -138.46 REMARK 500 6 PHE A 32 -113.14 -92.51 REMARK 500 6 ASP A 53 -14.75 68.10 REMARK 500 7 ARG A 17 -85.30 56.60 REMARK 500 7 SER A 22 -111.73 -135.48 REMARK 500 7 PHE A 32 -112.90 -85.25 REMARK 500 7 ASP A 37 -1.21 75.94 REMARK 500 7 ASP A 53 -8.68 74.16 REMARK 500 8 ARG A 17 -85.35 59.66 REMARK 500 8 SER A 22 -111.00 -142.69 REMARK 500 8 PHE A 32 -112.89 -85.58 REMARK 500 8 ASP A 53 -2.00 70.67 REMARK 500 9 ARG A 17 -85.02 55.30 REMARK 500 9 SER A 22 -111.25 -140.71 REMARK 500 9 PHE A 32 -112.91 -106.88 REMARK 500 10 ARG A 17 -86.80 54.65 REMARK 500 10 SER A 22 -112.07 -135.78 REMARK 500 10 PHE A 32 -113.16 -105.48 REMARK 500 10 ASP A 53 -19.55 68.81 REMARK 500 11 ARG A 17 -87.04 52.27 REMARK 500 11 SER A 22 -111.05 -140.76 REMARK 500 11 PHE A 32 -113.29 -90.71 REMARK 500 11 ASP A 53 -11.21 68.55 REMARK 500 12 ARG A 17 -84.18 60.62 REMARK 500 12 SER A 22 -111.18 -140.83 REMARK 500 12 PHE A 32 -113.01 -114.10 REMARK 500 12 ASP A 53 -17.01 71.67 REMARK 500 13 ARG A 17 -83.60 56.90 REMARK 500 13 SER A 22 -111.29 -131.96 REMARK 500 13 PHE A 32 -112.68 -80.90 REMARK 500 REMARK 500 THIS ENTRY HAS 79 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LEU A 57 SER A 58 11 147.08 REMARK 500 ASP A 53 GLY A 54 14 149.32 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 9 ARG A 35 0.10 SIDE CHAIN REMARK 500 10 ARG A 35 0.10 SIDE CHAIN REMARK 500 11 ARG A 25 0.09 SIDE CHAIN REMARK 500 15 ARG A 25 0.14 SIDE CHAIN REMARK 500 16 ARG A 17 0.08 SIDE CHAIN REMARK 500 17 ARG A 25 0.08 SIDE CHAIN REMARK 500 19 ARG A 25 0.09 SIDE CHAIN REMARK 500 19 ARG A 35 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16008 RELATED DB: BMRB REMARK 900 ENTRY CONTAINING CHEMICAL SHIFTS REMARK 900 RELATED ID: 399745 RELATED DB: TARGETDB DBREF 2KAF A 2 67 UNP P0C6U8 R1A_CVHSA 1473 1538 SEQADV 2KAF GLY A 1 UNP P0C6U8 EXPRESSION TAG SEQRES 1 A 67 GLY SER GLU GLU HIS PHE VAL GLU THR VAL SER LEU ALA SEQRES 2 A 67 GLY SER TYR ARG ASP TRP SER TYR SER GLY GLN ARG THR SEQRES 3 A 67 GLU LEU GLY VAL GLU PHE LEU LYS ARG GLY ASP LYS ILE SEQRES 4 A 67 VAL TYR HIS THR LEU GLU SER PRO VAL GLU PHE HIS LEU SEQRES 5 A 67 ASP GLY GLU VAL LEU SER LEU ASP LYS LEU LYS SER LEU SEQRES 6 A 67 LEU SER HELIX 1 1 GLY A 1 GLY A 14 1 14 HELIX 2 2 SER A 58 SER A 67 1 10 SHEET 1 A 2 SER A 15 TYR A 16 0 SHEET 2 A 2 TRP A 19 SER A 20 -1 O TRP A 19 N TYR A 16 SHEET 1 B 5 ARG A 25 THR A 26 0 SHEET 2 B 5 GLY A 29 ARG A 35 -1 O GLY A 29 N THR A 26 SHEET 3 B 5 LYS A 38 HIS A 42 -1 O VAL A 40 N PHE A 32 SHEET 4 B 5 PHE A 50 LEU A 52 -1 O HIS A 51 N TYR A 41 SHEET 5 B 5 GLU A 55 VAL A 56 -1 O GLU A 55 N LEU A 52 CISPEP 1 SER A 46 PRO A 47 1 -10.60 CISPEP 2 SER A 46 PRO A 47 2 -9.48 CISPEP 3 SER A 46 PRO A 47 3 -8.43 CISPEP 4 SER A 46 PRO A 47 4 -19.79 CISPEP 5 SER A 46 PRO A 47 5 -12.01 CISPEP 6 SER A 46 PRO A 47 6 -1.93 CISPEP 7 SER A 46 PRO A 47 7 -7.09 CISPEP 8 SER A 46 PRO A 47 8 -17.44 CISPEP 9 SER A 46 PRO A 47 9 -7.65 CISPEP 10 SER A 46 PRO A 47 10 -11.61 CISPEP 11 SER A 46 PRO A 47 11 -6.64 CISPEP 12 SER A 46 PRO A 47 12 -2.53 CISPEP 13 SER A 46 PRO A 47 13 -0.93 CISPEP 14 SER A 46 PRO A 47 14 -19.81 CISPEP 15 SER A 46 PRO A 47 15 -21.83 CISPEP 16 SER A 46 PRO A 47 16 -20.16 CISPEP 17 SER A 46 PRO A 47 17 -9.13 CISPEP 18 SER A 46 PRO A 47 18 -9.14 CISPEP 19 SER A 46 PRO A 47 19 -8.33 CISPEP 20 SER A 46 PRO A 47 20 -5.97 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