HEADER VIRAL PROTEIN, HYDROLASE 17-MAR-06 2GDT TITLE NMR STRUCTURE OF THE NONSTRUCTURAL PROTEIN 1 (NSP1) FROM THE SARS TITLE 2 CORONAVIRUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEADER PROTEIN; P65 HOMOLOG; NSP1 (EC 3.4.22.-); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NSP1-6; COMPND 5 EC: 3.4.22.-; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SARS CORONAVIRUS; SOURCE 3 ORGANISM_TAXID: 227859; 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: PSTEF KEYWDS LEADER PROTEIN, BETA-BARREL, ALPHA-BETA, VIRUS, REPLICASE, STRUCTURAL KEYWDS 2 GENOMICS, PSI-2, PROTEIN STRUCTURE INITIATIVE, JOINT CENTER FOR KEYWDS 3 STRUCTURAL GENOMICS, JCSG, VIRAL PROTEIN, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR M.S.ALMEIDA,T.HERRMANN,M.GERALT,M.A.JOHNSON,K.SAIKATENDU,J.JOSEPH, AUTHOR 2 R.C.SUBRAMANIAN,B.W.NEUMAN,M.J.BUCHMEIER,R.C.STEVENS,P.KUHN, AUTHOR 3 I.A.WILSON,K.WUTHRICH,JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG) REVDAT 6 20-OCT-21 2GDT 1 SEQADV REVDAT 5 19-FEB-20 2GDT 1 REMARK REVDAT 4 24-FEB-09 2GDT 1 VERSN REVDAT 3 20-NOV-07 2GDT 1 JRNL REVDAT 2 13-MAR-07 2GDT 1 REVDAT 1 06-FEB-07 2GDT 0 JRNL AUTH M.S.ALMEIDA,M.A.JOHNSON,T.HERRMANN,M.GERALT,K.WUTHRICH JRNL TITL NOVEL BETA-BARREL FOLD IN THE NUCLEAR MAGNETIC RESONANCE JRNL TITL 2 STRUCTURE OF THE REPLICASE NONSTRUCTURAL PROTEIN 1 FROM THE JRNL TITL 3 SEVERE ACUTE RESPIRATORY SYNDROME CORONAVIRUS. JRNL REF J.VIROL. V. 81 3151 2007 JRNL REFN ISSN 0022-538X JRNL PMID 17202208 JRNL DOI 10.1128/JVI.01939-06 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 1.3, OPALP REMARK 3 AUTHORS : BRUKER (TOPSPIN), LUGINBUHL (OPALP) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: MOLECULAR DYNAMICS USING CYANA 1.0.3. REMARK 3 ENERGY MINIMIZATION IN A WATER SHELL USING OPALP WITH AMBER FORCE REMARK 3 FIELD. REMARK 4 REMARK 4 2GDT COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-MAR-06. REMARK 100 THE DEPOSITION ID IS D_1000036994. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 25 MM SODIUM PHOSPHATE AND 250 REMARK 210 MM NACL REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2 MM NSP1-6; 25 MM NAPHOSPHATE REMARK 210 PH 7.0, 250 MM NACL, 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ATNOS/CANDID STANDALONE, CYANA REMARK 210 1.0.3 REMARK 210 METHOD USED : ATNOS/CANDID/CYANA REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 120 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: 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 O TYR A 86 HG1 THR A 92 1.59 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 3 ARG A 88 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 4 VAL A 95 CA - CB - CG1 ANGL. DEV. = 15.7 DEGREES REMARK 500 5 ARG A 32 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 9 ARG A 18 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 13 ARG A 18 CD - NE - CZ ANGL. DEV. = 9.2 DEGREES REMARK 500 14 ARG A 32 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 17 ARG A 13 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 18 ARG A 113 NE - CZ - NH1 ANGL. DEV. = 3.1 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 1 HIS A 2 162.14 64.80 REMARK 500 1 VAL A 15 65.02 -65.36 REMARK 500 1 THR A 39 38.89 -94.41 REMARK 500 1 PRO A 51 43.86 -84.37 REMARK 500 1 GLN A 52 -17.49 -142.28 REMARK 500 1 GLU A 54 -88.37 -82.49 REMARK 500 1 GLN A 55 -59.65 -156.39 REMARK 500 1 SER A 63 78.89 43.01 REMARK 500 1 ALA A 65 18.65 -163.42 REMARK 500 1 SER A 67 82.02 -150.71 REMARK 500 1 MET A 81 -72.20 -78.48 REMARK 500 1 TYR A 86 -70.71 65.38 REMARK 500 1 ILE A 91 -93.25 -65.69 REMARK 500 1 THR A 92 116.45 21.61 REMARK 500 1 THR A 103 101.99 69.17 REMARK 500 2 HIS A 2 165.59 62.21 REMARK 500 2 ASP A 22 -18.48 66.78 REMARK 500 2 THR A 39 39.90 -89.87 REMARK 500 2 GLU A 54 -86.73 -77.82 REMARK 500 2 GLN A 55 -56.42 -158.71 REMARK 500 2 ARG A 62 47.45 -70.40 REMARK 500 2 SER A 63 -176.43 52.15 REMARK 500 2 SER A 67 76.33 -165.46 REMARK 500 2 VAL A 74 177.75 52.50 REMARK 500 2 MET A 81 -75.31 -73.09 REMARK 500 2 ILE A 84 -67.55 -28.19 REMARK 500 2 TYR A 86 -37.72 72.77 REMARK 500 2 GLU A 102 -100.38 -55.56 REMARK 500 2 THR A 103 96.89 -164.88 REMARK 500 2 ASN A 115 -88.98 -92.55 REMARK 500 3 HIS A 2 166.41 67.79 REMARK 500 3 LEU A 16 -8.45 -49.82 REMARK 500 3 ASP A 22 -39.99 -157.42 REMARK 500 3 THR A 39 41.06 -84.24 REMARK 500 3 GLU A 54 -89.20 -72.07 REMARK 500 3 GLN A 55 -62.10 -160.48 REMARK 500 3 ARG A 62 76.75 -68.47 REMARK 500 3 SER A 63 -149.61 45.29 REMARK 500 3 ASP A 64 55.11 -91.49 REMARK 500 3 THR A 68 -147.73 43.04 REMARK 500 3 LYS A 73 96.32 -49.39 REMARK 500 3 ILE A 84 -70.53 -25.60 REMARK 500 3 TYR A 86 -48.99 72.46 REMARK 500 3 ARG A 88 -133.24 58.02 REMARK 500 3 SER A 89 -173.09 65.85 REMARK 500 3 THR A 103 105.58 61.00 REMARK 500 3 ASN A 115 -76.34 -63.64 REMARK 500 4 HIS A 2 158.23 66.74 REMARK 500 4 VAL A 15 65.40 -59.61 REMARK 500 4 LEU A 16 -35.95 -36.13 REMARK 500 REMARK 500 THIS ENTRY HAS 317 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 ASP A 22 SER A 23 1 146.30 REMARK 500 ILE A 91 THR A 92 1 148.28 REMARK 500 ARG A 62 SER A 63 4 144.42 REMARK 500 GLY A 71 HIS A 72 4 -146.81 REMARK 500 SER A 63 ASP A 64 6 146.24 REMARK 500 ASN A 115 GLY A 116 7 142.24 REMARK 500 GLY A 90 ILE A 91 10 145.54 REMARK 500 GLY A 83 ILE A 84 15 -143.65 REMARK 500 SER A 63 ASP A 64 16 -145.43 REMARK 500 ARG A 88 SER A 89 17 146.63 REMARK 500 ASN A 115 GLY A 116 17 -144.61 REMARK 500 ASP A 82 GLY A 83 19 -146.84 REMARK 500 LYS A 114 ASN A 115 19 148.44 REMARK 500 ARG A 113 LYS A 114 20 146.91 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 62 0.11 SIDE CHAIN REMARK 500 2 ARG A 62 0.10 SIDE CHAIN REMARK 500 2 ARG A 113 0.11 SIDE CHAIN REMARK 500 3 ARG A 113 0.08 SIDE CHAIN REMARK 500 4 ARG A 13 0.16 SIDE CHAIN REMARK 500 5 TYR A 57 0.07 SIDE CHAIN REMARK 500 5 TYR A 86 0.07 SIDE CHAIN REMARK 500 6 ARG A 88 0.08 SIDE CHAIN REMARK 500 7 ARG A 32 0.13 SIDE CHAIN REMARK 500 9 ARG A 62 0.12 SIDE CHAIN REMARK 500 12 ARG A 13 0.10 SIDE CHAIN REMARK 500 12 TYR A 86 0.07 SIDE CHAIN REMARK 500 12 ARG A 108 0.10 SIDE CHAIN REMARK 500 13 ARG A 13 0.08 SIDE CHAIN REMARK 500 13 ARG A 88 0.11 SIDE CHAIN REMARK 500 15 ARG A 13 0.08 SIDE CHAIN REMARK 500 16 ARG A 13 0.09 SIDE CHAIN REMARK 500 17 ARG A 18 0.12 SIDE CHAIN REMARK 500 17 TYR A 86 0.11 SIDE CHAIN REMARK 500 18 ARG A 13 0.13 SIDE CHAIN REMARK 500 18 ARG A 32 0.09 SIDE CHAIN REMARK 500 18 ARG A 88 0.07 SIDE CHAIN REMARK 500 19 ARG A 13 0.10 SIDE CHAIN REMARK 500 20 ARG A 18 0.10 SIDE CHAIN REMARK 500 20 ARG A 32 0.09 SIDE CHAIN REMARK 500 20 ARG A 62 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7014 RELATED DB: BMRB REMARK 900 CHEMICAL SHIFTS DBREF 2GDT A 1 116 UNP P59641 R1AB_CVHSA 12 127 SEQADV 2GDT GLY A 1 UNP P59641 THR 12 ENGINEERED MUTATION SEQRES 1 A 116 GLY HIS VAL GLN LEU SER LEU PRO VAL LEU GLN VAL ARG SEQRES 2 A 116 ASP VAL LEU VAL ARG GLY PHE GLY ASP SER VAL GLU GLU SEQRES 3 A 116 ALA LEU SER GLU ALA ARG GLU HIS LEU LYS ASN GLY THR SEQRES 4 A 116 CYS GLY LEU VAL GLU LEU GLU LYS GLY VAL LEU PRO GLN SEQRES 5 A 116 LEU GLU GLN PRO TYR VAL PHE ILE LYS ARG SER ASP ALA SEQRES 6 A 116 LEU SER THR ASN HIS GLY HIS LYS VAL VAL GLU LEU VAL SEQRES 7 A 116 ALA GLU MET ASP GLY ILE GLN TYR GLY ARG SER GLY ILE SEQRES 8 A 116 THR LEU GLY VAL LEU VAL PRO HIS VAL GLY GLU THR PRO SEQRES 9 A 116 ILE ALA TYR ARG ASN VAL LEU LEU ARG LYS ASN GLY HELIX 1 1 SER A 23 GLY A 38 1 16 HELIX 2 2 VAL A 49 LEU A 53 5 5 SHEET 1 A 2 VAL A 3 VAL A 9 0 SHEET 2 A 2 ALA A 106 LEU A 112 -1 O ARG A 108 N LEU A 7 SHEET 1 B 4 CYS A 40 VAL A 43 0 SHEET 2 B 4 GLY A 94 PRO A 98 -1 O VAL A 95 N VAL A 43 SHEET 3 B 4 TYR A 57 LYS A 61 -1 N VAL A 58 O LEU A 96 SHEET 4 B 4 GLU A 76 GLU A 80 -1 O VAL A 78 N PHE A 59 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 ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL ENDMDL MASTER 244 0 0 2 6 0 0 6 0 0 0 9 END