HEADER VIRAL PROTEIN 16-OCT-03 1R6R TITLE SOLUTION STRUCTURE OF DENGUE VIRUS CAPSID PROTEIN REVEALS A NEW FOLD COMPND MOL_ID: 1; COMPND 2 MOLECULE: GENOME POLYPROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: CAPSID PROTEIN C (RESIDUE 1-100); COMPND 5 SYNONYM: CORE PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DENGUE VIRUS 2 PUERTO RICO/PR159-S1/1969; SOURCE 3 ORGANISM_TAXID: 11066; SOURCE 4 STRAIN: PR-159-S1; SOURCE 5 GENE: CAPSID GENE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)[RIL]; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET30A KEYWDS ALPHA HELICAL, DIMER, VIRAL PROTEIN EXPDTA SOLUTION NMR NUMMDL 21 MDLTYP MINIMIZED AVERAGE AUTHOR L.MA,C.T.JONES,T.D.GROESCH,R.J.KUHN,C.B.POST REVDAT 5 22-MAY-24 1R6R 1 REMARK REVDAT 4 02-MAR-22 1R6R 1 REMARK REVDAT 3 24-FEB-09 1R6R 1 VERSN REVDAT 2 06-APR-04 1R6R 1 JRNL REVDAT 1 17-FEB-04 1R6R 0 JRNL AUTH L.MA,C.T.JONES,T.D.GROESCH,R.J.KUHN,C.B.POST JRNL TITL SOLUTION STRUCTURE OF DENGUE VIRUS CAPSID PROTEIN REVEALS JRNL TITL 2 ANOTHER FOLD JRNL REF PROC.NATL.ACAD.SCI.USA V. 101 3414 2004 JRNL REFN ISSN 0027-8424 JRNL PMID 14993605 JRNL DOI 10.1073/PNAS.0305892101 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 2.2, X-PLOR 3.8 REMARK 3 AUTHORS : DELAGIO, GRZESIEK, VUISTER, ZHU, PFEIFER, BAX REMARK 3 (NMRPIPE), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1R6R COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-OCT-03. REMARK 100 THE DEPOSITION ID IS D_1000020505. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300; 305 REMARK 210 PH : 6.0; 6.0 REMARK 210 IONIC STRENGTH : 50 MM SODIUM PHOSPHATE AND 200 REMARK 210 MM NACL; 50 MM SODIUM PHOSPHATE REMARK 210 AND 200 MM NACL REMARK 210 PRESSURE : 1 ATM; 1 ATM REMARK 210 SAMPLE CONTENTS : 0.8 MM DEN2C PROTEIN U-15N, 13C; REMARK 210 IN 90% H2O/10% D2O WITH 50 MM REMARK 210 SODIUM PHOSPHATE AND 200 MM NACL REMARK 210 AT PH 6.0. IN SHIGEMI TUBE; 1MM REMARK 210 OR 2 MM DEN2C PROTEIN U-15N; IN REMARK 210 90% H2O/10% D2O WITH 50 MM REMARK 210 SODIUM PHOSPHATE AND 200 MM NACL REMARK 210 AT PH 6.0. IN SHIGEMI TUBE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY; HNHA REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : SPARKY 3 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 54 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 REMARK 210 CONFORMERS, SELECTION CRITERIA : 20 ARBITRARILY SELECTED FROM REMARK 210 53/54 CONFORMERS WITH NO REMARK 210 CONSTRAINT VIOLATIONS LARGER REMARK 210 THAN 0.3 ANGSTROM OR 5 DEGREES. REMARK 210 MODEL 21 IS ENERGY MINIMIZED REMARK 210 STRUCTURE AVERAGED OVER THE 53 REMARK 210 MODELS. REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 21 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR REMARK 210 SPECTROSCOPY 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 VAL A 23 -26.00 -172.56 REMARK 500 1 MET A 37 -85.00 23.37 REMARK 500 1 ARG A 41 -146.17 56.76 REMARK 500 1 THR A 58 -8.68 -146.11 REMARK 500 1 PRO A 60 66.04 -104.70 REMARK 500 1 THR A 62 172.65 -57.96 REMARK 500 1 THR A 71 26.29 -163.68 REMARK 500 1 ILE A 72 -127.96 -114.80 REMARK 500 1 LYS A 74 -47.30 72.55 REMARK 500 1 ARG A 99 -62.14 68.41 REMARK 500 1 VAL B 23 -26.15 -172.53 REMARK 500 1 MET B 37 -77.32 -30.98 REMARK 500 1 ARG B 41 -147.85 56.85 REMARK 500 1 LEU B 44 19.79 56.92 REMARK 500 1 THR B 58 -8.68 -145.97 REMARK 500 1 PRO B 60 65.77 -104.87 REMARK 500 1 THR B 62 171.47 -57.85 REMARK 500 1 THR B 71 26.23 -163.75 REMARK 500 1 ILE B 72 -127.87 -114.92 REMARK 500 1 LYS B 74 -47.35 72.56 REMARK 500 1 ARG B 99 -62.31 68.38 REMARK 500 2 VAL A 23 -24.69 -169.09 REMARK 500 2 LEU A 35 30.37 -167.72 REMARK 500 2 ARG A 41 -99.14 54.00 REMARK 500 2 THR A 58 -9.73 -145.57 REMARK 500 2 PRO A 60 62.01 -105.35 REMARK 500 2 THR A 71 26.08 -164.22 REMARK 500 2 ILE A 72 -127.74 -104.19 REMARK 500 2 LYS A 74 -50.74 71.40 REMARK 500 2 VAL B 23 -24.23 -168.58 REMARK 500 2 LEU B 35 30.35 -167.46 REMARK 500 2 ARG B 41 -98.97 54.10 REMARK 500 2 THR B 58 -9.78 -145.18 REMARK 500 2 PRO B 60 62.27 -105.31 REMARK 500 2 THR B 71 26.23 -164.28 REMARK 500 2 ILE B 72 -127.88 -104.27 REMARK 500 2 LYS B 74 -50.91 71.26 REMARK 500 3 VAL A 23 -28.44 -172.35 REMARK 500 3 LEU A 35 55.81 -111.85 REMARK 500 3 ARG A 41 -97.80 52.36 REMARK 500 3 THR A 58 -8.96 -145.03 REMARK 500 3 PRO A 60 64.21 -105.09 REMARK 500 3 THR A 71 26.44 -167.12 REMARK 500 3 ILE A 72 -125.23 -98.32 REMARK 500 3 LYS A 74 -49.68 70.43 REMARK 500 3 ARG A 97 46.07 -95.63 REMARK 500 3 VAL B 23 -27.21 -171.77 REMARK 500 3 LEU B 35 30.77 -92.62 REMARK 500 3 MET B 37 -46.15 62.03 REMARK 500 3 ARG B 41 -97.31 52.44 REMARK 500 REMARK 500 THIS ENTRY HAS 364 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 22 0.25 SIDE CHAIN REMARK 500 1 ARG A 32 0.22 SIDE CHAIN REMARK 500 1 ARG A 41 0.29 SIDE CHAIN REMARK 500 1 ARG A 55 0.28 SIDE CHAIN REMARK 500 1 ARG A 68 0.21 SIDE CHAIN REMARK 500 1 ARG A 82 0.23 SIDE CHAIN REMARK 500 1 ARG A 85 0.31 SIDE CHAIN REMARK 500 1 ARG A 90 0.25 SIDE CHAIN REMARK 500 1 ARG A 97 0.32 SIDE CHAIN REMARK 500 1 ARG A 98 0.21 SIDE CHAIN REMARK 500 1 ARG A 99 0.29 SIDE CHAIN REMARK 500 1 ARG A 100 0.29 SIDE CHAIN REMARK 500 1 ARG B 22 0.25 SIDE CHAIN REMARK 500 1 ARG B 32 0.22 SIDE CHAIN REMARK 500 1 ARG B 41 0.29 SIDE CHAIN REMARK 500 1 ARG B 55 0.28 SIDE CHAIN REMARK 500 1 ARG B 68 0.21 SIDE CHAIN REMARK 500 1 ARG B 82 0.22 SIDE CHAIN REMARK 500 1 ARG B 85 0.31 SIDE CHAIN REMARK 500 1 ARG B 90 0.25 SIDE CHAIN REMARK 500 1 ARG B 97 0.32 SIDE CHAIN REMARK 500 1 ARG B 98 0.21 SIDE CHAIN REMARK 500 1 ARG B 99 0.29 SIDE CHAIN REMARK 500 1 ARG B 100 0.29 SIDE CHAIN REMARK 500 2 ARG A 22 0.32 SIDE CHAIN REMARK 500 2 ARG A 32 0.31 SIDE CHAIN REMARK 500 2 ARG A 41 0.31 SIDE CHAIN REMARK 500 2 ARG A 55 0.28 SIDE CHAIN REMARK 500 2 ARG A 68 0.21 SIDE CHAIN REMARK 500 2 ARG A 82 0.32 SIDE CHAIN REMARK 500 2 ARG A 85 0.31 SIDE CHAIN REMARK 500 2 ARG A 90 0.32 SIDE CHAIN REMARK 500 2 ARG A 97 0.32 SIDE CHAIN REMARK 500 2 ARG A 98 0.29 SIDE CHAIN REMARK 500 2 ARG A 99 0.31 SIDE CHAIN REMARK 500 2 ARG A 100 0.21 SIDE CHAIN REMARK 500 2 ARG B 22 0.32 SIDE CHAIN REMARK 500 2 ARG B 32 0.31 SIDE CHAIN REMARK 500 2 ARG B 41 0.31 SIDE CHAIN REMARK 500 2 ARG B 55 0.28 SIDE CHAIN REMARK 500 2 ARG B 68 0.21 SIDE CHAIN REMARK 500 2 ARG B 82 0.32 SIDE CHAIN REMARK 500 2 ARG B 85 0.31 SIDE CHAIN REMARK 500 2 ARG B 90 0.32 SIDE CHAIN REMARK 500 2 ARG B 97 0.32 SIDE CHAIN REMARK 500 2 ARG B 98 0.29 SIDE CHAIN REMARK 500 2 ARG B 99 0.31 SIDE CHAIN REMARK 500 2 ARG B 100 0.21 SIDE CHAIN REMARK 500 3 ARG A 22 0.22 SIDE CHAIN REMARK 500 3 ARG A 32 0.31 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 504 PLANE DEVIATIONS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5973 RELATED DB: BMRB REMARK 900 CHEMICAL SHIFT DATA OF THE SAME PROTEIN REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE RESIDUES 1-20 ARE MISSING FROM ALL THE REMARK 999 MODELS. THE NMR EXPERIMENTAL DATA WERE OBTAINED REMARK 999 USING PROTEIN INCLUDING THE MISSING RESIDUES. REMARK 999 SINCE THE N-TERMINAL 20 RESIDUES ARE USTRUCTURED, REMARK 999 THEY WERE EXCLUDED FROM THE STRUCTURE REFINEMENT. DBREF 1R6R A 1 100 UNP P12823 POLG_DEN2P 1 100 DBREF 1R6R B 1 100 UNP P12823 POLG_DEN2P 1 100 SEQRES 1 A 100 MET ASN ASP GLN ARG LYS LYS ALA ARG ASN THR PRO PHE SEQRES 2 A 100 ASN MET LEU LYS ARG GLU ARG ASN ARG VAL SER THR VAL SEQRES 3 A 100 GLN GLN LEU THR LYS ARG PHE SER LEU GLY MET LEU GLN SEQRES 4 A 100 GLY ARG GLY PRO LEU LYS LEU PHE MET ALA LEU VAL ALA SEQRES 5 A 100 PHE LEU ARG PHE LEU THR ILE PRO PRO THR ALA GLY ILE SEQRES 6 A 100 LEU LYS ARG TRP GLY THR ILE LYS LYS SER LYS ALA ILE SEQRES 7 A 100 ASN VAL LEU ARG GLY PHE ARG LYS GLU ILE GLY ARG MET SEQRES 8 A 100 LEU ASN ILE LEU ASN ARG ARG ARG ARG SEQRES 1 B 100 MET ASN ASP GLN ARG LYS LYS ALA ARG ASN THR PRO PHE SEQRES 2 B 100 ASN MET LEU LYS ARG GLU ARG ASN ARG VAL SER THR VAL SEQRES 3 B 100 GLN GLN LEU THR LYS ARG PHE SER LEU GLY MET LEU GLN SEQRES 4 B 100 GLY ARG GLY PRO LEU LYS LEU PHE MET ALA LEU VAL ALA SEQRES 5 B 100 PHE LEU ARG PHE LEU THR ILE PRO PRO THR ALA GLY ILE SEQRES 6 B 100 LEU LYS ARG TRP GLY THR ILE LYS LYS SER LYS ALA ILE SEQRES 7 B 100 ASN VAL LEU ARG GLY PHE ARG LYS GLU ILE GLY ARG MET SEQRES 8 B 100 LEU ASN ILE LEU ASN ARG ARG ARG ARG HELIX 1 1 VAL A 26 PHE A 33 1 8 HELIX 2 2 LEU A 44 THR A 58 1 15 HELIX 3 3 THR A 62 GLY A 70 1 9 HELIX 4 4 LYS A 74 ASN A 96 1 23 HELIX 5 5 VAL B 26 PHE B 33 1 8 HELIX 6 6 LEU B 44 THR B 58 1 15 HELIX 7 7 THR B 62 GLY B 70 1 9 HELIX 8 8 LYS B 74 ASN B 96 1 23 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