HEADER HYDROLASE 28-OCT-03 1R8V TITLE 3D STRUCTURE PREDICTION OF CLPP2 PROTEASE FROM ARABIDOPSIS TITLE 2 THALIANA, USING THE CRYSTAL STRUCTURE OF E. COLI CLPP TITLE 3 (1TYF) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT COMPND 3 (CLPP2); COMPND 4 CHAIN: A; COMPND 5 EC: 3.4.21.92 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 OTHER_DETAILS: ECOTYPE: COLUMBIA 0 KEYWDS SERINE PROTEASE, CLP PROTEASE, ARABIDOPSIS THALIANA EXPDTA THEORETICAL MODEL AUTHOR J.B.PELTIER,D.R.RIPOLL,G.FRISO,A.RUDELLA,Y.CAI,J.YTTERBERG, AUTHOR 2 L.GIACOMELLI,J.PILLARDY,K.J.VAN WIJK REVDAT 2 17-FEB-04 1R8V 1 JRNL REVDAT 1 18-NOV-03 1R8V 0 JRNL AUTH J.B.PELTIER,D.R.RIPOLL,G.FRISO,A.RUDELLA,Y.CAI, JRNL AUTH 2 J.YTTERBERG,L.GIACOMELLI,J.PILLARDY,K.J.VAN WIJK JRNL TITL CLP PROTEASE COMPLEXES FROM PHOTOSYNTHETIC AND JRNL TITL 2 NON-PHOTOSYNTHETIC PLASTIDS AND MITOCHONDRIA OF JRNL TITL 3 PLANTS, THEIR PREDICTED THREE-DIMENSIONAL JRNL TITL 4 STRUCTURES, AND FUNCTIONAL IMPLICATIONS. JRNL REF J.BIOL.CHEM. V. 279 4768 2004 JRNL REFN ASTM JBCHA3 US ISSN 0021-9258 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : MODELLER REMARK 3 AUTHORS : SALI REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1R8V COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-OCT-2003. REMARK 100 THE RCSB ID CODE IS RCSB020581. REMARK 220 REMARK 220 EXPERIMENTAL DETAILS REMARK 220 EXPERIMENT TYPE : THEORETICAL MODELLING REMARK 220 REMARK 220 REMARK: NULL REMARK 225 REMARK 225 THEORETICAL MODEL REMARK 225 THE COORDINATES IN THIS ENTRY REPRESENT A MODEL STRUCTURE. REMARK 225 PROTEIN DATA BANK CONVENTIONS REQUIRE THAT CRYST1 AND REMARK 225 SCALE RECORDS BE INCLUDED, BUT THE VALUES ON THESE REMARK 225 RECORDS ARE MEANINGLESS. 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 MET A 1 REMARK 465 MET A 2 REMARK 465 ARG A 3 REMARK 465 GLY A 4 REMARK 465 LEU A 5 REMARK 465 VAL A 6 REMARK 465 SER A 7 REMARK 465 GLY A 8 REMARK 465 ALA A 9 REMARK 465 LYS A 10 REMARK 465 MET A 11 REMARK 465 LEU A 12 REMARK 465 SER A 13 REMARK 465 SER A 14 REMARK 465 THR A 15 REMARK 465 PRO A 16 REMARK 465 SER A 17 REMARK 465 SER A 18 REMARK 465 MET A 19 REMARK 465 ALA A 20 REMARK 465 THR A 21 REMARK 465 SER A 22 REMARK 465 ILE A 23 REMARK 465 ALA A 24 REMARK 465 THR A 25 REMARK 465 GLY A 26 REMARK 465 ARG A 27 REMARK 465 ARG A 28 REMARK 465 SER A 29 REMARK 465 TYR A 30 REMARK 465 SER A 31 REMARK 465 LEU A 32 REMARK 465 ILE A 33 REMARK 465 PRO A 34 REMARK 465 MET A 35 REMARK 465 VAL A 36 REMARK 465 ILE A 37 REMARK 465 GLU A 38 REMARK 465 HIS A 39 REMARK 465 SER A 40 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),F6.3) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 ASP A 237 CG ASP A 237 OD2 0.118 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: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ILE A 219 N - CA - C ANGL. DEV. =-14.8 DEGREES REMARK 500 SER A 241 N - CA - C ANGL. DEV. =-22.6 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 SER A 127 -84.63 45.11 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 ARG A 222 PRO A 223 -144.12 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: AT5G23140 RELATED DB: TAIR DBREF 1R8V A 1 241 GB 18420643 NP_568427 1 241 SEQRES 1 A 241 MET MET ARG GLY LEU VAL SER GLY ALA LYS MET LEU SER SEQRES 2 A 241 SER THR PRO SER SER MET ALA THR SER ILE ALA THR GLY SEQRES 3 A 241 ARG ARG SER TYR SER LEU ILE PRO MET VAL ILE GLU HIS SEQRES 4 A 241 SER SER ARG GLY GLU ARG ALA TYR ASP ILE PHE SER ARG SEQRES 5 A 241 LEU LEU LYS GLU ARG ILE ILE CYS ILE ASN GLY PRO ILE SEQRES 6 A 241 ASN ASP ASP THR SER HIS VAL VAL VAL ALA GLN LEU LEU SEQRES 7 A 241 TYR LEU GLU SER GLU ASN PRO SER LYS PRO ILE HIS MET SEQRES 8 A 241 TYR LEU ASN SER PRO GLY GLY HIS VAL THR ALA GLY LEU SEQRES 9 A 241 ALA ILE TYR ASP THR MET GLN TYR ILE ARG SER PRO ILE SEQRES 10 A 241 SER THR ILE CYS LEU GLY GLN ALA ALA SER MET ALA SER SEQRES 11 A 241 LEU LEU LEU ALA ALA GLY ALA LYS GLY GLN ARG ARG SER SEQRES 12 A 241 LEU PRO ASN ALA THR VAL MET ILE HIS GLN PRO SER GLY SEQRES 13 A 241 GLY TYR SER GLY GLN ALA LYS ASP ILE THR ILE HIS THR SEQRES 14 A 241 LYS GLN ILE VAL ARG VAL TRP ASP ALA LEU ASN GLU LEU SEQRES 15 A 241 TYR VAL LYS HIS THR GLY GLN PRO LEU ASP VAL VAL ALA SEQRES 16 A 241 ASN ASN MET ASP ARG ASP HIS PHE MET THR PRO GLU GLU SEQRES 17 A 241 ALA LYS ALA PHE GLY ILE ILE ASP GLU VAL ILE ASP GLU SEQRES 18 A 241 ARG PRO LEU GLU LEU VAL LYS ASP ALA VAL GLY ASN GLU SEQRES 19 A 241 SER LYS ASP LYS SER SER SER HELIX 1 1 GLU A 44 GLU A 56 1 13 HELIX 2 2 ASP A 68 ASN A 84 1 17 HELIX 3 3 HIS A 99 ASP A 108 1 10 HELIX 4 4 SER A 127 ALA A 135 1 9 HELIX 5 5 GLN A 161 GLY A 188 1 28 HELIX 6 6 PRO A 190 MET A 198 1 9 HELIX 7 7 THR A 205 PHE A 212 1 8 HELIX 8 8 PRO A 223 LYS A 238 1 16 SHEET 1 A 4 ILE A 58 ASN A 62 0 SHEET 2 A 4 ILE A 89 SER A 95 1 O TYR A 92 N ILE A 59 SHEET 3 A 4 ILE A 117 ALA A 126 1 O SER A 118 N MET A 91 SHEET 4 A 4 ARG A 141 SER A 143 1 O ARG A 142 N THR A 119 SHEET 1 B 4 ILE A 58 ASN A 62 0 SHEET 2 B 4 ILE A 89 SER A 95 1 O TYR A 92 N ILE A 59 SHEET 3 B 4 ILE A 117 ALA A 126 1 O SER A 118 N MET A 91 SHEET 4 B 4 THR A 148 MET A 150 1 O THR A 148 N ALA A 125 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 MASTER 130 0 0 8 8 0 0 6 0 0 0 19 END