HEADER HYDROLASE 01-NOV-02 1N4T OBSLTE 06-MAR-07 1N4T 2ILX TITLE SOLUTION STRUCTURE OF THE CATALYTIC DOMAIN FROM RAT CNP COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2',3'-CYCLIC NUCLEOTIDE 3'-PHOSPHODIESTERASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC DOMAIN (RESIDUES 184-398); COMPND 5 EC: 3.1.4.37; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: RAT; SOURCE 4 GENE: CNP1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_COMMON: BACTERIA; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS MIXED ALPHA-BETA, OPEN BETA-SHEET STRUCTURE EXPDTA NMR, 20 STRUCTURES AUTHOR G.KOZLOV,J.LEE,P.GUTIERREZ,I.EKIEL,P.E.BRAUN,K.GEHRING REVDAT 2 06-MAR-07 1N4T 1 OBSLTE REVDAT 1 09-SEP-03 1N4T 0 JRNL AUTH G.KOZLOV,J.LEE,D.ELIAS,M.GRAVEL,P.GUTIERREZ, JRNL AUTH 2 I.EKIEL,P.E.BRAUN,K.GEHRING JRNL TITL STRUCTURAL EVIDENCE THAT BRAIN CYCLIC NUCLEOTIDE JRNL TITL 2 PHOSPHODIESTERASE IS A MEMBER OF THE 2H JRNL TITL 3 PHOSPHODIESTERASE SUPERFAMILY. JRNL REF J.BIOL.CHEM. V. 278 46021 2003 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 : CNS 1.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON A TOTAL REMARK 3 OF 2338 RESTRAINTS, 1925 ARE NOE-DERIVED DISTANCE CONSTRAINTS, REMARK 3 326 DIHEDRAL ANGLE RESTRAINTS, 87 DISTANCE RESTRAINTS FROM REMARK 3 HYDROGEN BONDS. REMARK 4 REMARK 4 1N4T COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS FILE IS A TEST VERSION. REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.100 (2007-05-01) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-NOV-2002. REMARK 100 THE RCSB ID CODE IS RCSB017519. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 310 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 0.15M NACL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1-2MM CNP U-15N; 50MM REMARK 210 PHOSPHATE BUFFER; 0.15M NACL; REMARK 210 1MM DTT; 0.1MM SODIUM AZIDE; REMARK 210 1-2MM CNP U-15N,13C; 50MM REMARK 210 PHOSPHATE BUFFER; 0.15M NACL; REMARK 210 1MM DTT; 0.1MM SODIUM AZIDE; REMARK 210 1-2MM CNP; 50MM PHOSPHATE REMARK 210 BUFFER; 0.15M NACL; 1MM DTT; REMARK 210 0.1MM SODIUM AZIDE REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_15N-SEPARATED_NOESY, 3D_ REMARK 210 13C-SEPARATED_NOESY, 2D NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ, 500 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS, DRX REMARK 210 SPECTROMETER MANUFACTURER : VARIAN, BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XWINNMR 2.1, GIFA 4.31, XEASY REMARK 210 1.3.13, ARIA 1.1 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 60 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE AND REMARK 210 2D HOMONUCLEAR TECHNIQUES. 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 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 REMARK 500 O ALA A 116 O LEU A 153 2.16 REMARK 500 O LEU A 204 O LYS A 207 2.18 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 1 GLY A 1 N GLY A 1 CA 0.039 REMARK 500 1 ARG A 199 CA ARG A 199 CB 0.024 REMARK 500 1 ARG A 199 CB ARG A 199 CG 0.022 REMARK 500 1 GLU A 209 CB GLU A 209 CG 0.022 REMARK 500 2 GLY A 1 N GLY A 1 CA 0.037 REMARK 500 2 ARG A 199 CA ARG A 199 CB 0.027 REMARK 500 3 GLY A 1 N GLY A 1 CA 0.038 REMARK 500 3 ARG A 199 CA ARG A 199 CB 0.021 REMARK 500 4 GLY A 1 N GLY A 1 CA 0.038 REMARK 500 4 ARG A 199 CB ARG A 199 CG 0.021 REMARK 500 5 GLY A 1 N GLY A 1 CA 0.038 REMARK 500 5 ARG A 199 CA ARG A 199 CB 0.026 REMARK 500 6 GLY A 1 N GLY A 1 CA 0.038 REMARK 500 6 ARG A 199 CA ARG A 199 CB 0.028 REMARK 500 6 ARG A 199 CB ARG A 199 CG 0.026 REMARK 500 7 GLY A 1 N GLY A 1 CA 0.038 REMARK 500 7 ARG A 199 CA ARG A 199 CB 0.026 REMARK 500 8 GLY A 1 N GLY A 1 CA 0.037 REMARK 500 8 ARG A 199 CA ARG A 199 CB 0.025 REMARK 500 9 GLY A 1 N GLY A 1 CA 0.037 REMARK 500 9 ARG A 199 CA ARG A 199 CB 0.031 REMARK 500 10 GLY A 1 N GLY A 1 CA 0.038 REMARK 500 10 ARG A 199 CA ARG A 199 CB 0.029 REMARK 500 10 ARG A 199 CB ARG A 199 CG 0.027 REMARK 500 11 GLY A 1 N GLY A 1 CA 0.037 REMARK 500 11 ARG A 199 CA ARG A 199 CB 0.026 REMARK 500 12 GLY A 1 N GLY A 1 CA 0.038 REMARK 500 12 LYS A 191 CA LYS A 191 CB -0.021 REMARK 500 12 ARG A 199 CA ARG A 199 CB 0.028 REMARK 500 13 GLY A 1 N GLY A 1 CA 0.037 REMARK 500 13 ARG A 199 CA ARG A 199 CB 0.027 REMARK 500 14 GLY A 1 N GLY A 1 CA 0.038 REMARK 500 14 ARG A 199 CA ARG A 199 CB 0.026 REMARK 500 15 GLY A 1 N GLY A 1 CA 0.038 REMARK 500 15 ARG A 199 CA ARG A 199 CB 0.029 REMARK 500 15 ARG A 199 CB ARG A 199 CG 0.027 REMARK 500 16 GLY A 1 N GLY A 1 CA 0.037 REMARK 500 16 ARG A 199 CA ARG A 199 CB 0.023 REMARK 500 16 ARG A 199 CB ARG A 199 CG 0.021 REMARK 500 17 GLY A 1 N GLY A 1 CA 0.038 REMARK 500 17 ARG A 199 CA ARG A 199 CB 0.025 REMARK 500 17 ARG A 199 CB ARG A 199 CG 0.021 REMARK 500 17 GLU A 209 CB GLU A 209 CG 0.022 REMARK 500 17 GLU A 209 CG GLU A 209 CD 0.021 REMARK 500 18 GLY A 1 N GLY A 1 CA 0.038 REMARK 500 18 ARG A 199 CA ARG A 199 CB 0.030 REMARK 500 18 ARG A 199 CB ARG A 199 CG 0.026 REMARK 500 19 GLY A 1 N GLY A 1 CA 0.037 REMARK 500 19 ARG A 199 CA ARG A 199 CB 0.027 REMARK 500 20 GLY A 1 N GLY A 1 CA 0.037 REMARK 500 20 ARG A 199 CA ARG A 199 CB 0.025 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 1 TRP A 12 N - CA - C ANGL. DEV. = -3.6 DEGREES REMARK 500 1 SER A 105 N - CA - C ANGL. DEV. = -4.6 DEGREES REMARK 500 1 VAL A 210 N - CA - C ANGL. DEV. = -4.0 DEGREES REMARK 500 2 SER A 105 N - CA - C ANGL. DEV. = -4.6 DEGREES REMARK 500 2 GLY A 181 N - CA - C ANGL. DEV. = 3.5 DEGREES REMARK 500 3 SER A 105 N - CA - C ANGL. DEV. = -5.0 DEGREES REMARK 500 3 VAL A 210 N - CA - C ANGL. DEV. = -3.6 DEGREES REMARK 500 4 TRP A 12 N - CA - C ANGL. DEV. = -3.7 DEGREES REMARK 500 4 SER A 105 N - CA - C ANGL. DEV. = -5.2 DEGREES REMARK 500 4 VAL A 210 N - CA - C ANGL. DEV. = -3.6 DEGREES REMARK 500 5 TRP A 12 N - CA - C ANGL. DEV. = -3.5 DEGREES REMARK 500 5 SER A 105 N - CA - C ANGL. DEV. = -5.4 DEGREES REMARK 500 6 TRP A 12 N - CA - C ANGL. DEV. = -3.6 DEGREES REMARK 500 6 SER A 105 N - CA - C ANGL. DEV. = -5.2 DEGREES REMARK 500 6 ALA A 118 N - CA - C ANGL. DEV. = -3.5 DEGREES REMARK 500 7 TRP A 12 N - CA - C ANGL. DEV. = -4.1 DEGREES REMARK 500 7 SER A 105 N - CA - C ANGL. DEV. = -5.1 DEGREES REMARK 500 8 SER A 105 N - CA - C ANGL. DEV. = -5.5 DEGREES REMARK 500 8 VAL A 210 N - CA - C ANGL. DEV. = -3.5 DEGREES REMARK 500 9 SER A 105 N - CA - C ANGL. DEV. = -4.8 DEGREES REMARK 500 9 VAL A 210 N - CA - C ANGL. DEV. = -4.0 DEGREES REMARK 500 10 SER A 105 N - CA - C ANGL. DEV. = -5.1 DEGREES REMARK 500 11 TRP A 12 N - CA - C ANGL. DEV. = -4.3 DEGREES REMARK 500 11 SER A 105 N - CA - C ANGL. DEV. = -5.2 DEGREES REMARK 500 11 VAL A 210 N - CA - C ANGL. DEV. = -3.6 DEGREES REMARK 500 12 SER A 105 N - CA - C ANGL. DEV. = -5.1 DEGREES REMARK 500 12 VAL A 210 N - CA - C ANGL. DEV. = -3.8 DEGREES REMARK 500 13 TRP A 12 N - CA - C ANGL. DEV. = -4.3 DEGREES REMARK 500 13 SER A 105 N - CA - C ANGL. DEV. = -5.1 DEGREES REMARK 500 13 VAL A 210 N - CA - C ANGL. DEV. = -3.6 DEGREES REMARK 500 14 SER A 105 N - CA - C ANGL. DEV. = -5.2 DEGREES REMARK 500 14 GLY A 181 N - CA - C ANGL. DEV. = 3.5 DEGREES REMARK 500 15 SER A 105 N - CA - C ANGL. DEV. = -5.3 DEGREES REMARK 500 16 SER A 105 N - CA - C ANGL. DEV. = -5.1 DEGREES REMARK 500 16 VAL A 210 N - CA - C ANGL. DEV. = -3.7 DEGREES REMARK 500 17 THR A 21 CA - CB - CG2 ANGL. DEV. = 3.7 DEGREES REMARK 500 17 SER A 105 N - CA - C ANGL. DEV. = -5.2 DEGREES REMARK 500 17 VAL A 210 N - CA - C ANGL. DEV. = -3.9 DEGREES REMARK 500 18 SER A 105 N - CA - C ANGL. DEV. = -5.1 DEGREES REMARK 500 19 TRP A 12 N - CA - C ANGL. DEV. = -3.9 DEGREES REMARK 500 19 SER A 105 N - CA - C ANGL. DEV. = -5.3 DEGREES REMARK 500 19 VAL A 210 N - CA - C ANGL. DEV. = -3.5 DEGREES REMARK 500 20 TRP A 12 N - CA - C ANGL. DEV. = -4.5 DEGREES REMARK 500 20 SER A 105 N - CA - C ANGL. DEV. = -5.0 DEGREES DBREF 1N4T A 5 219 UNP P13233 CN37_RAT 184 398 SEQADV 1N4T GLY A 1 UNP P13233 CLONING ARTIFACT SEQADV 1N4T SER A 2 UNP P13233 CLONING ARTIFACT SEQADV 1N4T HIS A 3 UNP P13233 CLONING ARTIFACT SEQADV 1N4T MET A 4 UNP P13233 CLONING ARTIFACT SEQRES 1 A 219 GLY SER HIS MET PHE LEU PRO LEU TYR PHE GLY TRP PHE SEQRES 2 A 219 LEU THR LYS LYS SER SER GLU THR LEU ARG LYS ALA GLY SEQRES 3 A 219 GLN VAL PHE LEU GLU GLU LEU GLY ASN HIS LYS ALA PHE SEQRES 4 A 219 LYS LYS GLU LEU ARG HIS PHE ILE SER GLY ASP GLU PRO SEQRES 5 A 219 LYS GLU LYS LEU ASP LEU VAL SER TYR PHE GLY LYS ARG SEQRES 6 A 219 PRO PRO GLY VAL LEU HIS CYS THR THR LYS PHE CYS ASP SEQRES 7 A 219 TYR GLY LYS ALA THR GLY ALA GLU GLU TYR ALA GLN GLN SEQRES 8 A 219 ASP VAL VAL ARG ARG SER TYR GLY LYS ALA PHE LYS LEU SEQRES 9 A 219 SER ILE SER ALA LEU PHE VAL THR PRO LYS THR ALA GLY SEQRES 10 A 219 ALA GLN VAL VAL LEU ASN GLU GLN GLU LEU GLN LEU TRP SEQRES 11 A 219 PRO SER ASP LEU ASP LYS PRO SER SER SER GLU SER LEU SEQRES 12 A 219 PRO PRO GLY SER ARG ALA HIS VAL THR LEU GLY CYS ALA SEQRES 13 A 219 ALA ASP VAL GLN PRO VAL GLN THR GLY LEU ASP LEU LEU SEQRES 14 A 219 GLU ILE LEU GLN GLN VAL LYS GLY GLY SER GLN GLY GLU SEQRES 15 A 219 GLU VAL GLY GLU LEU PRO ARG GLY LYS LEU TYR SER LEU SEQRES 16 A 219 GLY LYS GLY ARG TRP MET LEU SER LEU ALA LYS LYS MET SEQRES 17 A 219 GLU VAL LYS ALA ILE PHE THR GLY TYR TYR GLY HELIX 1 1 THR A 21 LYS A 37 1 17 HELIX 2 2 ALA A 38 LEU A 43 1 6 HELIX 3 3 THR A 83 TYR A 98 1 16 HELIX 4 4 ASN A 123 ASP A 135 1 13 HELIX 5 5 PRO A 161 LYS A 176 1 16 SHEET 1 A 4 LEU A 70 THR A 74 0 SHEET 2 A 4 PHE A 10 LEU A 14 -1 N TRP A 12 O CYS A 72 SHEET 3 A 4 GLU A 182 GLY A 185 -1 O VAL A 184 N GLY A 11 SHEET 4 A 4 LEU A 192 SER A 194 -1 O SER A 194 N GLU A 183 SHEET 1 B 2 PHE A 102 LEU A 104 0 SHEET 2 B 2 VAL A 210 ALA A 212 -1 O VAL A 210 N LEU A 104 SHEET 1 C 3 LEU A 109 VAL A 111 0 SHEET 2 C 3 ALA A 116 ALA A 118 -1 O GLY A 117 N PHE A 110 SHEET 3 C 3 VAL A 151 LEU A 153 -1 O LEU A 153 N ALA A 116 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