HEADER BINDING PROTEIN/HYDROLASE 06-FEB-03 1NWD TITLE SOLUTION STRUCTURE OF CA2+/CALMODULIN BOUND TO THE C-TERMINAL DOMAIN TITLE 2 OF PETUNIA GLUTAMATE DECARBOXYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CALMODULIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: GLUTAMATE DECARBOXYLASE; COMPND 7 CHAIN: B, C; COMPND 8 FRAGMENT: C-TERMINAL CALMODULIN BINDING DOMAIN (RESIDUES 470-495); COMPND 9 SYNONYM: GAD; COMPND 10 EC: 4.1.1.15; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XENOPUS LAEVIS; SOURCE 3 ORGANISM_COMMON: AFRICAN CLAWED FROG; SOURCE 4 ORGANISM_TAXID: 8355; SOURCE 5 GENE: (CALM1 OR CAM1 OR CALM OR CAM) AND (CALM2 OR CAM2 OR CAMB) AND SOURCE 6 (CALM3 OR CAM3 OR CAMC); SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: AR58; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PAS; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: PETUNIA X HYBRIDA; SOURCE 14 ORGANISM_TAXID: 4102; SOURCE 15 GENE: GAD; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 17 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 18 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 19 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 20 EXPRESSION_SYSTEM_PLASMID: PGEX-2T KEYWDS CALMODULIN-PEPTIDE COMPLEX, CALMODULIN, GAD, GLUTAMATE DECARBOXYLASE, KEYWDS 2 DIMER, BINDING PROTEIN-HYDROLASE COMPLEX EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.L.YAP,T.YUAN,T.K.MAL,H.J.VOGEL,M.IKURA REVDAT 3 23-FEB-22 1NWD 1 REMARK SEQADV LINK REVDAT 2 24-FEB-09 1NWD 1 VERSN REVDAT 1 08-APR-03 1NWD 0 JRNL AUTH K.L.YAP,T.YUAN,T.K.MAL,H.J.VOGEL,M.IKURA JRNL TITL STRUCTURAL BASIS FOR SIMULTANEOUS BINDING OF TWO JRNL TITL 2 CARBOXY-TERMINAL PEPTIDES OF PLANT GLUTAMATE DECARBOXYLASE JRNL TITL 3 TO CALMODULIN JRNL REF J.MOL.BIOL. V. 328 193 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12684008 JRNL DOI 10.1016/S0022-2836(03)00271-7 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 TITL CALCIUM-CALMODULIN-INDUCED DIMERIZATION OF THE REMARK 1 TITL 2 CARBOXYL-TERMINAL DOMAIN FROM PETUNIA GLUTAMATE REMARK 1 TITL 3 DECARBOXYLASE REMARK 1 REF J.BIOL.CHEM. V. 273 30328 1998 REMARK 1 REFN ISSN 0021-9258 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: NULL REMARK 4 REMARK 4 1NWD COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-FEB-03. REMARK 100 THE DEPOSITION ID IS D_1000018280. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 6.3 REMARK 210 IONIC STRENGTH : 100 MM KCL, 10 MM CACL2 REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : 1 MM CALMODULIN; 2.2 MM GAD REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : NULL REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : DYANA 1.5, XEASY 6300, NMRPIPE REMARK 210 FOR SOLARIS 2 REMARK 210 METHOD USED : SIMULATED ANNEALING AND TORSION REMARK 210 ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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 : 4 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING ISOTOPE-EDITED AND REMARK 210 FILTERED TRIPLE RESONANCE NMR EXPERIMENTS ON A NUMBER OF COMPLEX REMARK 210 SAMPLES WITH VARIOUS COMBINATIONS OF 15-N, 13-C AND 2-H REMARK 210 LABELING. SEE CITATION REFERENCE FOR DETAILS. 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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: 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 LYS A 75 152.50 74.45 REMARK 500 1 MET A 76 153.70 73.74 REMARK 500 1 THR A 79 -87.44 -78.13 REMARK 500 1 ASP A 95 -64.55 -171.07 REMARK 500 1 GLU A 114 83.16 -156.62 REMARK 500 1 LYS A 115 88.69 -69.10 REMARK 500 1 ILE A 125 -62.45 -101.45 REMARK 500 1 ARG A 126 20.89 -77.48 REMARK 500 1 ALA A 128 69.28 -159.15 REMARK 500 1 ASP A 133 25.73 -152.29 REMARK 500 1 THR A 146 55.44 -119.42 REMARK 500 1 HIS B 3 -66.80 -149.59 REMARK 500 2 ASN A 42 79.15 -119.48 REMARK 500 2 VAL A 55 38.30 -99.02 REMARK 500 2 LYS A 75 122.67 94.72 REMARK 500 2 MET A 76 131.26 80.20 REMARK 500 2 ASP A 78 -155.75 -134.48 REMARK 500 2 ASN A 97 24.13 -147.03 REMARK 500 2 ASP A 133 9.52 -150.23 REMARK 500 2 HIS B 3 124.39 -173.64 REMARK 500 2 LYS B 27 107.16 -162.47 REMARK 500 2 SER C 2 -57.09 -150.14 REMARK 500 3 ILE A 27 78.00 -111.90 REMARK 500 3 ARG A 74 -113.75 -86.75 REMARK 500 3 LYS A 75 -131.90 -152.57 REMARK 500 3 THR A 79 -78.61 -73.93 REMARK 500 3 PHE A 92 -71.17 -73.22 REMARK 500 3 TYR A 99 90.70 -162.59 REMARK 500 3 LYS A 115 55.40 -90.20 REMARK 500 3 ALA A 128 75.66 -151.99 REMARK 500 3 ASP A 133 25.46 -148.37 REMARK 500 3 THR A 146 59.55 -105.71 REMARK 500 3 SER B 2 -75.22 -142.28 REMARK 500 4 ASN A 42 78.10 -113.66 REMARK 500 4 LYS A 75 128.09 79.44 REMARK 500 4 MET A 76 117.06 76.64 REMARK 500 4 PHE A 92 -72.82 -79.69 REMARK 500 4 THR A 117 105.24 -52.56 REMARK 500 4 ALA A 128 50.86 -150.20 REMARK 500 4 ASP A 133 43.59 -145.16 REMARK 500 4 GLU A 139 -9.97 -58.95 REMARK 500 4 SER B 2 -71.17 70.53 REMARK 500 4 SER C 2 -70.64 -153.46 REMARK 500 5 LEU A 39 -71.29 -54.72 REMARK 500 5 ALA A 73 -64.79 -94.17 REMARK 500 5 LYS A 75 121.38 84.23 REMARK 500 5 MET A 76 136.76 68.69 REMARK 500 5 THR A 79 -87.05 -75.34 REMARK 500 5 ASP A 95 -55.20 -178.27 REMARK 500 5 TYR A 99 89.76 -158.00 REMARK 500 REMARK 500 THIS ENTRY HAS 264 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 TYR A 138 0.09 SIDE CHAIN REMARK 500 8 TYR A 99 0.08 SIDE CHAIN REMARK 500 8 PHE B 21 0.07 SIDE CHAIN REMARK 500 10 TYR A 99 0.06 SIDE CHAIN REMARK 500 11 PHE A 68 0.09 SIDE CHAIN REMARK 500 13 TYR A 138 0.07 SIDE CHAIN REMARK 500 14 PHE A 89 0.07 SIDE CHAIN REMARK 500 18 PHE A 12 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 149 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 22 OD2 REMARK 620 2 ASP A 24 OD1 106.5 REMARK 620 3 ASP A 24 OD2 71.3 41.0 REMARK 620 4 THR A 26 OG1 160.3 53.8 90.8 REMARK 620 5 GLU A 31 OE2 66.8 99.9 104.0 111.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 150 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 62 O REMARK 620 2 ASP A 64 OD1 70.2 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 151 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 93 OD2 REMARK 620 2 ASN A 97 OD1 83.7 REMARK 620 3 GLU A 104 OE1 60.4 122.1 REMARK 620 4 GLN A 135 OE1 177.2 98.5 116.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 152 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 129 OD1 REMARK 620 2 ASP A 129 OD2 40.8 REMARK 620 3 ASP A 133 OD1 126.9 142.5 REMARK 620 4 ASP A 133 N 90.7 83.0 60.0 REMARK 620 5 GLN A 135 O 97.0 75.0 135.6 135.1 REMARK 620 6 GLU A 140 OE1 58.4 82.1 124.5 145.4 69.5 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 149 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 150 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 151 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 152 REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SCIENTIFIC ORGANISM FOR CALMODULIN REMARK 999 IN THIS ENTRY IS XENOPUS LEAVIS (AFRICAN REMARK 999 CLAWED FROG) AND THE SEQUENCE IS IDENTICAL REMARK 999 TO THAT OF THE HUMAN CALMODULIN (SWISS-PROT REMARK 999 ACCESSSION CALM_HUMAN P02593). THERE IS NO REMARK 999 SEPARATE SEQUENCE FOR XENOPUS LAEVIS AND REMARK 999 BECAUSE IT IS 100% IDENTICAL TO THAT OF REMARK 999 HUMAN, SWISS-PROT ALSO LISTS XENOPUS LAEVIS REMARK 999 AS A SOURCE FOR THIS SEQUENCE ACCESSION REMARK 999 NUMBER. DBREF 1NWD A 1 148 UNP P62155 CALM_XENLA 1 148 DBREF 1NWD B 3 28 UNP Q07346 DCE_PETHY 470 495 DBREF 1NWD C 3 28 UNP Q07346 DCE_PETHY 470 495 SEQADV 1NWD GLY B 1 UNP Q07346 CLONING ARTIFACT SEQADV 1NWD SER B 2 UNP Q07346 CLONING ARTIFACT SEQADV 1NWD GLY C 1 UNP Q07346 CLONING ARTIFACT SEQADV 1NWD SER C 2 UNP Q07346 CLONING ARTIFACT SEQRES 1 A 148 ALA ASP GLN LEU THR GLU GLU GLN ILE ALA GLU PHE LYS SEQRES 2 A 148 GLU ALA PHE SER LEU PHE ASP LYS ASP GLY ASP GLY THR SEQRES 3 A 148 ILE THR THR LYS GLU LEU GLY THR VAL MET ARG SER LEU SEQRES 4 A 148 GLY GLN ASN PRO THR GLU ALA GLU LEU GLN ASP MET ILE SEQRES 5 A 148 ASN GLU VAL ASP ALA ASP GLY ASN GLY THR ILE ASP PHE SEQRES 6 A 148 PRO GLU PHE LEU THR MET MET ALA ARG LYS MET LYS ASP SEQRES 7 A 148 THR ASP SER GLU GLU GLU ILE ARG GLU ALA PHE ARG VAL SEQRES 8 A 148 PHE ASP LYS ASP GLY ASN GLY TYR ILE SER ALA ALA GLU SEQRES 9 A 148 LEU ARG HIS VAL MET THR ASN LEU GLY GLU LYS LEU THR SEQRES 10 A 148 ASP GLU GLU VAL ASP GLU MET ILE ARG GLU ALA ASP ILE SEQRES 11 A 148 ASP GLY ASP GLY GLN VAL ASN TYR GLU GLU PHE VAL GLN SEQRES 12 A 148 MET MET THR ALA LYS SEQRES 1 B 28 GLY SER HIS LYS LYS THR ASP SER GLU VAL GLN LEU GLU SEQRES 2 B 28 MET ILE THR ALA TRP LYS LYS PHE VAL GLU GLU LYS LYS SEQRES 3 B 28 LYS LYS SEQRES 1 C 28 GLY SER HIS LYS LYS THR ASP SER GLU VAL GLN LEU GLU SEQRES 2 C 28 MET ILE THR ALA TRP LYS LYS PHE VAL GLU GLU LYS LYS SEQRES 3 C 28 LYS LYS HET CA A 149 1 HET CA A 150 1 HET CA A 151 1 HET CA A 152 1 HETNAM CA CALCIUM ION FORMUL 4 CA 4(CA 2+) HELIX 1 1 GLU A 6 ASP A 20 1 15 HELIX 2 2 THR A 28 GLY A 40 1 13 HELIX 3 3 THR A 44 GLU A 54 1 11 HELIX 4 4 PHE A 65 ALA A 73 1 9 HELIX 5 5 SER A 81 ASP A 93 1 13 HELIX 6 6 SER A 101 GLU A 114 1 14 HELIX 7 7 ASP A 118 MET A 124 1 7 HELIX 8 8 ASN A 137 THR A 146 1 10 HELIX 9 9 THR B 6 LYS B 26 1 21 HELIX 10 10 THR C 6 LYS C 26 1 21 SHEET 1 A 2 THR A 26 ILE A 27 0 SHEET 2 A 2 ILE A 63 ASP A 64 -1 O ILE A 63 N ILE A 27 LINK OD2 ASP A 22 CA CA A 149 1555 1555 3.24 LINK OD1 ASP A 24 CA CA A 149 1555 1555 3.12 LINK OD2 ASP A 24 CA CA A 149 1555 1555 3.21 LINK OG1 THR A 26 CA CA A 149 1555 1555 3.12 LINK OE2 GLU A 31 CA CA A 149 1555 1555 3.18 LINK O THR A 62 CA CA A 150 1555 1555 3.04 LINK OD1 ASP A 64 CA CA A 150 1555 1555 3.04 LINK OD2 ASP A 93 CA CA A 151 1555 1555 2.94 LINK OD1 ASN A 97 CA CA A 151 1555 1555 3.01 LINK OE1 GLU A 104 CA CA A 151 1555 1555 3.06 LINK OD1 ASP A 129 CA CA A 152 1555 1555 2.90 LINK OD2 ASP A 129 CA CA A 152 1555 1555 3.34 LINK OD1 ASP A 133 CA CA A 152 1555 1555 2.92 LINK N ASP A 133 CA CA A 152 1555 1555 3.23 LINK OE1 GLN A 135 CA CA A 151 1555 1555 2.90 LINK O GLN A 135 CA CA A 152 1555 1555 2.84 LINK OE1 GLU A 140 CA CA A 152 1555 1555 3.16 SITE 1 AC1 4 ASP A 22 ASP A 24 THR A 26 GLU A 31 SITE 1 AC2 4 ASP A 58 THR A 62 ASP A 64 GLU A 67 SITE 1 AC3 7 ASP A 93 ASN A 97 TYR A 99 ILE A 100 SITE 2 AC3 7 SER A 101 GLU A 104 GLN A 135 SITE 1 AC4 6 ASP A 129 ASP A 131 GLY A 132 ASP A 133 SITE 2 AC4 6 GLN A 135 GLU A 140 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