HEADER METAL BINDING PROTEIN 06-AUG-10 2L1W TITLE THE SOLUTION STRUCTURE OF SOYBEAN CALMODULIN ISOFORM 4 COMPLEXED WITH TITLE 2 THE VACUOLAR CALCIUM ATPASE BCA1 PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CALMODULIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: VACUOLAR CALCIUM ATPASE BCA1 PEPTIDE; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GLYCINE MAX; SOURCE 3 ORGANISM_COMMON: SOYBEANS; SOURCE 4 ORGANISM_TAXID: 3847; SOURCE 5 GENE: SCAM-4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET30B; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 OTHER_DETAILS: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. KEYWDS CALMODULIN, CALMODULIN COMPLEX, SOYBEAN CALMODULIN, VACUOLAR CALCIUM KEYWDS 2 ATPASE, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 25 AUTHOR H.ISHIDA,H.J.VOGEL REVDAT 2 01-MAY-24 2L1W 1 REMARK LINK REVDAT 1 29-SEP-10 2L1W 0 JRNL AUTH H.ISHIDA,H.VOGEL JRNL TITL THE SOLUTION STRUCTURE OF A PLANT CALMODULIN AND THE JRNL TITL 2 CAM-BINDING DOMAIN OF THE VACUOLAR CALCIUM-ATPASE BCA1 JRNL TITL 3 REVEALS A NEW BINDING AND ACTIVATION MECHANISM JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE, X-PLOR NIH REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), SCHWIETERS, KUSZEWSKI, TJANDRA AND REMARK 3 CLORE (X-PLOR NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2L1W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000101852. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303; 303 REMARK 210 PH : 7; 7 REMARK 210 IONIC STRENGTH : 0.1; 0.3 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 0.300 MM [U-98% 13C; U-98% 15N] REMARK 210 PROTEIN_1-1, 0.375 MM PROTEIN_2- REMARK 210 2, 5 MM CALCIUM ION-3, 100 MM REMARK 210 POTASSIUM CHLORIDE-4, 10 MM DTT- REMARK 210 5, 90% H2O/10% D2O; 0.300 MM [U- REMARK 210 98% 13C; U-98% 15N] PROTEIN_1-6, REMARK 210 0.375 MM PROTEIN_2-7, 5 MM REMARK 210 CALCIUM ION-8, 100 MM POTASSIUM REMARK 210 CHLORIDE-9, 10 MM DTT-10, 100% REMARK 210 D2O; 0.300 MM [U-98% 13C; U-98% REMARK 210 15N] PROTEIN_1-11, 0.255 MM REMARK 210 PROTEIN_2-12, 5 MM CALCIUM ION- REMARK 210 13, 100 MM POTASSIUM CHLORIDE-14, REMARK 210 10 MM DTT-15, 90% H2O/10% D2O; REMARK 210 0.300 MM [U-98% 13C; U-98% 15N] REMARK 210 PROTEIN_1-16, 0.255 MM PROTEIN_2- REMARK 210 17, 5 MM CALCIUM ION-18, 100 MM REMARK 210 POTASSIUM CHLORIDE-19, 10 MM DTT- REMARK 210 20, 100% D2O; 0.300 MM [U-98% REMARK 210 15N] PROTEIN_1-21, 0.375 MM REMARK 210 PROTEIN_2-22, 5 MM CALCIUM ION- REMARK 210 23, 300 MM POTASSIUM CHLORIDE-24, REMARK 210 10 MM DTT-25, 16 MG/ML PF1 REMARK 210 PHAGE-26, 20 MM BIS-TRIS-27, 90% REMARK 210 H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 HNCO; 3D HN(CA)CO; 3D H(CCO)NH; REMARK 210 3D HBHA(CO)NH; 3D C(CO)NH; 3D REMARK 210 HCCH-TOCSY; 3D 1H-15N NOESY; 3D REMARK 210 1H-13C NOESY; 3D 13C/F3-FILTER REMARK 210 13C/F1-EDITED NOESY; 2D 13C,15N- REMARK 210 FILTER NOESY; 2D 13C-FLITER COSY; REMARK 210 IPAP-1H-15N HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 700 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRDRAW, NMRVIEW, X-PLOR NIH REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 25 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: 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: 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 H2 ALA B 19 H ARG B 20 1.28 REMARK 500 O ILE A 110 H GLY A 113 1.55 REMARK 500 O ASP A 93 H GLN A 96 1.56 REMARK 500 OD2 ASP A 93 H GLY A 98 1.59 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 LEU A 4 106.50 55.54 REMARK 500 1 ASP A 22 38.07 -93.61 REMARK 500 1 ASP A 40 20.68 81.45 REMARK 500 1 ALA A 57 -74.15 -48.68 REMARK 500 1 ASP A 58 10.57 -64.29 REMARK 500 1 VAL A 76 73.83 -157.28 REMARK 500 1 LYS A 77 -99.17 -122.17 REMARK 500 1 ASP A 78 -87.15 -176.38 REMARK 500 1 THR A 79 -8.56 73.28 REMARK 500 1 VAL A 108 -16.73 -48.76 REMARK 500 1 MET A 109 -78.48 -90.25 REMARK 500 1 ASN A 111 -9.29 -52.04 REMARK 500 1 MET A 146 -91.01 -83.72 REMARK 500 1 VAL A 148 -26.07 76.93 REMARK 500 1 ALA B 34 74.37 35.31 REMARK 500 1 PHE B 37 69.91 67.53 REMARK 500 2 ILE A 3 176.78 60.08 REMARK 500 2 LEU A 4 2.52 -173.45 REMARK 500 2 GLU A 6 -8.92 -52.28 REMARK 500 2 ASP A 22 33.32 -92.65 REMARK 500 2 LEU A 39 14.90 -61.55 REMARK 500 2 ASP A 40 44.11 70.59 REMARK 500 2 VAL A 76 -123.00 -141.65 REMARK 500 2 LYS A 77 146.83 -33.61 REMARK 500 2 THR A 79 66.62 60.05 REMARK 500 2 GLN A 96 59.02 35.72 REMARK 500 2 MET A 109 -75.59 -31.37 REMARK 500 2 ASN A 111 -8.70 -47.15 REMARK 500 2 MET A 146 -151.58 -89.36 REMARK 500 2 THR A 147 -59.87 -2.98 REMARK 500 2 VAL A 148 1.92 97.64 REMARK 500 2 ALA B 34 91.78 -36.38 REMARK 500 2 PHE B 37 67.73 61.28 REMARK 500 3 ASP A 2 82.87 46.36 REMARK 500 3 LEU A 4 45.97 -143.31 REMARK 500 3 GLU A 6 -9.78 -50.42 REMARK 500 3 GLN A 41 -94.35 -64.92 REMARK 500 3 ASN A 42 83.40 -178.43 REMARK 500 3 PRO A 43 -153.43 -54.41 REMARK 500 3 VAL A 55 50.96 -112.51 REMARK 500 3 LYS A 74 9.90 -65.55 REMARK 500 3 LYS A 75 52.66 -147.84 REMARK 500 3 VAL A 76 -70.45 -138.58 REMARK 500 3 LYS A 77 -90.93 31.00 REMARK 500 3 ASP A 78 -50.02 -127.84 REMARK 500 3 THR A 79 -62.17 68.93 REMARK 500 3 ASP A 80 141.78 -173.03 REMARK 500 3 MET A 109 -75.39 -33.34 REMARK 500 3 LEU A 112 -123.82 -84.08 REMARK 500 3 MET A 146 -153.64 -50.54 REMARK 500 REMARK 500 THIS ENTRY HAS 450 RAMACHANDRAN OUTLIERS. 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 179 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 20 OD1 REMARK 620 2 ASP A 22 OD1 88.4 REMARK 620 3 ASP A 24 OD2 131.8 51.2 REMARK 620 4 CYS A 26 O 72.6 152.1 130.5 REMARK 620 5 GLU A 31 OE2 112.3 64.9 76.8 140.9 REMARK 620 6 GLU A 31 OE1 63.4 69.2 112.7 116.7 49.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 192 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 56 OD2 REMARK 620 2 ASP A 58 OD1 134.3 REMARK 620 3 ASN A 60 OD1 89.9 86.7 REMARK 620 4 THR A 62 O 53.5 145.1 58.4 REMARK 620 5 GLU A 67 OE2 80.3 94.0 166.9 120.0 REMARK 620 6 GLU A 67 OE1 60.8 140.5 132.7 74.3 48.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 221 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 93 OD1 REMARK 620 2 ASP A 95 OD1 56.5 REMARK 620 3 ASP A 95 OD2 100.5 49.2 REMARK 620 4 ASN A 97 OD1 53.0 84.0 93.9 REMARK 620 5 TYR A 99 O 63.5 119.9 149.7 55.9 REMARK 620 6 GLU A 104 OE2 102.0 60.5 63.6 144.5 141.8 REMARK 620 7 GLU A 104 OE1 79.7 80.7 110.1 130.4 92.9 48.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 234 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 129 OD1 REMARK 620 2 ASP A 131 OD2 109.9 REMARK 620 3 ASP A 133 OD1 57.1 101.3 REMARK 620 4 GLN A 135 O 74.3 159.5 63.4 REMARK 620 5 GLU A 140 OE2 105.0 53.1 144.7 146.7 REMARK 620 6 GLU A 140 OE1 96.1 101.5 149.7 97.9 48.8 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 179 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 192 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 221 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 234 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2RO8 RELATED DB: PDB REMARK 900 RELATED ID: 2RO9 RELATED DB: PDB REMARK 900 RELATED ID: 2ROA RELATED DB: PDB REMARK 900 RELATED ID: 2ROB RELATED DB: PDB REMARK 900 RELATED ID: 2KN2 RELATED DB: PDB REMARK 900 RELATED ID: 2KSZ RELATED DB: PDB DBREF 2L1W A 1 149 UNP Q39890 Q39890_SOYBN 2 150 DBREF 2L1W B 19 43 PDB 2L1W 2L1W 19 43 SEQRES 1 A 149 ALA ASP ILE LEU SER GLU GLU GLN ILE VAL ASP PHE LYS SEQRES 2 A 149 GLU ALA PHE GLY LEU PHE ASP LYS ASP GLY ASP GLY CYS SEQRES 3 A 149 ILE THR VAL GLU GLU LEU ALA THR VAL ILE ARG SER LEU SEQRES 4 A 149 ASP GLN ASN PRO THR GLU GLU GLU LEU GLN ASP MET ILE SEQRES 5 A 149 SER GLU VAL ASP ALA ASP GLY ASN GLY THR ILE GLU PHE SEQRES 6 A 149 ASP GLU PHE LEU SER LEU MET ALA LYS LYS VAL LYS ASP SEQRES 7 A 149 THR ASP ALA GLU GLU GLU LEU LYS GLU ALA PHE LYS VAL SEQRES 8 A 149 PHE ASP LYS ASP GLN ASN GLY TYR ILE SER ALA SER GLU SEQRES 9 A 149 LEU ARG HIS VAL MET ILE ASN LEU GLY GLU LYS LEU THR SEQRES 10 A 149 ASP GLU GLU VAL GLU GLN MET ILE LYS GLU ALA ASP LEU SEQRES 11 A 149 ASP GLY ASP GLY GLN VAL ASN TYR GLU GLU PHE VAL LYS SEQRES 12 A 149 MET MET MET THR VAL ARG SEQRES 1 B 25 ALA ARG GLN ARG TRP ARG SER SER VAL SER ILE VAL LYS SEQRES 2 B 25 ASN ARG ALA ARG ARG PHE ARG MET ILE SER ASN LEU HET CA A 179 1 HET CA A 192 1 HET CA A 221 1 HET CA A 234 1 HETNAM CA CALCIUM ION FORMUL 3 CA 4(CA 2+) HELIX 1 1 SER A 5 ASP A 20 1 16 HELIX 2 2 VAL A 29 SER A 38 1 10 HELIX 3 3 THR A 44 ASP A 56 1 13 HELIX 4 4 PHE A 65 LYS A 75 1 11 HELIX 5 5 ASP A 80 ASP A 93 1 14 HELIX 6 6 ALA A 102 ASN A 111 1 10 HELIX 7 7 THR A 117 ASP A 129 1 13 HELIX 8 8 TYR A 138 THR A 147 1 10 HELIX 9 9 ALA B 19 ALA B 34 1 16 HELIX 10 10 PHE B 37 LEU B 43 1 7 SHEET 1 A 2 CYS A 26 THR A 28 0 SHEET 2 A 2 THR A 62 GLU A 64 -1 O ILE A 63 N ILE A 27 SHEET 1 B 2 TYR A 99 SER A 101 0 SHEET 2 B 2 GLN A 135 ASN A 137 -1 O VAL A 136 N ILE A 100 LINK OD1 ASP A 20 CA CA A 179 1555 1555 2.60 LINK OD1 ASP A 22 CA CA A 179 1555 1555 2.78 LINK OD2 ASP A 24 CA CA A 179 1555 1555 2.65 LINK O CYS A 26 CA CA A 179 1555 1555 2.81 LINK OE2 GLU A 31 CA CA A 179 1555 1555 2.60 LINK OE1 GLU A 31 CA CA A 179 1555 1555 2.57 LINK OD2 ASP A 56 CA CA A 192 1555 1555 2.59 LINK OD1 ASP A 58 CA CA A 192 1555 1555 2.76 LINK OD1 ASN A 60 CA CA A 192 1555 1555 2.60 LINK O THR A 62 CA CA A 192 1555 1555 2.77 LINK OE2 GLU A 67 CA CA A 192 1555 1555 2.61 LINK OE1 GLU A 67 CA CA A 192 1555 1555 2.63 LINK OD1 ASP A 93 CA CA A 221 1555 1555 2.65 LINK OD1 ASP A 95 CA CA A 221 1555 1555 2.58 LINK OD2 ASP A 95 CA CA A 221 1555 1555 2.60 LINK OD1 ASN A 97 CA CA A 221 1555 1555 2.61 LINK O TYR A 99 CA CA A 221 1555 1555 2.56 LINK OE2 GLU A 104 CA CA A 221 1555 1555 2.60 LINK OE1 GLU A 104 CA CA A 221 1555 1555 2.60 LINK OD1 ASP A 129 CA CA A 234 1555 1555 2.59 LINK OD2 ASP A 131 CA CA A 234 1555 1555 2.65 LINK OD1 ASP A 133 CA CA A 234 1555 1555 2.60 LINK O GLN A 135 CA CA A 234 1555 1555 2.68 LINK OE2 GLU A 140 CA CA A 234 1555 1555 2.60 LINK OE1 GLU A 140 CA CA A 234 1555 1555 2.60 SITE 1 AC1 5 ASP A 20 ASP A 22 ASP A 24 CYS A 26 SITE 2 AC1 5 GLU A 31 SITE 1 AC2 5 ASP A 56 ASP A 58 ASN A 60 THR A 62 SITE 2 AC2 5 GLU A 67 SITE 1 AC3 5 ASP A 93 ASP A 95 ASN A 97 TYR A 99 SITE 2 AC3 5 GLU A 104 SITE 1 AC4 6 ASP A 129 ASP A 131 ASP A 133 GLN A 135 SITE 2 AC4 6 ASN A 137 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