PDB Short entry for 1F55 HEADER TRANSPORT PROTEIN 13-JUN-00 1F55 TITLE SOLUTION STRUCTURE OF THE CALCIUM BOUND N-TERMINAL DOMAIN OF YEAST TITLE 2 CALMODULIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CALMODULIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: INTRACELLULAR CALCIUM SENSOR SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 4932; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-30B(+) AND PIC10 KEYWDS EF-HAND, HELIX-LOOP-HELIX, TRANSPORT PROTEIN EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR H.ISHIDA,K.TAKAHASHI,K.NAKASHIMA,Y.KUMAKI,M.NAKATA,K.HIKICHI,M.YAZAWA REVDAT 3 16-FEB-22 1F55 1 REMARK LINK REVDAT 2 24-FEB-09 1F55 1 VERSN REVDAT 1 15-JUL-03 1F55 0 JRNL AUTH H.ISHIDA,K.TAKAHASHI,K.NAKASHIMA,Y.KUMAKI,M.NAKATA, JRNL AUTH 2 K.HIKICHI,M.YAZAWA JRNL TITL SOLUTION STRUCTURES OF THE N-TERMINAL DOMAIN OF YEAST JRNL TITL 2 CALMODULIN: CA2+-DEPENDENT CONFORMATIONAL CHANGE AND ITS JRNL TITL 3 FUNCTIONAL IMPLICATION JRNL REF BIOCHEMISTRY V. 39 13660 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 11076504 JRNL DOI 10.1021/BI000582X REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851, X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER (X-PLOR), BRUNGER (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REMARK 3 THE STRUCTURES ARE BASED ON A TOTAL OF 920 RESTRAINTS, 863 ARE NOE- REMARK 3 DERIVED REMARK 3 DISTANCE CONSTRAINTS, 17 DIHEDRAL ANGLE RESTRAINTS, 28 DISTANCE REMARK 3 RESTRAINTS REMARK 3 FROM HYDROGEN BONDS, 12 CALCIUM-LIGAND DISTANCE RESTRAINTS REMARK 4 REMARK 4 1F55 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-JUN-00. REMARK 100 THE DEPOSITION ID IS D_1000011255. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 6.8 REMARK 210 IONIC STRENGTH : 50MM KCL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 5 MM N-TERMINAL DOMAIN OF YEAST REMARK 210 CALMODULIN; 50 MM KCL; 15 MM REMARK 210 CACL2; 90% H2O, 10% D2O; 3 MM N- REMARK 210 TERMINAL DOMAIN OF YEAST REMARK 210 CALMODULIN U-15N; 50 MM KCL; 9 REMARK 210 MM CACL2; 90% H2O, 10% D2O; 3 MM REMARK 210 N-TERMINAL DOMAIN OF YEAST REMARK 210 CALMODULIN; 50 MM KCL; 9 MM REMARK 210 CACL2; 99.99% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; DQF-COSY; 2D TOCSY; REMARK 210 3D_15N-SEPARATED_NOESY; 3D_15N- REMARK 210 SEPARATED_TOCSY; 15N-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : A REMARK 210 SPECTROMETER MANUFACTURER : JEOL REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: THE STRUCTURE WAS DETERMINED USING DOUBLE-RESONANCE NMR REMARK 210 SPECTROSCOPY ON 15N-LABELED PROTEIN 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 O LEU A 4 HG1 THR A 5 1.51 REMARK 500 O PHE A 12 H PHE A 16 1.56 REMARK 500 OD1 ASP A 20 H ASP A 22 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 -108.97 -115.68 REMARK 500 1 THR A 5 -144.35 49.76 REMARK 500 1 LEU A 41 -42.98 -144.10 REMARK 500 1 ASP A 56 90.35 -64.15 REMARK 500 1 PHE A 65 -71.35 -44.71 REMARK 500 1 MET A 72 -92.00 -58.95 REMARK 500 1 ARG A 74 -142.22 61.07 REMARK 500 1 GLN A 75 -46.06 -163.76 REMARK 500 1 LEU A 76 -76.24 -132.55 REMARK 500 2 LEU A 4 -119.42 -92.82 REMARK 500 2 THR A 5 -145.08 52.24 REMARK 500 2 ASP A 22 20.02 -155.38 REMARK 500 2 ASN A 23 29.78 42.23 REMARK 500 2 SER A 28 -158.77 -106.13 REMARK 500 2 GLU A 31 -71.32 -42.34 REMARK 500 2 SER A 42 64.15 -176.92 REMARK 500 2 ASP A 56 95.28 -56.22 REMARK 500 2 PHE A 65 -71.33 -43.32 REMARK 500 2 SER A 66 -35.12 -34.93 REMARK 500 2 MET A 72 -90.07 -51.66 REMARK 500 2 ARG A 74 129.79 61.47 REMARK 500 2 GLN A 75 -54.63 -143.48 REMARK 500 2 LEU A 76 175.25 -47.56 REMARK 500 3 ASN A 3 94.53 57.47 REMARK 500 3 LEU A 4 -106.35 -81.54 REMARK 500 3 THR A 5 -146.17 51.40 REMARK 500 3 ASP A 22 20.53 -162.91 REMARK 500 3 ASN A 23 27.14 41.40 REMARK 500 3 LEU A 39 -62.71 -134.70 REMARK 500 3 SER A 42 48.32 -158.15 REMARK 500 3 SER A 44 145.71 69.53 REMARK 500 3 ASN A 60 34.34 -97.60 REMARK 500 3 HIS A 61 13.82 58.36 REMARK 500 3 PHE A 65 -70.07 -50.28 REMARK 500 3 MET A 72 -79.61 -68.50 REMARK 500 3 GLN A 75 -147.09 64.26 REMARK 500 4 ASN A 3 -145.79 -128.46 REMARK 500 4 LEU A 4 -115.13 -84.73 REMARK 500 4 THR A 5 -145.98 52.04 REMARK 500 4 SER A 29 -87.20 -53.22 REMARK 500 4 GLU A 31 -79.05 -42.66 REMARK 500 4 LEU A 41 172.90 -54.65 REMARK 500 4 SER A 44 147.02 67.67 REMARK 500 4 PHE A 65 -71.11 -58.05 REMARK 500 4 MET A 72 -80.54 -61.54 REMARK 500 4 SER A 73 164.03 -44.24 REMARK 500 5 SER A 2 -74.29 -144.37 REMARK 500 5 LEU A 4 -134.03 -114.87 REMARK 500 5 THR A 5 -142.30 50.33 REMARK 500 5 ASP A 22 26.48 -172.41 REMARK 500 REMARK 500 THIS ENTRY HAS 368 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 37 0.15 SIDE CHAIN REMARK 500 1 ARG A 74 0.30 SIDE CHAIN REMARK 500 2 ARG A 37 0.23 SIDE CHAIN REMARK 500 2 ARG A 74 0.27 SIDE CHAIN REMARK 500 3 ARG A 37 0.29 SIDE CHAIN REMARK 500 3 ARG A 74 0.28 SIDE CHAIN REMARK 500 4 ARG A 37 0.23 SIDE CHAIN REMARK 500 4 ARG A 74 0.30 SIDE CHAIN REMARK 500 5 ARG A 37 0.17 SIDE CHAIN REMARK 500 5 ARG A 74 0.24 SIDE CHAIN REMARK 500 6 ARG A 37 0.31 SIDE CHAIN REMARK 500 6 ARG A 74 0.20 SIDE CHAIN REMARK 500 7 ARG A 37 0.29 SIDE CHAIN REMARK 500 7 ARG A 74 0.32 SIDE CHAIN REMARK 500 8 ARG A 37 0.30 SIDE CHAIN REMARK 500 8 ARG A 74 0.30 SIDE CHAIN REMARK 500 9 ARG A 37 0.32 SIDE CHAIN REMARK 500 9 ARG A 74 0.20 SIDE CHAIN REMARK 500 10 ARG A 37 0.25 SIDE CHAIN REMARK 500 10 ARG A 74 0.22 SIDE CHAIN REMARK 500 11 ARG A 37 0.28 SIDE CHAIN REMARK 500 11 ARG A 74 0.15 SIDE CHAIN REMARK 500 12 ARG A 37 0.22 SIDE CHAIN REMARK 500 12 ARG A 74 0.31 SIDE CHAIN REMARK 500 13 ARG A 37 0.32 SIDE CHAIN REMARK 500 13 ARG A 74 0.26 SIDE CHAIN REMARK 500 14 ARG A 37 0.28 SIDE CHAIN REMARK 500 14 ARG A 74 0.24 SIDE CHAIN REMARK 500 15 ARG A 37 0.23 SIDE CHAIN REMARK 500 15 ARG A 74 0.31 SIDE CHAIN REMARK 500 16 ARG A 37 0.28 SIDE CHAIN REMARK 500 16 ARG A 74 0.26 SIDE CHAIN REMARK 500 17 ARG A 37 0.21 SIDE CHAIN REMARK 500 17 ARG A 74 0.28 SIDE CHAIN REMARK 500 18 ARG A 37 0.32 SIDE CHAIN REMARK 500 18 ARG A 74 0.21 SIDE CHAIN REMARK 500 19 ARG A 37 0.20 SIDE CHAIN REMARK 500 19 ARG A 74 0.23 SIDE CHAIN REMARK 500 20 ARG A 37 0.17 SIDE CHAIN REMARK 500 20 ARG A 74 0.28 SIDE CHAIN REMARK 500 21 ARG A 37 0.28 SIDE CHAIN REMARK 500 21 ARG A 74 0.15 SIDE CHAIN REMARK 500 22 ARG A 37 0.31 SIDE CHAIN REMARK 500 22 ARG A 74 0.31 SIDE CHAIN REMARK 500 23 ARG A 37 0.13 SIDE CHAIN REMARK 500 23 ARG A 74 0.20 SIDE CHAIN REMARK 500 24 ARG A 37 0.09 SIDE CHAIN REMARK 500 24 ARG A 74 0.28 SIDE CHAIN REMARK 500 25 ARG A 37 0.08 SIDE CHAIN REMARK 500 25 ARG A 74 0.20 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 60 PLANE DEVIATIONS. 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 101 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 20 OD2 REMARK 620 2 ASP A 20 OD1 40.9 REMARK 620 3 ASP A 22 OD2 115.7 76.7 REMARK 620 4 ASN A 24 OD1 102.0 108.9 81.1 REMARK 620 5 SER A 26 O 51.6 72.3 134.8 140.0 REMARK 620 6 GLU A 31 OE1 103.5 84.1 78.2 152.2 66.7 REMARK 620 7 GLU A 31 OE2 86.6 49.3 49.2 126.7 85.6 45.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 102 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 56 OD1 REMARK 620 2 ASP A 58 OD2 78.0 REMARK 620 3 ASP A 58 OD1 52.0 43.3 REMARK 620 4 ASN A 60 OD1 49.4 58.1 70.9 REMARK 620 5 ASN A 60 ND2 92.4 53.3 92.0 43.4 REMARK 620 6 GLN A 62 O 52.0 109.9 103.0 52.2 80.2 REMARK 620 7 GLU A 67 OE1 84.7 123.2 84.1 134.0 176.0 100.0 REMARK 620 8 GLU A 67 OE2 119.7 99.5 85.1 155.0 134.3 144.8 46.1 REMARK 620 N 1 2 3 4 5 6 7 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 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1F54 RELATED DB: PDB REMARK 900 1F54 IS THE APO-FORM OF THE SAME PROTEIN DBREF 1F55 A 1 77 UNP P06787 CALM_YEAST 2 78 SEQRES 1 A 77 SER SER ASN LEU THR GLU GLU GLN ILE ALA GLU PHE LYS SEQRES 2 A 77 GLU ALA PHE ALA LEU PHE ASP LYS ASP ASN ASN GLY SER SEQRES 3 A 77 ILE SER SER SER GLU LEU ALA THR VAL MET ARG SER LEU SEQRES 4 A 77 GLY LEU SER PRO SER GLU ALA GLU VAL ASN ASP LEU MET SEQRES 5 A 77 ASN GLU ILE ASP VAL ASP GLY ASN HIS GLN ILE GLU PHE SEQRES 6 A 77 SER GLU PHE LEU ALA LEU MET SER ARG GLN LEU LYS HET CA A 101 1 HET CA A 102 1 HETNAM CA CALCIUM ION FORMUL 2 CA 2(CA 2+) HELIX 1 1 THR A 5 ASP A 20 1 16 HELIX 2 2 SER A 29 LEU A 41 1 13 HELIX 3 3 SER A 44 ASP A 56 1 13 HELIX 4 4 PHE A 65 MET A 72 1 8 SHEET 1 A 2 SER A 26 SER A 28 0 SHEET 2 A 2 GLN A 62 GLU A 64 -1 O ILE A 63 N ILE A 27 LINK OD2 ASP A 20 CA CA A 101 1555 1555 3.25 LINK OD1 ASP A 20 CA CA A 101 1555 1555 2.80 LINK OD2 ASP A 22 CA CA A 101 1555 1555 2.81 LINK OD1 ASN A 24 CA CA A 101 1555 1555 2.82 LINK O SER A 26 CA CA A 101 1555 1555 2.81 LINK OE1 GLU A 31 CA CA A 101 1555 1555 2.80 LINK OE2 GLU A 31 CA CA A 101 1555 1555 2.81 LINK OD1 ASP A 56 CA CA A 102 1555 1555 2.80 LINK OD2 ASP A 58 CA CA A 102 1555 1555 3.13 LINK OD1 ASP A 58 CA CA A 102 1555 1555 2.48 LINK OD1 ASN A 60 CA CA A 102 1555 1555 2.79 LINK ND2 ASN A 60 CA CA A 102 1555 1555 3.07 LINK O GLN A 62 CA CA A 102 1555 1555 2.48 LINK OE1 GLU A 67 CA CA A 102 1555 1555 2.78 LINK OE2 GLU A 67 CA CA A 102 1555 1555 2.73 SITE 1 AC1 5 ASP A 20 ASP A 22 ASN A 24 SER A 26 SITE 2 AC1 5 GLU A 31 SITE 1 AC2 6 ASP A 56 ASP A 58 ASN A 60 GLN A 62 SITE 2 AC2 6 ILE A 63 GLU A 67 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