HEADER METAL BINDING PROTEIN 08-AUG-08 2K7D TITLE NMR STRUCTURE OF CA2+-BOUND CABP1 C-DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CALCIUM-BINDING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 72 TO 156; COMPND 5 SYNONYM: CABP1, CALBRAIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CABP1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET3B KEYWDS EF-HAND, CALCIUM, CABP1, IP3 RECEPTOR, ALTERNATIVE SPLICING, CELL KEYWDS 2 MEMBRANE, CYTOPLASM, CYTOSKELETON, LIPOPROTEIN, MEMBRANE, MYRISTATE, KEYWDS 3 METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 15 AUTHOR J.AMES REVDAT 4 22-MAY-24 2K7D 1 REMARK REVDAT 3 16-MAR-22 2K7D 1 REMARK REVDAT 2 24-FEB-09 2K7D 1 VERSN REVDAT 1 25-NOV-08 2K7D 0 JRNL AUTH J.AMES JRNL TITL NMR STRUCTURE OF CA2+-BOUND CABP1 C-DOMAIN 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 3.1 REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), BRUNGER, A. (X-PLOR) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: XPLOR-NIH YASAP PROTOCOL REMARK 4 REMARK 4 2K7D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-AUG-08. REMARK 100 THE DEPOSITION ID IS D_1000100768. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 300 REMARK 210 PH : 7.4 REMARK 210 IONIC STRENGTH : 0.05 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.0 MM [U-99% 13C; U-99% 15N] REMARK 210 CABP1, 50 MM SODIUM CHLORIDE, 5 REMARK 210 MM CALCIUM, 10 MM TRIS, 90% H2O/ REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HCCH-TOCSY; 3D 1H-15N NOESY; REMARK 210 3D 1H-15N TOCSY; 3D 1H-13C NOESY; REMARK 210 2D 1H-1H NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NULL REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 50 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 15 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: 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 SER A 120 H LEU A 124 1.45 REMARK 500 OD1 ASP A 157 H GLU A 160 1.46 REMARK 500 OE2 GLU A 118 HH11 ARG A 155 1.50 REMARK 500 O MET A 128 H LEU A 132 1.59 REMARK 500 OD1 ASP A 112 CA CA A 501 1.67 REMARK 500 REMARK 500 REMARK: NULL 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),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 1 HIS A 134 CG HIS A 134 ND1 -0.121 REMARK 500 1 HIS A 138 CG HIS A 138 ND1 -0.120 REMARK 500 2 HIS A 134 CG HIS A 134 ND1 -0.120 REMARK 500 2 HIS A 138 CG HIS A 138 ND1 -0.121 REMARK 500 3 HIS A 134 CG HIS A 134 ND1 -0.121 REMARK 500 3 HIS A 138 CG HIS A 138 ND1 -0.121 REMARK 500 4 HIS A 134 CG HIS A 134 ND1 -0.120 REMARK 500 4 HIS A 138 CG HIS A 138 ND1 -0.120 REMARK 500 5 HIS A 134 CG HIS A 134 ND1 -0.123 REMARK 500 5 HIS A 138 CG HIS A 138 ND1 -0.120 REMARK 500 6 HIS A 134 CG HIS A 134 ND1 -0.121 REMARK 500 6 HIS A 138 CG HIS A 138 ND1 -0.119 REMARK 500 7 HIS A 134 CG HIS A 134 ND1 -0.120 REMARK 500 7 HIS A 138 CG HIS A 138 ND1 -0.122 REMARK 500 8 HIS A 134 CG HIS A 134 ND1 -0.120 REMARK 500 8 HIS A 138 CG HIS A 138 ND1 -0.120 REMARK 500 9 HIS A 134 CG HIS A 134 ND1 -0.120 REMARK 500 9 HIS A 138 CG HIS A 138 ND1 -0.121 REMARK 500 10 HIS A 134 CG HIS A 134 ND1 -0.120 REMARK 500 10 HIS A 138 CG HIS A 138 ND1 -0.120 REMARK 500 11 HIS A 134 CG HIS A 134 ND1 -0.120 REMARK 500 11 HIS A 138 CG HIS A 138 ND1 -0.119 REMARK 500 12 HIS A 134 CG HIS A 134 ND1 -0.120 REMARK 500 12 HIS A 138 CG HIS A 138 ND1 -0.120 REMARK 500 13 HIS A 134 CG HIS A 134 ND1 -0.121 REMARK 500 13 HIS A 138 CG HIS A 138 ND1 -0.120 REMARK 500 14 HIS A 134 CG HIS A 134 ND1 -0.121 REMARK 500 14 HIS A 138 CG HIS A 138 ND1 -0.122 REMARK 500 15 HIS A 134 CG HIS A 134 ND1 -0.120 REMARK 500 15 HIS A 138 CG HIS A 138 ND1 -0.120 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 ILE A 99 151.51 -45.38 REMARK 500 1 ASN A 114 -95.73 -94.60 REMARK 500 1 ASP A 116 -3.52 -142.23 REMARK 500 1 LEU A 132 -73.40 -88.06 REMARK 500 1 HIS A 134 -175.82 63.81 REMARK 500 1 GLN A 135 168.98 65.20 REMARK 500 1 VAL A 136 -164.23 -119.76 REMARK 500 1 ASP A 149 -39.07 177.10 REMARK 500 1 LEU A 150 89.32 23.94 REMARK 500 1 ASN A 151 -4.39 -52.26 REMARK 500 1 PHE A 158 -25.25 -37.86 REMARK 500 1 SER A 166 166.69 -49.55 REMARK 500 2 ASP A 97 129.92 68.09 REMARK 500 2 MET A 98 83.82 -68.49 REMARK 500 2 ILE A 99 -165.96 -60.32 REMARK 500 2 ASN A 114 -149.22 -118.16 REMARK 500 2 LEU A 132 -147.79 -81.99 REMARK 500 2 GLN A 135 76.32 -63.21 REMARK 500 2 ASP A 140 -70.52 -49.53 REMARK 500 2 ARG A 146 -69.08 -90.74 REMARK 500 2 ASP A 147 -12.45 -45.65 REMARK 500 2 ASN A 151 -60.44 -104.24 REMARK 500 2 SER A 166 -127.44 -71.47 REMARK 500 3 ILE A 99 -169.04 -60.67 REMARK 500 3 ASP A 116 -72.28 -76.17 REMARK 500 3 LEU A 132 -128.16 -94.74 REMARK 500 3 HIS A 134 -67.48 -94.63 REMARK 500 3 VAL A 136 19.47 -147.84 REMARK 500 3 LEU A 150 11.82 -141.14 REMARK 500 3 ASP A 153 -149.56 -95.21 REMARK 500 3 SER A 166 -131.07 -101.67 REMARK 500 4 MET A 98 10.75 -170.04 REMARK 500 4 VAL A 101 -12.97 -48.95 REMARK 500 4 THR A 113 -15.35 -47.01 REMARK 500 4 ASN A 114 -89.88 -101.64 REMARK 500 4 GLN A 135 -127.89 -85.22 REMARK 500 4 VAL A 148 -124.50 -68.43 REMARK 500 4 ASP A 149 89.13 52.47 REMARK 500 4 ASN A 151 -91.04 -90.67 REMARK 500 4 ASP A 153 -69.07 -90.81 REMARK 500 4 PHE A 158 -32.34 -38.96 REMARK 500 4 MET A 165 -79.84 -90.13 REMARK 500 4 SER A 166 80.20 35.86 REMARK 500 5 ASP A 97 -50.89 -147.42 REMARK 500 5 VAL A 101 -70.16 -82.13 REMARK 500 5 ASN A 114 -80.04 -103.46 REMARK 500 5 LEU A 132 -146.64 -85.95 REMARK 500 5 ASP A 149 -176.25 -57.58 REMARK 500 5 LEU A 150 -38.33 -169.49 REMARK 500 5 SER A 166 -154.31 -131.68 REMARK 500 REMARK 500 THIS ENTRY HAS 139 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 105 0.15 SIDE CHAIN REMARK 500 1 ARG A 109 0.25 SIDE CHAIN REMARK 500 1 ARG A 125 0.08 SIDE CHAIN REMARK 500 1 ARG A 129 0.27 SIDE CHAIN REMARK 500 1 ARG A 139 0.16 SIDE CHAIN REMARK 500 1 ARG A 146 0.18 SIDE CHAIN REMARK 500 1 ARG A 155 0.32 SIDE CHAIN REMARK 500 1 ARG A 163 0.31 SIDE CHAIN REMARK 500 1 ARG A 167 0.32 SIDE CHAIN REMARK 500 2 ARG A 105 0.31 SIDE CHAIN REMARK 500 2 ARG A 109 0.26 SIDE CHAIN REMARK 500 2 ARG A 125 0.29 SIDE CHAIN REMARK 500 2 ARG A 129 0.31 SIDE CHAIN REMARK 500 2 ARG A 139 0.13 SIDE CHAIN REMARK 500 2 ARG A 146 0.28 SIDE CHAIN REMARK 500 2 ARG A 155 0.17 SIDE CHAIN REMARK 500 2 ARG A 163 0.14 SIDE CHAIN REMARK 500 3 ARG A 105 0.29 SIDE CHAIN REMARK 500 3 ARG A 109 0.30 SIDE CHAIN REMARK 500 3 ARG A 125 0.30 SIDE CHAIN REMARK 500 3 ARG A 129 0.29 SIDE CHAIN REMARK 500 3 ARG A 139 0.25 SIDE CHAIN REMARK 500 3 ARG A 146 0.24 SIDE CHAIN REMARK 500 3 ARG A 163 0.22 SIDE CHAIN REMARK 500 3 ARG A 167 0.32 SIDE CHAIN REMARK 500 4 ARG A 105 0.32 SIDE CHAIN REMARK 500 4 ARG A 125 0.16 SIDE CHAIN REMARK 500 4 ARG A 129 0.17 SIDE CHAIN REMARK 500 4 ARG A 139 0.30 SIDE CHAIN REMARK 500 4 ARG A 146 0.25 SIDE CHAIN REMARK 500 4 ARG A 155 0.30 SIDE CHAIN REMARK 500 4 ARG A 163 0.17 SIDE CHAIN REMARK 500 4 ARG A 167 0.31 SIDE CHAIN REMARK 500 5 ARG A 105 0.32 SIDE CHAIN REMARK 500 5 ARG A 109 0.31 SIDE CHAIN REMARK 500 5 ARG A 125 0.30 SIDE CHAIN REMARK 500 5 ARG A 129 0.23 SIDE CHAIN REMARK 500 5 ARG A 139 0.19 SIDE CHAIN REMARK 500 5 ARG A 146 0.27 SIDE CHAIN REMARK 500 5 ARG A 155 0.17 SIDE CHAIN REMARK 500 5 ARG A 163 0.21 SIDE CHAIN REMARK 500 5 ARG A 167 0.28 SIDE CHAIN REMARK 500 6 ARG A 105 0.09 SIDE CHAIN REMARK 500 6 ARG A 109 0.18 SIDE CHAIN REMARK 500 6 ARG A 125 0.32 SIDE CHAIN REMARK 500 6 ARG A 129 0.17 SIDE CHAIN REMARK 500 6 ARG A 139 0.32 SIDE CHAIN REMARK 500 6 ARG A 146 0.21 SIDE CHAIN REMARK 500 6 ARG A 155 0.28 SIDE CHAIN REMARK 500 6 ARG A 163 0.32 SIDE CHAIN REMARK 500 REMARK 500 THIS ENTRY HAS 130 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 501 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 114 OD1 REMARK 620 2 ASP A 116 OD1 121.0 REMARK 620 3 GLU A 118 O 170.2 59.6 REMARK 620 4 GLU A 123 OE2 109.1 115.9 77.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 502 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 149 OD1 REMARK 620 2 ASN A 151 OD1 73.7 REMARK 620 3 ASP A 153 OD2 144.2 77.3 REMARK 620 4 ARG A 155 O 148.0 138.2 63.4 REMARK 620 5 GLU A 160 OE2 48.1 54.8 125.1 142.5 REMARK 620 N 1 2 3 4 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2K7B RELATED DB: PDB REMARK 900 RELATED ID: 2K7C RELATED DB: PDB REMARK 900 RELATED ID: 15623 RELATED DB: BMRB DBREF 2K7D A 96 167 UNP Q9NZU7 CABP1_HUMAN 156 227 SEQRES 1 A 72 ALA ASP MET ILE GLY VAL LYS GLU LEU ARG ASP ALA PHE SEQRES 2 A 72 ARG GLU PHE ASP THR ASN GLY ASP GLY GLU ILE SER THR SEQRES 3 A 72 SER GLU LEU ARG GLU ALA MET ARG LYS LEU LEU GLY HIS SEQRES 4 A 72 GLN VAL GLY HIS ARG ASP ILE GLU GLU ILE ILE ARG ASP SEQRES 5 A 72 VAL ASP LEU ASN GLY ASP GLY ARG VAL ASP PHE GLU GLU SEQRES 6 A 72 PHE VAL ARG MET MET SER ARG HET CA A 501 1 HET CA A 502 1 HETNAM CA CALCIUM ION FORMUL 2 CA 2(CA 2+) HELIX 1 1 VAL A 101 ASP A 112 1 12 HELIX 2 2 SER A 120 LEU A 132 1 13 HELIX 3 3 HIS A 138 VAL A 148 1 11 HELIX 4 4 PHE A 158 SER A 166 1 9 SHEET 1 A 2 GLU A 118 ILE A 119 0 SHEET 2 A 2 VAL A 156 ASP A 157 -1 O VAL A 156 N ILE A 119 LINK OD1 ASN A 114 CA CA A 501 1555 1555 2.78 LINK OD1 ASP A 116 CA CA A 501 1555 1555 2.26 LINK O GLU A 118 CA CA A 501 1555 1555 2.80 LINK OE2 GLU A 123 CA CA A 501 1555 1555 2.06 LINK OD1 ASP A 149 CA CA A 502 1555 1555 2.89 LINK OD1 ASN A 151 CA CA A 502 1555 1555 2.81 LINK OD2 ASP A 153 CA CA A 502 1555 1555 2.84 LINK O ARG A 155 CA CA A 502 1555 1555 2.88 LINK OE2 GLU A 160 CA CA A 502 1555 1555 2.86 SITE 1 AC1 4 ASP A 112 ASN A 114 ASP A 116 GLU A 118 SITE 1 AC2 4 ASP A 149 ASN A 151 ASP A 153 ASP A 157 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