HEADER METAL BINDING PROTEIN 06-MAR-06 2G9B TITLE NMR SOLUTION STRUCTURE OF CA2+-LOADED CALBINDIN D28K COMPND MOL_ID: 1; COMPND 2 MOLECULE: CALBINDIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: VITAMIN D-DEPENDENT CALCIUM-BINDING PROTEIN, AVIAN-TYPE, COMPND 5 CALBINDIN D28, D-28K, SPOT 35 PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RATTUS NORVEGICUS; SOURCE 3 ORGANISM_COMMON: NORWAY RAT; SOURCE 4 ORGANISM_TAXID: 10116; SOURCE 5 GENE: CALB1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-4T KEYWDS EF-HAND, CA2+-BINDING, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 10 AUTHOR D.J.KOJETIN,R.A.VENTERS,D.R.KORDYS,R.J.THOMPSON,R.KUMAR,J.CAVANAGH REVDAT 5 29-MAY-24 2G9B 1 REMARK REVDAT 4 09-MAR-22 2G9B 1 REMARK SEQADV REVDAT 3 24-FEB-09 2G9B 1 VERSN REVDAT 2 18-JUL-06 2G9B 1 JRNL REVDAT 1 04-JUL-06 2G9B 0 JRNL AUTH D.J.KOJETIN,R.A.VENTERS,D.R.KORDYS,R.J.THOMPSON,R.KUMAR, JRNL AUTH 2 J.CAVANAGH JRNL TITL STRUCTURE, BINDING INTERFACE AND HYDROPHOBIC TRANSITIONS OF JRNL TITL 2 CA(2+)-LOADED CALBINDIN-D(28K). JRNL REF NAT.STRUCT.MOL.BIOL. V. 13 641 2006 JRNL REFN ISSN 1545-9993 JRNL PMID 16799559 JRNL DOI 10.1038/NSMB1112 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0, XPLOR-NIH 2.9.4A REMARK 3 AUTHORS : BRUNGER, A.T., ADAMS, P.D., CLORE, G.M., DELANO, REMARK 3 W.L., GROS, P., GROSSE-KUNSTLEVE, R.W., JIANG, J.- REMARK 3 S., KUSZEWSKI, J., NILGES, M., PANNU, N.S., READ, REMARK 3 R.J., RICE, L.M., SIMONSON, T., WARREN, G.L. (CNS), REMARK 3 SCHWIETERS, C.D. ET AL. (XPLOR-NIH) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE STRUCTURES ARE BASED ON 6882 NOE REMARK 3 DISTANCE CONSTRAINTS, 432 DIHEDRAL ANGLE RESTRAINTS, 36 HYDROGEN REMARK 3 BOND RESTRAINTS AND 304 RESIDUAL DIPOLAR COUPLING RESTRAINTS REMARK 4 REMARK 4 2G9B COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAR-06. REMARK 100 THE DEPOSITION ID IS D_1000036850. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298; 323 REMARK 210 PH : 7.0; 6.2 REMARK 210 IONIC STRENGTH : 6 MM CACL2; 6 MM CACL2 REMARK 210 PRESSURE : AMBIENT; AMBIENT REMARK 210 SAMPLE CONTENTS : 1MM CALBINDIN D28K; U-15N,13C; REMARK 210 10 MM TRIS, 1 MM DTT, 0.02% NAN3, REMARK 210 6 MM CACL2, 90% H2O, 10% D2O; REMARK 210 1MM CALBINDIN D28K; U-15N,13C; REMARK 210 10 MM TRIS, 1 MM DTT, 0.02% NAN3, REMARK 210 6 MM CACL2, 100% D2O; 1MM REMARK 210 CALBINDIN D28K; U-2H,15N,13C; REMARK 210 ILE (D1 ONLY), LEU, VAL METHYL REMARK 210 PROTONATED; 10 MM TRIS, 1 MM DTT, REMARK 210 0.02% NAN3, 6 MM CACL2, 90% H2O, REMARK 210 10% D2O; 1MM CALBINDIN D28K; U- REMARK 210 2H,15N; 10 MM TRIS, 1 MM DTT, REMARK 210 0.02% NAN3, 6 MM CACL2, 90% H2O, REMARK 210 10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 4D_13C/15N-SEPARATED_NOESY; REMARK 210 4D_13C/13C-SEPARATED_NOESY; 3D_CT_13C_METHYL-SEPARATED_NOESY; (4, REMARK 210 2)D_CT_13C/13C_METHYL-SEPARATED_NOESY; (4,2)D_13C/15N-SEPARATED_ REMARK 210 NOESY; 4D_15N/15N-SEPARATED_NOESY; (4,2)D_13C_ALI/13C_ARO- REMARK 210 SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 2.3, NMRVIEW 5.0 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS, REMARK 210 MOLECULAR DYNAMICS SIMULATED REMARK 210 ANNEALING REFINEMENT IN EXPLICIT REMARK 210 SOLVENT (WATER) REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 900 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 10 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS, STRUCTURES REMARK 210 WITH THE LOWEST RESTRAINT ENERGY REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: THIS STRUCTURE WAS DETERMINED USING A COMBINATION OF 3D, REMARK 210 4D AND (4,2)D PROJECTION RECONSTRUCTION TECHNIQUES ON REMARK 210 PERDEUTERATED AND FULLY PROTONATED SAMPLES. 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-10 REMARK 465 RES C SSSEQI REMARK 465 GLY A -1 REMARK 465 SER A 0 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 OE2 GLU A 3 HZ3 LYS A 49 1.58 REMARK 500 OD2 ASP A 111 H SER A 115 1.59 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 5 TRP A 107 CD2 TRP A 107 CE3 -0.095 REMARK 500 REMARK 500 REMARK: NULL 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 PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 6 TYR A 146 CB - CG - CD2 ANGL. DEV. = -3.6 DEGREES 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 SER A 9 -172.17 60.89 REMARK 500 1 LEU A 10 65.81 -106.71 REMARK 500 1 ILE A 11 107.58 -35.06 REMARK 500 1 PHE A 23 17.13 -151.45 REMARK 500 1 ALA A 25 -71.86 -43.23 REMARK 500 1 LEU A 39 -79.57 -57.49 REMARK 500 1 ILE A 40 -40.41 -24.97 REMARK 500 1 LYS A 49 -71.96 -69.89 REMARK 500 1 ALA A 50 -1.85 -60.00 REMARK 500 1 PRO A 56 -4.85 -49.07 REMARK 500 1 GLN A 67 17.52 -144.36 REMARK 500 1 LYS A 72 134.85 -174.43 REMARK 500 1 THR A 84 -84.14 -61.62 REMARK 500 1 GLU A 85 84.93 -155.87 REMARK 500 1 LYS A 98 -69.68 -153.25 REMARK 500 1 THR A 112 -81.58 23.90 REMARK 500 1 ASP A 113 19.84 -142.11 REMARK 500 1 HIS A 114 74.41 70.91 REMARK 500 1 PHE A 117 135.92 -170.48 REMARK 500 1 GLU A 119 -154.07 -96.77 REMARK 500 1 LYS A 136 -71.93 -121.68 REMARK 500 1 THR A 137 -26.16 154.09 REMARK 500 1 VAL A 138 79.26 51.59 REMARK 500 1 ASP A 139 162.33 -48.45 REMARK 500 1 PHE A 154 21.81 -147.26 REMARK 500 1 ASN A 157 18.50 -144.49 REMARK 500 1 LEU A 164 -71.33 -67.30 REMARK 500 1 THR A 165 33.52 -55.39 REMARK 500 1 GLN A 174 -77.49 -123.86 REMARK 500 1 LYS A 185 115.82 -27.95 REMARK 500 1 CYS A 187 143.44 146.71 REMARK 500 1 GLU A 208 -8.54 -47.22 REMARK 500 1 ILE A 228 -2.94 -52.15 REMARK 500 1 ASN A 237 -82.59 -47.89 REMARK 500 1 THR A 250 -31.55 -157.38 REMARK 500 1 ALA A 253 12.81 -147.46 REMARK 500 1 ALA A 258 -28.02 167.71 REMARK 500 2 SER A 9 -177.59 61.60 REMARK 500 2 LEU A 10 59.77 -110.60 REMARK 500 2 ILE A 11 93.05 -29.25 REMARK 500 2 ALA A 13 36.93 -88.31 REMARK 500 2 SER A 14 -54.01 -125.96 REMARK 500 2 PHE A 23 18.74 -144.64 REMARK 500 2 ASP A 24 76.89 -108.07 REMARK 500 2 LEU A 39 -81.54 -58.02 REMARK 500 2 ILE A 40 -30.47 -32.93 REMARK 500 2 ALA A 50 2.05 -59.29 REMARK 500 2 LEU A 52 -160.67 -101.55 REMARK 500 2 GLN A 67 16.81 -140.58 REMARK 500 2 ASP A 70 39.58 -99.52 REMARK 500 REMARK 500 THIS ENTRY HAS 362 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 2 ARG A 249 0.09 SIDE CHAIN REMARK 500 3 ARG A 47 0.08 SIDE CHAIN REMARK 500 4 TYR A 205 0.08 SIDE CHAIN REMARK 500 6 ARG A 47 0.07 SIDE CHAIN REMARK 500 7 TYR A 205 0.08 SIDE CHAIN REMARK 500 8 TYR A 110 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2F33 RELATED DB: PDB REMARK 900 NMR SOLUTION STRUCTURE OF CA2+-LOADED CALBINDIN D28K, NOT REFINED REMARK 900 IN EXPLICIT SOLVENT DBREF 2G9B A 1 261 UNP P07171 CALB1_RAT 1 261 SEQADV 2G9B GLY A -1 UNP P07171 CLONING ARTIFACT SEQADV 2G9B SER A 0 UNP P07171 CLONING ARTIFACT SEQRES 1 A 263 GLY SER MET ALA GLU SER HIS LEU GLN SER SER LEU ILE SEQRES 2 A 263 THR ALA SER GLN PHE PHE GLU ILE TRP LEU HIS PHE ASP SEQRES 3 A 263 ALA ASP GLY SER GLY TYR LEU GLU GLY LYS GLU LEU GLN SEQRES 4 A 263 ASN LEU ILE GLN GLU LEU LEU GLN ALA ARG LYS LYS ALA SEQRES 5 A 263 GLY LEU GLU LEU SER PRO GLU MET LYS THR PHE VAL ASP SEQRES 6 A 263 GLN TYR GLY GLN ARG ASP ASP GLY LYS ILE GLY ILE VAL SEQRES 7 A 263 GLU LEU ALA HIS VAL LEU PRO THR GLU GLU ASN PHE LEU SEQRES 8 A 263 LEU LEU PHE ARG CYS GLN GLN LEU LYS SER CYS GLU GLU SEQRES 9 A 263 PHE MET LYS THR TRP ARG LYS TYR ASP THR ASP HIS SER SEQRES 10 A 263 GLY PHE ILE GLU THR GLU GLU LEU LYS ASN PHE LEU LYS SEQRES 11 A 263 ASP LEU LEU GLU LYS ALA ASN LYS THR VAL ASP ASP THR SEQRES 12 A 263 LYS LEU ALA GLU TYR THR ASP LEU MET LEU LYS LEU PHE SEQRES 13 A 263 ASP SER ASN ASN ASP GLY LYS LEU GLU LEU THR GLU MET SEQRES 14 A 263 ALA ARG LEU LEU PRO VAL GLN GLU ASN PHE LEU LEU LYS SEQRES 15 A 263 PHE GLN GLY ILE LYS MET CYS GLY LYS GLU PHE ASN LYS SEQRES 16 A 263 ALA PHE GLU LEU TYR ASP GLN ASP GLY ASN GLY TYR ILE SEQRES 17 A 263 ASP GLU ASN GLU LEU ASP ALA LEU LEU LYS ASP LEU CYS SEQRES 18 A 263 GLU LYS ASN LYS GLN GLU LEU ASP ILE ASN ASN ILE SER SEQRES 19 A 263 THR TYR LYS LYS ASN ILE MET ALA LEU SER ASP GLY GLY SEQRES 20 A 263 LYS LEU TYR ARG THR ASP LEU ALA LEU ILE LEU SER ALA SEQRES 21 A 263 GLY ASP ASN HELIX 1 1 MET A 1 LEU A 6 1 6 HELIX 2 2 SER A 14 HIS A 22 1 9 HELIX 3 3 LYS A 34 GLY A 51 1 18 HELIX 4 4 GLU A 57 GLY A 66 1 10 HELIX 5 5 GLY A 74 ALA A 79 1 6 HELIX 6 6 PHE A 88 ARG A 93 1 6 HELIX 7 7 GLU A 101 TYR A 110 1 10 HELIX 8 8 GLU A 119 GLU A 132 1 14 HELIX 9 9 ASP A 139 PHE A 154 1 16 HELIX 10 10 GLU A 163 ALA A 168 1 6 HELIX 11 11 LEU A 179 LYS A 185 1 7 HELIX 12 12 CYS A 187 ASP A 199 1 13 HELIX 13 13 GLU A 208 GLU A 220 1 13 HELIX 14 14 ASN A 230 MET A 239 1 10 SHEET 1 A 2 LEU A 31 GLU A 32 0 SHEET 2 A 2 LYS A 72 ILE A 73 -1 O ILE A 73 N LEU A 31 SHEET 1 B 2 ILE A 206 ASP A 207 0 SHEET 2 B 2 LYS A 246 LEU A 247 -1 O LEU A 247 N ILE A 206 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