HEADER CONTRACTILE PROTEIN 26-SEP-11 3TZ1 TITLE CRYSTAL STRUCTURE OF THE CA2+-SATURATED C-TERMINAL DOMAIN OF AKAZARA TITLE 2 SCALLOP TROPONIN C IN COMPLEX WITH A TROPONIN I FRAGMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: TROPONIN C; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN, UNP RESIDUES 81-153; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: TROPONIN I; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: UNP RESIDUES 143-166; COMPND 10 SYNONYM: TNI; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CHLAMYS NIPPONENSIS AKAZARA; SOURCE 3 ORGANISM_COMMON: AKAZARA SCALLOP; SOURCE 4 ORGANISM_TAXID: 6571; SOURCE 5 GENE: TROPONIN C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET16B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: CHLAMYS NIPPONENSIS AKAZARA; SOURCE 14 ORGANISM_COMMON: AKAZARA SCALLOP; SOURCE 15 ORGANISM_TAXID: 6571 KEYWDS PROTEIN-PEPTIDE COMPLEX, EF HAND, CA2+-SENSOR, CONTRACTILE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR F.YUMOTO,Y.S.KATO,I.OHTSUKI,M.TANOKURA REVDAT 2 20-MAR-24 3TZ1 1 REMARK SEQADV LINK REVDAT 1 23-JAN-13 3TZ1 0 JRNL AUTH Y.S.KATO,F.YUMOTO,H.TANAKA,T.MIYAKAWA,Y.MIYAUCHI, JRNL AUTH 2 D.TAKESHITA,Y.SAWANO,T.OJIMA,I.OHTSUKI,M.TANOKURA JRNL TITL STRUCTURE OF THE CA2+-SATURATED C-TERMINAL DOMAIN OF SCALLOP JRNL TITL 2 TROPONIN C IN COMPLEX WITH A TROPONIN I FRAGMENT JRNL REF BIOL.CHEM. V. 394 55 2012 JRNL REFN ISSN 1431-6730 JRNL PMID 23096565 JRNL DOI 10.1515/HSZ-2012-0152 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.1_743) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 7950 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.630 REMARK 3 FREE R VALUE TEST SET COUNT : 368 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 28.3244 - 2.5937 0.99 2585 148 0.2115 0.2200 REMARK 3 2 2.5937 - 2.0589 1.00 2516 110 0.1797 0.2773 REMARK 3 3 2.0589 - 1.7987 0.99 2481 110 0.2078 0.2772 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.44 REMARK 3 B_SOL : 55.34 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.330 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.950 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.87 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.70150 REMARK 3 B22 (A**2) : -10.25340 REMARK 3 B33 (A**2) : 3.55190 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.005 756 REMARK 3 ANGLE : 0.978 1006 REMARK 3 CHIRALITY : 0.082 116 REMARK 3 PLANARITY : 0.005 127 REMARK 3 DIHEDRAL : 13.852 302 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 82:100) REMARK 3 ORIGIN FOR THE GROUP (A): -18.1328 10.4245 -10.5537 REMARK 3 T TENSOR REMARK 3 T11: 0.2568 T22: 0.2397 REMARK 3 T33: 0.2071 T12: -0.0188 REMARK 3 T13: 0.0132 T23: 0.0011 REMARK 3 L TENSOR REMARK 3 L11: 0.0676 L22: 0.3667 REMARK 3 L33: 0.2801 L12: -0.0170 REMARK 3 L13: 0.0368 L23: 0.2170 REMARK 3 S TENSOR REMARK 3 S11: -0.0981 S12: 0.1964 S13: 0.0565 REMARK 3 S21: -0.4312 S22: -0.0010 S23: 0.2635 REMARK 3 S31: -0.1710 S32: -0.0385 S33: -0.0119 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 101:130) REMARK 3 ORIGIN FOR THE GROUP (A): -10.5327 -1.2151 1.2370 REMARK 3 T TENSOR REMARK 3 T11: 0.2260 T22: 0.2030 REMARK 3 T33: 0.2236 T12: 0.0135 REMARK 3 T13: -0.0479 T23: 0.0006 REMARK 3 L TENSOR REMARK 3 L11: 0.6085 L22: 0.3276 REMARK 3 L33: 0.5721 L12: 0.1239 REMARK 3 L13: 0.1799 L23: 0.1944 REMARK 3 S TENSOR REMARK 3 S11: 0.0086 S12: -0.2360 S13: -0.1900 REMARK 3 S21: 0.0682 S22: -0.0354 S23: -0.2881 REMARK 3 S31: 0.4535 S32: -0.0491 S33: -0.0033 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESSEQ 131:152) REMARK 3 ORIGIN FOR THE GROUP (A): -18.7123 -1.7820 -10.5517 REMARK 3 T TENSOR REMARK 3 T11: 0.2563 T22: 0.2609 REMARK 3 T33: 0.1859 T12: 0.0113 REMARK 3 T13: -0.0338 T23: -0.0342 REMARK 3 L TENSOR REMARK 3 L11: 0.2037 L22: 1.1779 REMARK 3 L33: 0.8046 L12: -0.3369 REMARK 3 L13: -0.1133 L23: -0.4728 REMARK 3 S TENSOR REMARK 3 S11: 0.2303 S12: 0.3708 S13: -0.6098 REMARK 3 S21: -0.5028 S22: 0.0823 S23: 0.3506 REMARK 3 S31: 0.4507 S32: -0.3483 S33: 0.0820 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' REMARK 3 ORIGIN FOR THE GROUP (A): -19.3603 3.9113 1.2281 REMARK 3 T TENSOR REMARK 3 T11: 0.1704 T22: 0.1742 REMARK 3 T33: 0.2204 T12: -0.0155 REMARK 3 T13: 0.0195 T23: -0.0150 REMARK 3 L TENSOR REMARK 3 L11: 0.6199 L22: 0.1393 REMARK 3 L33: 0.3670 L12: -0.0933 REMARK 3 L13: 0.0134 L23: -0.2250 REMARK 3 S TENSOR REMARK 3 S11: 0.0294 S12: -0.1145 S13: -0.0314 REMARK 3 S21: 0.2329 S22: 0.0422 S23: 0.1927 REMARK 3 S31: 0.1495 S32: -0.0248 S33: 0.0011 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3TZ1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000068098. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-MAR-06; 31-OCT-06 REMARK 200 TEMPERATURE (KELVIN) : 95; 95 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY; PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A; AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000; 0.97854, 0.9791, 0.974 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210; ADSC QUANTUM REMARK 200 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8036 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.05300 REMARK 200 R SYM (I) : 0.05300 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.26600 REMARK 200 FOR SHELL : 5.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.03 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 4000, 0.1 M SODIUM ACETATE PH REMARK 280 4.6 AND 0.2 M AMMONIUM ACETATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 16.06500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.98300 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.07550 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.98300 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.06500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.07550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 79 REMARK 465 GLU A 80 REMARK 465 ASP A 81 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 1 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 12 O REMARK 620 2 ASP A 131 OD1 172.0 REMARK 620 3 ASP A 133 OD1 94.4 81.3 REMARK 620 4 SER A 135 OG 81.9 90.6 78.8 REMARK 620 5 THR A 137 O 98.1 82.5 149.1 75.2 REMARK 620 6 GLU A 142 OE2 91.6 94.5 81.2 158.3 126.3 REMARK 620 7 GLU A 142 OE1 81.8 106.1 131.2 146.8 78.7 50.5 REMARK 620 N 1 2 3 4 5 6 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 1 DBREF 3TZ1 A 80 152 UNP Q27428 Q27428_CHLNI 81 153 DBREF 3TZ1 B 143 166 UNP Q7M3Y3 TNNI_CHLNI 143 166 SEQADV 3TZ1 MET A 79 UNP Q27428 EXPRESSION TAG SEQRES 1 A 74 MET GLU ASP LEU ASP GLU ARG GLU LEU LYS GLU ALA PHE SEQRES 2 A 74 ARG VAL LEU ASP LYS GLU LYS LYS GLY VAL ILE LYS VAL SEQRES 3 A 74 ASP VAL LEU ARG TRP ILE LEU LYS SER LEU GLY ASP GLU SEQRES 4 A 74 LEU THR GLU ASP GLU ILE GLU ASN MET ILE ALA GLU THR SEQRES 5 A 74 ASP THR ASP GLY SER GLY THR VAL ASP TYR GLU GLU PHE SEQRES 6 A 74 LYS CYS LEU MET MET SER SER ASP ALA SEQRES 1 B 24 GLY LEU SER PRO GLU LYS LYS LYS MET LEU LYS LYS LEU SEQRES 2 B 24 ILE MET GLN LYS ALA ALA GLU ASP LEU ALA ASN HET CA A 1 1 HETNAM CA CALCIUM ION FORMUL 3 CA CA 2+ FORMUL 4 HOH *27(H2 O) HELIX 1 1 ASP A 83 ASP A 95 1 13 HELIX 2 2 VAL A 104 GLY A 115 1 12 HELIX 3 3 THR A 119 ASP A 131 1 13 HELIX 4 4 ASP A 139 SER A 149 1 11 HELIX 5 5 SER B 145 ALA B 165 1 21 SHEET 1 A 2 ILE A 102 LYS A 103 0 SHEET 2 A 2 THR A 137 VAL A 138 -1 O VAL A 138 N ILE A 102 LINK CA CA A 1 O HOH A 12 1555 1555 2.63 LINK CA CA A 1 OD1 ASP A 131 1555 1555 2.34 LINK CA CA A 1 OD1 ASP A 133 1555 1555 2.33 LINK CA CA A 1 OG SER A 135 1555 1555 2.69 LINK CA CA A 1 O THR A 137 1555 1555 2.35 LINK CA CA A 1 OE2 GLU A 142 1555 1555 2.58 LINK CA CA A 1 OE1 GLU A 142 1555 1555 2.59 SITE 1 AC1 6 HOH A 12 ASP A 131 ASP A 133 SER A 135 SITE 2 AC1 6 THR A 137 GLU A 142 CRYST1 32.130 42.151 59.966 90.00 90.00 90.00 P 21 21 21 4 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 0.031124 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023724 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016676 0.00000