HEADER TRANSPORT PROTEIN 04-APR-14 4P9I TITLE CRYSTAL STRUCTURE OF MOUSE RYANODINE RECEPTOR 2 SPRY2 DOMAIN (1080- TITLE 2 1253) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RYANODINE RECEPTOR 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1080-1253; COMPND 5 SYNONYM: RYR2,CARDIAC MUSCLE RYANODINE RECEPTOR,CARDIAC MUSCLE COMPND 6 RYANODINE RECEPTOR-CALCIUM RELEASE CHANNEL,TYPE 2 RYANODINE RECEPTOR; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: RYR2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA KEYWDS ION CHANNEL, SIGNALLING, METAL TRANSPORT, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.LAU,F.VAN PETEGEM REVDAT 6 27-DEC-23 4P9I 1 REMARK REVDAT 5 08-JAN-20 4P9I 1 REMARK REVDAT 4 18-APR-18 4P9I 1 JRNL REVDAT 3 22-NOV-17 4P9I 1 REMARK REVDAT 2 06-SEP-17 4P9I 1 SOURCE REMARK REVDAT 1 05-NOV-14 4P9I 0 JRNL AUTH K.LAU,F.VAN PETEGEM JRNL TITL CRYSTAL STRUCTURES OF WILD TYPE AND DISEASE MUTANT FORMS OF JRNL TITL 2 THE RYANODINE RECEPTOR SPRY2 DOMAIN. JRNL REF NAT COMMUN V. 5 5397 2014 JRNL REFN ESSN 2041-1723 JRNL PMID 25370123 JRNL DOI 10.1038/NCOMMS6397 REMARK 2 REMARK 2 RESOLUTION. 1.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: DEV_1637) 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) : 1.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.10 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.6 REMARK 3 NUMBER OF REFLECTIONS : 33932 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.139 REMARK 3 R VALUE (WORKING SET) : 0.138 REMARK 3 FREE R VALUE : 0.163 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1697 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 47.1237 - 3.0677 1.00 3119 164 0.1552 0.1672 REMARK 3 2 3.0677 - 2.4349 1.00 2985 157 0.1526 0.1636 REMARK 3 3 2.4349 - 2.1272 0.99 2940 155 0.1312 0.1578 REMARK 3 4 2.1272 - 1.9327 1.00 2930 154 0.1236 0.1443 REMARK 3 5 1.9327 - 1.7941 1.00 2906 154 0.1243 0.1638 REMARK 3 6 1.7941 - 1.6884 1.00 2908 153 0.1183 0.1558 REMARK 3 7 1.6884 - 1.6038 1.00 2898 152 0.1092 0.1547 REMARK 3 8 1.6038 - 1.5340 1.00 2901 153 0.1120 0.1583 REMARK 3 9 1.5340 - 1.4749 0.94 2720 143 0.1227 0.2169 REMARK 3 10 1.4749 - 1.4240 0.83 2376 125 0.1257 0.1489 REMARK 3 11 1.4240 - 1.3795 0.68 1981 105 0.1359 0.1734 REMARK 3 12 1.3795 - 1.3401 0.55 1571 82 0.1477 0.2065 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.590 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL 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 : 0.007 1325 REMARK 3 ANGLE : 1.168 1787 REMARK 3 CHIRALITY : 0.073 179 REMARK 3 PLANARITY : 0.005 234 REMARK 3 DIHEDRAL : 11.352 463 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 4P9I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000200984. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUN-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33935 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.340 REMARK 200 RESOLUTION RANGE LOW (A) : 47.095 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.6 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM FORMATE, PEG 3350, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.11500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.49000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.11500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 33.49000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1338 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1413 LIES ON A SPECIAL POSITION. 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 GLY A 1080 REMARK 465 THR A 1081 REMARK 465 GLY A 1082 REMARK 465 GLU A 1083 REMARK 465 CYS A 1122 REMARK 465 GLN A 1123 REMARK 465 PRO A 1124 REMARK 465 ASP A 1125 REMARK 465 LEU A 1126 REMARK 465 SER A 1252 REMARK 465 LYS A 1253 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A1084 CG CD NE CZ NH1 NH2 REMARK 470 GLU A1127 CG CD OE1 OE2 REMARK 470 GLU A1180 CD OE1 OE2 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 ASP A1131 -158.44 -123.09 REMARK 500 ALA A1142 66.57 62.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1465 DISTANCE = 6.44 ANGSTROMS REMARK 525 HOH A1510 DISTANCE = 6.37 ANGSTROMS REMARK 525 HOH A1527 DISTANCE = 6.27 ANGSTROMS DBREF 4P9I A 1080 1253 UNP E9Q401 RYR2_MOUSE 1080 1253 SEQRES 1 A 174 GLY THR GLY GLU ARG PHE ARG ILE PHE ARG ALA GLU LYS SEQRES 2 A 174 THR TYR ALA VAL LYS ALA GLY ARG TRP TYR PHE GLU PHE SEQRES 3 A 174 GLU ALA VAL THR ALA GLY ASP MET ARG VAL GLY TRP SER SEQRES 4 A 174 ARG PRO GLY CYS GLN PRO ASP LEU GLU LEU GLY SER ASP SEQRES 5 A 174 ASP ARG ALA PHE ALA PHE ASP GLY PHE LYS ALA GLN ARG SEQRES 6 A 174 TRP HIS GLN GLY ASN GLU HIS TYR GLY ARG SER TRP GLN SEQRES 7 A 174 ALA GLY ASP VAL VAL GLY CYS MET VAL ASP MET ASN GLU SEQRES 8 A 174 HIS THR MET MET PHE THR LEU ASN GLY GLU ILE LEU LEU SEQRES 9 A 174 ASP ASP SER GLY SER GLU LEU ALA PHE LYS ASP PHE ASP SEQRES 10 A 174 VAL GLY ASP GLY PHE ILE PRO VAL CYS SER LEU GLY VAL SEQRES 11 A 174 ALA GLN VAL GLY ARG MET ASN PHE GLY LYS ASP VAL SER SEQRES 12 A 174 THR LEU LYS TYR PHE THR ILE CYS GLY LEU GLN GLU GLY SEQRES 13 A 174 TYR GLU PRO PHE ALA VAL ASN THR ASN ARG ASP ILE THR SEQRES 14 A 174 MET TRP LEU SER LYS FORMUL 2 HOH *227(H2 O) HELIX 1 AA1 GLU A 1091 ALA A 1095 5 5 HELIX 2 AA2 ASP A 1220 LEU A 1224 5 5 HELIX 3 AA3 ALA A 1240 THR A 1243 5 4 SHEET 1 AA1 6 ARG A1086 ARG A1089 0 SHEET 2 AA1 6 ILE A1202 LEU A1207 -1 O LEU A1207 N ARG A1086 SHEET 3 AA1 6 MET A1113 SER A1118 -1 N SER A1118 O ILE A1202 SHEET 4 AA1 6 ALA A1134 ASP A1138 -1 O PHE A1137 N VAL A1115 SHEET 5 AA1 6 GLN A1143 TRP A1145 -1 O GLN A1143 N ASP A1138 SHEET 6 AA1 6 ASN A1149 HIS A1151 -1 O GLU A1150 N ARG A1144 SHEET 1 AA2 5 GLU A1180 ILE A1181 0 SHEET 2 AA2 5 THR A1172 LEU A1177 -1 N LEU A1177 O GLU A1180 SHEET 3 AA2 5 VAL A1161 ASP A1167 -1 N ASP A1167 O THR A1172 SHEET 4 AA2 5 ARG A1100 ALA A1107 -1 N PHE A1105 O VAL A1162 SHEET 5 AA2 5 GLY A1213 ASN A1216 -1 O ASN A1216 N GLU A1104 SHEET 1 AA3 5 PHE A1192 LYS A1193 0 SHEET 2 AA3 5 THR A1172 LEU A1177 -1 N MET A1173 O PHE A1192 SHEET 3 AA3 5 VAL A1161 ASP A1167 -1 N ASP A1167 O THR A1172 SHEET 4 AA3 5 ARG A1100 ALA A1107 -1 N PHE A1105 O VAL A1162 SHEET 5 AA3 5 GLU A1237 PRO A1238 1 O GLU A1237 N ARG A1100 CRYST1 36.290 66.230 66.980 90.00 90.00 90.00 P 2 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 0.027556 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015099 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014930 0.00000