HEADER METAL TRANSPORT 24-APR-12 4ETT TITLE CRYSTAL STRUCTURE OF RABBIT RYANODINE RECEPTOR 1 MUTANT E2764K COMPND MOL_ID: 1; COMPND 2 MOLECULE: RYANODINE RECEPTOR 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RYR-1, RYR1, SKELETAL MUSCLE CALCIUM RELEASE CHANNEL, COMPND 5 SKELETAL MUSCLE RYANODINE RECEPTOR, SKELETAL MUSCLE-TYPE RYANODINE COMPND 6 RECEPTOR, TYPE 1 RYANODINE RECEPTOR; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS; SOURCE 3 ORGANISM_COMMON: RABBIT; SOURCE 4 ORGANISM_TAXID: 9986; SOURCE 5 GENE: RYR1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA(DE3)PLACI; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28HMT KEYWDS RYANODINE RECEPTOR CALCIUM RELEASE CHANNEL, PHOSPHORYLATION, MUSCLE, KEYWDS 2 SKELETAL, METAL TRANSPORT EXPDTA X-RAY DIFFRACTION AUTHOR Z.YUCHI,K.LAU,F.VAN PETEGEM REVDAT 5 13-SEP-23 4ETT 1 REMARK SEQADV REVDAT 4 17-JUL-19 4ETT 1 REMARK REVDAT 3 15-NOV-17 4ETT 1 REMARK REVDAT 2 17-OCT-12 4ETT 1 JRNL REVDAT 1 13-JUN-12 4ETT 0 JRNL AUTH Z.YUCHI,K.LAU,F.VAN PETEGEM JRNL TITL DISEASE MUTATIONS IN THE RYANODINE RECEPTOR CENTRAL REGION: JRNL TITL 2 CRYSTAL STRUCTURES OF A PHOSPHORYLATION HOT SPOT DOMAIN. JRNL REF STRUCTURE V. 20 1201 2012 JRNL REFN ISSN 0969-2126 JRNL PMID 22705209 JRNL DOI 10.1016/J.STR.2012.04.015 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6_289 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.050 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.5 REMARK 3 NUMBER OF REFLECTIONS : 10258 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.223 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.770 REMARK 3 FREE R VALUE TEST SET COUNT : 489 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE 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 : 0.39 REMARK 3 B_SOL : 45.30 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.89120 REMARK 3 B22 (A**2) : 1.28070 REMARK 3 B33 (A**2) : 6.61050 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : 0.037 NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 4ETT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 29-APR-12. REMARK 100 THE DEPOSITION ID IS D_1000072060. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-FEB-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.542 REMARK 200 MONOCHROMATOR : VARIMAX VHF REMARK 200 OPTICS : DOUBLE CRYSTAL MONOCHROMATOR, REMARK 200 MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000, DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11079 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.195 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 (%) : 98.5 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.30100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4ERT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3350, 25% GLYCEROL, 0.1M HEPES, REMARK 280 PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 28.12200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.34650 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.12200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 57.34650 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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. (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 SER A 2731 REMARK 465 ASN A 2732 REMARK 465 ALA A 2733 REMARK 465 ASN A 2734 REMARK 465 GLU A 2832 REMARK 465 ARG A 2833 REMARK 465 THR A 2834 REMARK 465 GLU A 2835 REMARK 465 LYS A 2836 REMARK 465 LYS A 2837 REMARK 465 LYS A 2838 REMARK 465 THR A 2839 REMARK 465 ARG A 2840 REMARK 465 LYS A 2841 REMARK 465 ILE A 2842 REMARK 465 SER A 2843 REMARK 465 GLN A 2844 REMARK 465 THR A 2845 REMARK 465 ALA A 2846 REMARK 465 GLN A 2847 REMARK 465 THR A 2848 REMARK 465 TYR A 2849 REMARK 465 ASP A 2850 REMARK 465 PRO A 2851 REMARK 465 ARG A 2852 REMARK 465 GLU A 2853 REMARK 465 GLY A 2854 REMARK 465 GLY A 2940 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 GLU A2741 CG CD OE1 OE2 REMARK 470 LEU A2743 CG CD1 CD2 REMARK 470 GLU A2779 CG CD OE1 OE2 REMARK 470 GLU A2783 CG CD OE1 OE2 REMARK 470 LYS A2795 CG CD CE NZ REMARK 470 LYS A2800 CG CD CE NZ REMARK 470 GLU A2830 CG CD OE1 OE2 REMARK 470 GLU A2831 CG CD OE1 OE2 REMARK 470 GLU A2870 CG CD OE1 OE2 REMARK 470 LYS A2897 CG CD CE NZ REMARK 470 LYS A2914 CG CD CE NZ REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 3001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 3002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 3003 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 3004 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ERT RELATED DB: PDB REMARK 900 RYR1 2734-2940 REMARK 900 RELATED ID: 4ERV RELATED DB: PDB REMARK 900 RYR3 2597-2800 REMARK 900 RELATED ID: 4ESU RELATED DB: PDB REMARK 900 RYR1 S2776M REMARK 900 RELATED ID: 4ETU RELATED DB: PDB REMARK 900 RYR1 R2939S REMARK 900 RELATED ID: 4ETV RELATED DB: PDB REMARK 900 RYR2 K2879A DBREF 4ETT A 2734 2940 UNP P11716 RYR1_RABIT 2734 2940 SEQADV 4ETT SER A 2731 UNP P11716 EXPRESSION TAG SEQADV 4ETT ASN A 2732 UNP P11716 EXPRESSION TAG SEQADV 4ETT ALA A 2733 UNP P11716 EXPRESSION TAG SEQADV 4ETT LYS A 2764 UNP P11716 GLU 2764 ENGINEERED MUTATION SEQRES 1 A 210 SER ASN ALA ASN PHE ASP PRO ARG PRO VAL GLU THR LEU SEQRES 2 A 210 ASN VAL ILE ILE PRO GLU LYS LEU ASP SER PHE ILE ASN SEQRES 3 A 210 LYS PHE ALA GLU TYR THR HIS LYS LYS TRP ALA PHE ASP SEQRES 4 A 210 LYS ILE GLN ASN ASN TRP SER TYR GLY GLU ASN VAL ASP SEQRES 5 A 210 GLU GLU LEU LYS THR HIS PRO MET LEU ARG PRO TYR LYS SEQRES 6 A 210 THR PHE SER GLU LYS ASP LYS GLU ILE TYR ARG TRP PRO SEQRES 7 A 210 ILE LYS GLU SER LEU LYS ALA MET ILE ALA TRP GLU TRP SEQRES 8 A 210 THR ILE GLU LYS ALA ARG GLU GLY GLU GLU GLU ARG THR SEQRES 9 A 210 GLU LYS LYS LYS THR ARG LYS ILE SER GLN THR ALA GLN SEQRES 10 A 210 THR TYR ASP PRO ARG GLU GLY TYR ASN PRO GLN PRO PRO SEQRES 11 A 210 ASP LEU SER GLY VAL THR LEU SER ARG GLU LEU GLN ALA SEQRES 12 A 210 MET ALA GLU GLN LEU ALA GLU ASN TYR HIS ASN THR TRP SEQRES 13 A 210 GLY ARG LYS LYS LYS GLN GLU LEU GLU ALA LYS GLY GLY SEQRES 14 A 210 GLY THR HIS PRO LEU LEU VAL PRO TYR ASP THR LEU THR SEQRES 15 A 210 ALA LYS GLU LYS ALA ARG ASP ARG GLU LYS ALA GLN GLU SEQRES 16 A 210 LEU LEU LYS PHE LEU GLN MET ASN GLY TYR ALA VAL THR SEQRES 17 A 210 ARG GLY HET GOL A3001 6 HET GOL A3002 6 HET GOL A3003 6 HET GOL A3004 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 4(C3 H8 O3) FORMUL 6 HOH *103(H2 O) HELIX 1 1 PRO A 2748 LYS A 2750 5 3 HELIX 2 2 LEU A 2751 ASN A 2773 1 23 HELIX 3 3 PRO A 2793 PHE A 2797 5 5 HELIX 4 4 SER A 2798 TRP A 2819 1 22 HELIX 5 5 ASP A 2861 VAL A 2865 5 5 HELIX 6 6 SER A 2868 LYS A 2897 1 30 HELIX 7 7 PRO A 2907 LEU A 2911 5 5 HELIX 8 8 THR A 2912 ASN A 2933 1 22 SHEET 1 A 2 THR A2822 LYS A2825 0 SHEET 2 A 2 TYR A2935 THR A2938 -1 O ALA A2936 N GLU A2824 SITE 1 AC1 7 ASP A2736 ARG A2738 ARG A2827 GLU A2828 SITE 2 AC1 7 ASN A2884 HOH A3104 HOH A3131 SITE 1 AC2 5 PRO A2748 LEU A2751 THR A2822 ILE A2823 SITE 2 AC2 5 HOH A3191 SITE 1 AC3 8 ASP A2736 ARG A2738 ILE A2747 LYS A2810 SITE 2 AC3 8 LYS A2814 ARG A2827 HOH A3182 HOH A3202 SITE 1 AC4 7 LEU A2785 HIS A2883 TRP A2886 LEU A2904 SITE 2 AC4 7 GLU A2915 ARG A2918 ASP A2919 CRYST1 32.110 56.244 114.693 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 0.031143 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017780 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008719 0.00000