HEADER TRANSFERASE 10-SEP-22 8B1N TITLE CRYSTAL STRUCTURE OF TRMD-TM1570 FROM CALDITERRIVIBRIO NITROREDUCENS TITLE 2 IN COMPLEX WITH S-ADENOSYL-L-METHIONINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRNA (GUANINE-N(1)-)-METHYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: M1G-METHYLTRANSFERASE,TRNA [GM37] METHYLTRANSFERASE; COMPND 5 EC: 2.1.1.228; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CALDITERRIVIBRIO NITROREDUCENS DSM 19672; SOURCE 3 ORGANISM_TAXID: 768670; SOURCE 4 STRAIN: DSM 19672 / NBRC 101217 / YU37-1; SOURCE 5 GENE: TRMD, CALNI_2012; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS TRMD-TM1570, TRMD, TM1570, METHYL TRANSFERASE, KNOTTED PROTEIN, KEYWDS 2 DOUBLE KNOTTED PROTEIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.KLUZA,I.LEWANDOWSKA,R.AUGUSTYNIAK,J.SULKOWSKA REVDAT 3 03-JUL-24 8B1N 1 JRNL REVDAT 2 31-JAN-24 8B1N 1 REMARK REVDAT 1 28-SEP-22 8B1N 0 JRNL AUTH A.P.PERLINSKA,M.L.NGUYEN,S.P.PILLA,E.STASZOR,I.LEWANDOWSKA, JRNL AUTH 2 A.BERNAT,E.PURTA,R.AUGUSTYNIAK,J.M.BUJNICKI,J.I.SULKOWSKA JRNL TITL ARE THERE DOUBLE KNOTS IN PROTEINS? PREDICTION AND IN VITRO JRNL TITL 2 VERIFICATION BASED ON TRMD-TM1570 FUSION FROM C. JRNL TITL 3 NITROREDUCENS. JRNL REF FRONT MOL BIOSCI V. 10 23830 2023 JRNL REFN ESSN 2296-889X JRNL PMID 38903539 JRNL DOI 10.3389/FMOLB.2023.1223830 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.92 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 75168 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.170 REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.790 REMARK 3 FREE R VALUE TEST SET COUNT : 2100 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 48.9200 - 4.9300 0.99 5182 150 0.1687 0.2137 REMARK 3 2 4.9300 - 3.9100 1.00 4975 143 0.1234 0.1509 REMARK 3 3 3.9100 - 3.4200 1.00 4934 142 0.1452 0.1789 REMARK 3 4 3.4200 - 3.1100 1.00 4876 140 0.1611 0.2091 REMARK 3 5 3.1100 - 2.8800 1.00 4885 140 0.1728 0.2128 REMARK 3 6 2.8800 - 2.7100 1.00 4864 140 0.1784 0.2281 REMARK 3 7 2.7100 - 2.5800 1.00 4847 138 0.1740 0.2155 REMARK 3 8 2.5800 - 2.4700 1.00 4840 139 0.1728 0.2180 REMARK 3 9 2.4700 - 2.3700 1.00 4842 139 0.1844 0.2386 REMARK 3 10 2.3700 - 2.2900 1.00 4820 139 0.1971 0.2422 REMARK 3 11 2.2900 - 2.2200 1.00 4846 139 0.2123 0.2501 REMARK 3 12 2.2200 - 2.1500 1.00 4802 138 0.2147 0.2652 REMARK 3 13 2.1500 - 2.1000 1.00 4798 138 0.2379 0.2597 REMARK 3 14 2.1000 - 2.0500 1.00 4815 138 0.2640 0.2927 REMARK 3 15 2.0500 - 2.0000 0.99 4742 137 0.2901 0.3357 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) : 0.229 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.687 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.87 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 7119 REMARK 3 ANGLE : 0.824 9661 REMARK 3 CHIRALITY : 0.053 1083 REMARK 3 PLANARITY : 0.004 1224 REMARK 3 DIHEDRAL : 17.221 2675 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -2 THROUGH 159 ) REMARK 3 ORIGIN FOR THE GROUP (A): 59.5030 79.0885 80.1762 REMARK 3 T TENSOR REMARK 3 T11: 0.1838 T22: 0.2166 REMARK 3 T33: 0.3048 T12: 0.0175 REMARK 3 T13: 0.0492 T23: 0.0117 REMARK 3 L TENSOR REMARK 3 L11: 1.6516 L22: 2.3258 REMARK 3 L33: 1.2576 L12: -0.2996 REMARK 3 L13: -0.0676 L23: 0.4684 REMARK 3 S TENSOR REMARK 3 S11: -0.0314 S12: -0.0760 S13: 0.1300 REMARK 3 S21: 0.2059 S22: -0.0168 S23: 0.4335 REMARK 3 S31: -0.0572 S32: -0.1691 S33: 0.0471 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 248 THROUGH 430 ) REMARK 3 ORIGIN FOR THE GROUP (A): 116.0491 64.9927 83.4999 REMARK 3 T TENSOR REMARK 3 T11: 0.2466 T22: 0.2566 REMARK 3 T33: 0.1833 T12: 0.0016 REMARK 3 T13: 0.0235 T23: 0.0433 REMARK 3 L TENSOR REMARK 3 L11: 3.4804 L22: 4.7469 REMARK 3 L33: 1.8996 L12: -0.1426 REMARK 3 L13: 0.3206 L23: 0.2652 REMARK 3 S TENSOR REMARK 3 S11: 0.0817 S12: 0.1447 S13: 0.1834 REMARK 3 S21: -0.0711 S22: -0.0421 S23: -0.3064 REMARK 3 S31: -0.2029 S32: 0.1400 S33: -0.0388 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 0 THROUGH 159 ) REMARK 3 ORIGIN FOR THE GROUP (A): 68.4943 72.1441 57.7820 REMARK 3 T TENSOR REMARK 3 T11: 0.2668 T22: 0.2969 REMARK 3 T33: 0.1987 T12: 0.0244 REMARK 3 T13: -0.0344 T23: 0.0410 REMARK 3 L TENSOR REMARK 3 L11: 1.9454 L22: 2.6871 REMARK 3 L33: 1.5939 L12: -0.2922 REMARK 3 L13: -0.0508 L23: 0.5358 REMARK 3 S TENSOR REMARK 3 S11: 0.0383 S12: 0.3413 S13: 0.0530 REMARK 3 S21: -0.4652 S22: -0.0365 S23: 0.2239 REMARK 3 S31: -0.1119 S32: -0.1239 S33: -0.0051 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 160 THROUGH 241 ) REMARK 3 ORIGIN FOR THE GROUP (A): 76.4238 96.4879 82.4844 REMARK 3 T TENSOR REMARK 3 T11: 0.3006 T22: 0.2384 REMARK 3 T33: 0.3803 T12: -0.0267 REMARK 3 T13: -0.0259 T23: -0.0396 REMARK 3 L TENSOR REMARK 3 L11: 3.4007 L22: 5.3831 REMARK 3 L33: 2.6110 L12: -0.2929 REMARK 3 L13: -1.1807 L23: 1.3285 REMARK 3 S TENSOR REMARK 3 S11: 0.0590 S12: -0.1483 S13: 0.4057 REMARK 3 S21: 0.1234 S22: 0.1185 S23: -0.4398 REMARK 3 S31: -0.2791 S32: 0.2314 S33: -0.1602 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 247 THROUGH 429 ) REMARK 3 ORIGIN FOR THE GROUP (A): 96.7373 65.2971 99.9222 REMARK 3 T TENSOR REMARK 3 T11: 0.3137 T22: 0.3094 REMARK 3 T33: 0.2082 T12: 0.0787 REMARK 3 T13: 0.0579 T23: -0.0081 REMARK 3 L TENSOR REMARK 3 L11: 2.8745 L22: 2.1065 REMARK 3 L33: 2.8790 L12: 0.0710 REMARK 3 L13: 0.2712 L23: -0.7360 REMARK 3 S TENSOR REMARK 3 S11: -0.0612 S12: -0.3540 S13: 0.0488 REMARK 3 S21: 0.2357 S22: 0.0000 S23: 0.0591 REMARK 3 S31: -0.2228 S32: -0.2409 S33: 0.0650 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 160 THROUGH 247) REMARK 3 ORIGIN FOR THE GROUP (A): 84.6450 56.6657 67.8975 REMARK 3 T TENSOR REMARK 3 T11: 0.2384 T22: 0.2399 REMARK 3 T33: 0.2327 T12: 0.0653 REMARK 3 T13: 0.0248 T23: 0.0253 REMARK 3 L TENSOR REMARK 3 L11: 3.1310 L22: 2.5733 REMARK 3 L33: 4.6055 L12: 0.3796 REMARK 3 L13: 1.7728 L23: 1.0212 REMARK 3 S TENSOR REMARK 3 S11: 0.0632 S12: 0.0678 S13: -0.3545 REMARK 3 S21: 0.0831 S22: -0.0001 S23: -0.0063 REMARK 3 S31: 0.3408 S32: 0.1564 S33: -0.0640 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 8B1N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-SEP-22. REMARK 100 THE DEPOSITION ID IS D_1292125149. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-APR-22 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 : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 75191 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 49.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.810 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.6800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.12 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.4 REMARK 200 DATA REDUNDANCY IN SHELL : 8.69 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.430 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: 5WYR, 3DCM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SAMPLE: 5.7 MG/ML TRMD-TM1570 REMARK 280 IN 50 MM HEPES BUFFER PH 7.4, 300 MM NACL, 5% GLYCEROL, WITH REMARK 280 ADDITION OF 3 MM SAM, 0.1% DDM AND 3000X DILUTED SEEDS STOCK. REMARK 280 RESERVOIR SOLUTION: 0.2 M MGCL2, 0.1 M TRIS PH 7.0, 10% PEG REMARK 280 8000., VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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+1/2,Y+1/2,-Z 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 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 48.39000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 99.78000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 48.39000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 99.78000 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 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 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 A 985 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 ASP A 431 REMARK 465 ILE A 432 REMARK 465 LEU A 433 REMARK 465 GLY B -2 REMARK 465 PRO B -1 REMARK 465 GLY B 242 REMARK 465 VAL B 243 REMARK 465 GLN B 244 REMARK 465 ARG B 245 REMARK 465 LYS B 246 REMARK 465 GLY B 313 REMARK 465 TYR B 314 REMARK 465 GLY B 315 REMARK 465 ALA B 316 REMARK 465 THR B 317 REMARK 465 TYR B 318 REMARK 465 ASN B 319 REMARK 465 GLU B 320 REMARK 465 ASN B 321 REMARK 465 ARG B 322 REMARK 465 LYS B 323 REMARK 465 GLU B 324 REMARK 465 ALA B 325 REMARK 465 PHE B 326 REMARK 465 GLU B 327 REMARK 465 GLU B 430 REMARK 465 ASP B 431 REMARK 465 ILE B 432 REMARK 465 LEU B 433 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 ASP A 161 CG OD1 OD2 REMARK 470 GLN A 244 CG CD OE1 NE2 REMARK 470 ARG A 245 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 246 CG CD CE NZ REMARK 470 LYS A 261 CG CD CE NZ REMARK 470 GLU A 262 CG CD OE1 OE2 REMARK 470 LYS A 264 CG CD CE NZ REMARK 470 GLU A 301 CG CD OE1 OE2 REMARK 470 LYS A 312 CG CD CE NZ REMARK 470 LYS A 340 CG CD CE NZ REMARK 470 GLU A 344 CG CD OE1 OE2 REMARK 470 GLU A 430 CG CD OE1 OE2 REMARK 470 HIS B 0 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 25 CG CD CE NZ REMARK 470 GLU B 44 CG CD OE1 OE2 REMARK 470 LYS B 46 CG CD CE NZ REMARK 470 GLU B 162 CG CD OE1 OE2 REMARK 470 GLU B 167 CG CD OE1 OE2 REMARK 470 ARG B 230 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 241 CG CD NE CZ NH1 NH2 REMARK 470 TYR B 247 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ARG B 308 CG CD NE CZ NH1 NH2 REMARK 470 TRP B 310 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP B 310 CZ3 CH2 REMARK 470 LYS B 312 CG CD CE NZ REMARK 470 LYS B 340 CG CD CE NZ REMARK 470 LYS B 362 CG CD CE NZ REMARK 470 LYS B 370 CG CD CE NZ REMARK 470 GLN B 429 CG CD OE1 NE2 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 TYR A 42 50.46 -96.40 REMARK 500 GLU A 44 43.23 -143.57 REMARK 500 TYR A 114 -135.14 57.63 REMARK 500 ASN A 163 107.76 -174.40 REMARK 500 PHE A 170 -48.98 71.39 REMARK 500 ASN A 409 32.67 -143.87 REMARK 500 TYR B 42 40.65 -107.25 REMARK 500 TYR B 114 -134.29 59.49 REMARK 500 ASN B 163 109.45 -171.51 REMARK 500 PHE B 170 -42.00 71.61 REMARK 500 THR B 240 56.94 -113.14 REMARK 500 THR B 356 149.60 -170.39 REMARK 500 ASN B 409 33.36 -145.62 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 A 957 DISTANCE = 6.26 ANGSTROMS 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 MG B 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 115 OE1 REMARK 620 2 GLU B 167 O 160.8 REMARK 620 3 GLU B 168 OE1 91.9 89.8 REMARK 620 4 GLU B 176 OE2 113.3 85.4 97.2 REMARK 620 5 HOH B 603 O 87.2 73.6 94.7 155.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 501 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 167 O REMARK 620 2 GLU A 168 OE1 89.9 REMARK 620 3 GLU A 176 OE2 86.2 94.6 REMARK 620 4 HOH A 739 O 79.6 168.6 80.5 REMARK 620 5 GLU B 115 OE1 161.5 92.3 111.9 99.1 REMARK 620 6 HOH B 611 O 70.2 103.8 149.8 76.8 91.4 REMARK 620 N 1 2 3 4 5 DBREF 8B1N A 1 433 UNP E4THH1 E4THH1_CALNY 1 433 DBREF 8B1N B 1 433 UNP E4THH1 E4THH1_CALNY 1 433 SEQADV 8B1N GLY A -2 UNP E4THH1 EXPRESSION TAG SEQADV 8B1N PRO A -1 UNP E4THH1 EXPRESSION TAG SEQADV 8B1N HIS A 0 UNP E4THH1 EXPRESSION TAG SEQADV 8B1N GLY B -2 UNP E4THH1 EXPRESSION TAG SEQADV 8B1N PRO B -1 UNP E4THH1 EXPRESSION TAG SEQADV 8B1N HIS B 0 UNP E4THH1 EXPRESSION TAG SEQRES 1 A 436 GLY PRO HIS MET LYS ARG TYR ASN VAL ILE THR ILE PHE SEQRES 2 A 436 PRO GLU MET ILE ASN GLU ILE PHE LYS TYR GLY VAL LEU SEQRES 3 A 436 SER LYS GLY ILE ASP ILE GLY LEU PHE ARG VAL ASN PRO SEQRES 4 A 436 ILE ASN LEU ARG ASP TYR THR GLU ASP LYS HIS LYS THR SEQRES 5 A 436 VAL ASP ASP TYR GLN TYR GLY GLY GLY HIS GLY LEU VAL SEQRES 6 A 436 MET LYS PRO GLU PRO ILE TYR LYS ALA ILE ALA ASP LEU SEQRES 7 A 436 LYS SER LYS LYS ASP THR HIS VAL VAL PHE LEU ASP PRO SEQRES 8 A 436 ARG GLY GLU GLN PHE THR GLN LYS THR ALA GLU ARG LEU SEQRES 9 A 436 TYR ASN TYR ASP ASP ILE THR PHE VAL CYS GLY ARG TYR SEQRES 10 A 436 GLU GLY ILE ASP ASP ARG VAL ARG GLU LEU MET ALA ASP SEQRES 11 A 436 GLU MET ILE SER ILE GLY ASP PHE VAL ILE THR GLY GLY SEQRES 12 A 436 GLU LEU ALA ALA VAL THR ILE ILE ASP ALA VAL ALA ARG SEQRES 13 A 436 LEU ILE PRO GLY VAL LEU GLY ASP GLU ASN SER PRO ASN SEQRES 14 A 436 GLU GLU SER PHE THR THR GLY LEU LEU GLU TYR PRO HIS SEQRES 15 A 436 PHE THR ARG PRO ALA GLU PHE MET GLY LYS LYS VAL PRO SEQRES 16 A 436 GLU VAL LEU ILE SER GLY ASN HIS GLU GLU ILE ARG ARG SEQRES 17 A 436 TRP ARG LEU THR GLU SER ILE LYS THR THR LEU GLN ASN SEQRES 18 A 436 ARG PRO ASP MET ILE LEU ARG LYS SER LEU SER ARG GLU SEQRES 19 A 436 GLU GLU GLN ILE LEU TRP SER LEU THR ARG GLY VAL GLN SEQRES 20 A 436 ARG LYS TYR ASN ILE TYR VAL ALA LEU MET HIS TYR PRO SEQRES 21 A 436 MET ARG ASP LYS GLU GLY LYS VAL VAL THR THR SER ILE SEQRES 22 A 436 THR ASN MET ASP LEU HIS ASP ILE SER ARG SER CYS ARG SEQRES 23 A 436 THR PHE GLY VAL LYS ASN TYR PHE VAL VAL ASN PRO MET SEQRES 24 A 436 PRO ALA GLN ARG GLU ILE ALA SER ARG VAL VAL ARG HIS SEQRES 25 A 436 TRP ILE LYS GLY TYR GLY ALA THR TYR ASN GLU ASN ARG SEQRES 26 A 436 LYS GLU ALA PHE GLU TYR THR ILE ILE THR ASP SER LEU SEQRES 27 A 436 ALA SER VAL ILE LYS SER ILE GLU GLU LYS GLU SER GLY SEQRES 28 A 436 SER PRO ILE ILE ILE ALA THR THR ALA ARG TYR GLN GLN SEQRES 29 A 436 LYS ALA ILE SER ILE GLU LYS LEU LYS GLU ILE ALA ASP SEQRES 30 A 436 ARG PRO ILE LEU LEU LEU PHE GLY THR GLY TRP GLY PHE SEQRES 31 A 436 VAL ASP ASP ILE LEU GLU PHE ALA ASP TYR VAL LEU LYS SEQRES 32 A 436 PRO ILE HIS GLY VAL GLY ASP PHE ASN HIS LEU SER VAL SEQRES 33 A 436 ARG SER ALA VAL ALA ILE TYR LEU ASP ARG ILE ASN ARG SEQRES 34 A 436 SER PHE GLN GLU ASP ILE LEU SEQRES 1 B 436 GLY PRO HIS MET LYS ARG TYR ASN VAL ILE THR ILE PHE SEQRES 2 B 436 PRO GLU MET ILE ASN GLU ILE PHE LYS TYR GLY VAL LEU SEQRES 3 B 436 SER LYS GLY ILE ASP ILE GLY LEU PHE ARG VAL ASN PRO SEQRES 4 B 436 ILE ASN LEU ARG ASP TYR THR GLU ASP LYS HIS LYS THR SEQRES 5 B 436 VAL ASP ASP TYR GLN TYR GLY GLY GLY HIS GLY LEU VAL SEQRES 6 B 436 MET LYS PRO GLU PRO ILE TYR LYS ALA ILE ALA ASP LEU SEQRES 7 B 436 LYS SER LYS LYS ASP THR HIS VAL VAL PHE LEU ASP PRO SEQRES 8 B 436 ARG GLY GLU GLN PHE THR GLN LYS THR ALA GLU ARG LEU SEQRES 9 B 436 TYR ASN TYR ASP ASP ILE THR PHE VAL CYS GLY ARG TYR SEQRES 10 B 436 GLU GLY ILE ASP ASP ARG VAL ARG GLU LEU MET ALA ASP SEQRES 11 B 436 GLU MET ILE SER ILE GLY ASP PHE VAL ILE THR GLY GLY SEQRES 12 B 436 GLU LEU ALA ALA VAL THR ILE ILE ASP ALA VAL ALA ARG SEQRES 13 B 436 LEU ILE PRO GLY VAL LEU GLY ASP GLU ASN SER PRO ASN SEQRES 14 B 436 GLU GLU SER PHE THR THR GLY LEU LEU GLU TYR PRO HIS SEQRES 15 B 436 PHE THR ARG PRO ALA GLU PHE MET GLY LYS LYS VAL PRO SEQRES 16 B 436 GLU VAL LEU ILE SER GLY ASN HIS GLU GLU ILE ARG ARG SEQRES 17 B 436 TRP ARG LEU THR GLU SER ILE LYS THR THR LEU GLN ASN SEQRES 18 B 436 ARG PRO ASP MET ILE LEU ARG LYS SER LEU SER ARG GLU SEQRES 19 B 436 GLU GLU GLN ILE LEU TRP SER LEU THR ARG GLY VAL GLN SEQRES 20 B 436 ARG LYS TYR ASN ILE TYR VAL ALA LEU MET HIS TYR PRO SEQRES 21 B 436 MET ARG ASP LYS GLU GLY LYS VAL VAL THR THR SER ILE SEQRES 22 B 436 THR ASN MET ASP LEU HIS ASP ILE SER ARG SER CYS ARG SEQRES 23 B 436 THR PHE GLY VAL LYS ASN TYR PHE VAL VAL ASN PRO MET SEQRES 24 B 436 PRO ALA GLN ARG GLU ILE ALA SER ARG VAL VAL ARG HIS SEQRES 25 B 436 TRP ILE LYS GLY TYR GLY ALA THR TYR ASN GLU ASN ARG SEQRES 26 B 436 LYS GLU ALA PHE GLU TYR THR ILE ILE THR ASP SER LEU SEQRES 27 B 436 ALA SER VAL ILE LYS SER ILE GLU GLU LYS GLU SER GLY SEQRES 28 B 436 SER PRO ILE ILE ILE ALA THR THR ALA ARG TYR GLN GLN SEQRES 29 B 436 LYS ALA ILE SER ILE GLU LYS LEU LYS GLU ILE ALA ASP SEQRES 30 B 436 ARG PRO ILE LEU LEU LEU PHE GLY THR GLY TRP GLY PHE SEQRES 31 B 436 VAL ASP ASP ILE LEU GLU PHE ALA ASP TYR VAL LEU LYS SEQRES 32 B 436 PRO ILE HIS GLY VAL GLY ASP PHE ASN HIS LEU SER VAL SEQRES 33 B 436 ARG SER ALA VAL ALA ILE TYR LEU ASP ARG ILE ASN ARG SEQRES 34 B 436 SER PHE GLN GLU ASP ILE LEU HET MG A 501 1 HET CL A 502 1 HET CL A 503 1 HET SAM A 504 54 HET SAM A 505 27 HET GOL A 506 6 HET GOL A 507 6 HET GOL A 508 6 HET GOL A 509 6 HET GOL A 510 6 HET GOL A 511 6 HET MG B 501 1 HET CL B 502 1 HET CL B 503 1 HET SAM B 504 27 HET SAM B 505 54 HET GOL B 506 6 HET GOL B 507 6 HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM SAM S-ADENOSYLMETHIONINE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 MG 2(MG 2+) FORMUL 4 CL 4(CL 1-) FORMUL 6 SAM 4(C15 H22 N6 O5 S) FORMUL 8 GOL 8(C3 H8 O3) FORMUL 21 HOH *665(H2 O) HELIX 1 AA1 PHE A 10 PHE A 18 1 9 HELIX 2 AA2 TYR A 20 ILE A 29 1 10 HELIX 3 AA3 ARG A 40 THR A 43 5 4 HELIX 4 AA4 LYS A 64 LYS A 79 1 16 HELIX 5 AA5 THR A 94 ASN A 103 1 10 HELIX 6 AA6 ASP A 118 ALA A 126 1 9 HELIX 7 AA7 GLY A 140 ARG A 153 1 14 HELIX 8 AA8 PRO A 192 GLY A 198 1 7 HELIX 9 AA9 ASN A 199 ARG A 219 1 21 HELIX 10 AB1 ARG A 219 LYS A 226 1 8 HELIX 11 AB2 SER A 229 ARG A 241 1 13 HELIX 12 AB3 THR A 271 PHE A 285 1 15 HELIX 13 AB4 MET A 296 LYS A 312 1 17 HELIX 14 AB5 TYR A 314 ASN A 319 1 6 HELIX 15 AB6 ASN A 319 GLU A 327 1 9 HELIX 16 AB7 SER A 334 SER A 347 1 14 HELIX 17 AB8 ILE A 366 ILE A 372 1 7 HELIX 18 AB9 VAL A 388 ALA A 395 1 8 HELIX 19 AC1 SER A 412 GLU A 430 1 19 HELIX 20 AC2 PHE B 10 PHE B 18 1 9 HELIX 21 AC3 TYR B 20 ILE B 29 1 10 HELIX 22 AC4 ARG B 40 THR B 43 5 4 HELIX 23 AC5 LYS B 64 SER B 77 1 14 HELIX 24 AC6 THR B 94 ASN B 103 1 10 HELIX 25 AC7 ASP B 118 ALA B 126 1 9 HELIX 26 AC8 GLY B 140 ARG B 153 1 14 HELIX 27 AC9 PRO B 192 GLY B 198 1 7 HELIX 28 AD1 ASN B 199 ARG B 219 1 21 HELIX 29 AD2 ARG B 219 LYS B 226 1 8 HELIX 30 AD3 SER B 229 THR B 240 1 12 HELIX 31 AD4 THR B 271 PHE B 285 1 15 HELIX 32 AD5 MET B 296 LYS B 312 1 17 HELIX 33 AD6 SER B 334 SER B 347 1 14 HELIX 34 AD7 SER B 365 ALA B 373 1 9 HELIX 35 AD8 VAL B 388 ALA B 395 1 8 HELIX 36 AD9 SER B 412 GLN B 429 1 18 SHEET 1 AA1 6 PHE A 32 ASN A 38 0 SHEET 2 AA1 6 LYS A 2 THR A 8 1 N VAL A 6 O ILE A 37 SHEET 3 AA1 6 ASP A 106 VAL A 110 1 O PHE A 109 N ASN A 5 SHEET 4 AA1 6 HIS A 82 LEU A 86 1 N VAL A 84 O THR A 108 SHEET 5 AA1 6 GLU A 128 SER A 131 1 O GLU A 128 N PHE A 85 SHEET 6 AA1 6 GLU A 91 GLN A 92 1 N GLU A 91 O SER A 131 SHEET 1 AA2 2 ASP A 51 TYR A 53 0 SHEET 2 AA2 2 LEU A 61 MET A 63 -1 O VAL A 62 N ASP A 52 SHEET 1 AA3 2 GLU A 185 PHE A 186 0 SHEET 2 AA3 2 LYS A 189 LYS A 190 -1 O LYS A 189 N PHE A 186 SHEET 1 AA4 6 THR A 329 THR A 332 0 SHEET 2 AA4 6 ASN A 289 VAL A 293 1 N VAL A 292 O ILE A 330 SHEET 3 AA4 6 ILE A 249 MET A 254 1 N VAL A 251 O PHE A 291 SHEET 4 AA4 6 ILE A 377 PHE A 381 1 O LEU A 379 N TYR A 250 SHEET 5 AA4 6 ILE A 351 ALA A 354 1 N ILE A 353 O LEU A 380 SHEET 6 AA4 6 TYR A 397 VAL A 398 1 O TYR A 397 N ALA A 354 SHEET 1 AA5 2 MET A 258 ARG A 259 0 SHEET 2 AA5 2 VAL A 265 VAL A 266 -1 O VAL A 266 N MET A 258 SHEET 1 AA6 6 PHE B 32 ASN B 38 0 SHEET 2 AA6 6 LYS B 2 THR B 8 1 N VAL B 6 O ILE B 37 SHEET 3 AA6 6 ASP B 106 VAL B 110 1 O PHE B 109 N ASN B 5 SHEET 4 AA6 6 HIS B 82 LEU B 86 1 N VAL B 84 O THR B 108 SHEET 5 AA6 6 GLU B 128 SER B 131 1 O GLU B 128 N PHE B 85 SHEET 6 AA6 6 GLU B 91 GLN B 92 1 N GLU B 91 O SER B 131 SHEET 1 AA7 2 ASP B 51 TYR B 53 0 SHEET 2 AA7 2 LEU B 61 MET B 63 -1 O VAL B 62 N ASP B 52 SHEET 1 AA8 2 GLU B 185 PHE B 186 0 SHEET 2 AA8 2 LYS B 189 LYS B 190 -1 O LYS B 189 N PHE B 186 SHEET 1 AA9 6 THR B 329 THR B 332 0 SHEET 2 AA9 6 ASN B 289 VAL B 293 1 N VAL B 292 O ILE B 330 SHEET 3 AA9 6 ILE B 249 MET B 254 1 N VAL B 251 O PHE B 291 SHEET 4 AA9 6 ILE B 377 PHE B 381 1 O PHE B 381 N MET B 254 SHEET 5 AA9 6 ILE B 351 ALA B 354 1 N ILE B 353 O LEU B 380 SHEET 6 AA9 6 TYR B 397 VAL B 398 1 O TYR B 397 N ALA B 354 SHEET 1 AB1 2 MET B 258 ARG B 259 0 SHEET 2 AB1 2 VAL B 265 VAL B 266 -1 O VAL B 266 N MET B 258 LINK OE1 GLU A 115 MG MG B 501 1555 1555 2.77 LINK O GLU A 167 MG MG A 501 1555 1555 2.31 LINK OE1 GLU A 168 MG MG A 501 1555 1555 2.04 LINK OE2 GLU A 176 MG MG A 501 1555 1555 2.19 LINK MG MG A 501 O HOH A 739 1555 1555 2.27 LINK MG MG A 501 OE1 GLU B 115 1555 1555 2.75 LINK MG MG A 501 O HOH B 611 1555 1555 2.26 LINK O GLU B 167 MG MG B 501 1555 1555 2.30 LINK OE1 GLU B 168 MG MG B 501 1555 1555 2.07 LINK OE2 GLU B 176 MG MG B 501 1555 1555 2.24 LINK MG MG B 501 O HOH B 603 1555 1555 2.26 CISPEP 1 ARG A 182 PRO A 183 0 6.07 CISPEP 2 TYR A 256 PRO A 257 0 -9.73 CISPEP 3 ARG B 182 PRO B 183 0 5.82 CISPEP 4 TYR B 256 PRO B 257 0 -6.33 CRYST1 96.780 199.560 56.700 90.00 90.00 90.00 P 21 21 2 8 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 0.010333 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005011 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017637 0.00000