HEADER RNA BINDING PROTEIN 24-NOV-22 8BS4 TITLE CRYSTAL STRUCTURE OF YTHDF1 YTH DOMAIN DIMER COMPND MOL_ID: 1; COMPND 2 MOLECULE: YTH DOMAIN-CONTAINING FAMILY PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DF1,DERMATOMYOSITIS ASSOCIATED WITH CANCER PUTATIVE COMPND 5 AUTOANTIGEN 1,DACA-1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: YTHDF1, C20ORF21; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS YTHDF1, DIMER, YTH, M6A, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.K.BEDI,A.CAFLISCH REVDAT 1 13-DEC-23 8BS4 0 JRNL AUTH R.K.BEDI,A.CAFLISCH JRNL TITL CRYSTAL STRUCTURE OF YTHDF1 YTH DOMAIN DIMER JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.83 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 30899 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.216 REMARK 3 R VALUE (WORKING SET) : 0.215 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1546 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 44.8300 - 4.6700 1.00 2931 154 0.2073 0.2269 REMARK 3 2 4.6700 - 3.7100 1.00 2744 144 0.1716 0.1969 REMARK 3 3 3.7000 - 3.2400 1.00 2698 143 0.2014 0.2198 REMARK 3 4 3.2400 - 2.9400 1.00 2663 140 0.2209 0.2963 REMARK 3 5 2.9400 - 2.7300 1.00 2658 140 0.2424 0.2741 REMARK 3 6 2.7300 - 2.5700 1.00 2632 138 0.2614 0.3400 REMARK 3 7 2.5700 - 2.4400 1.00 2629 139 0.2532 0.3031 REMARK 3 8 2.4400 - 2.3300 1.00 2618 137 0.2739 0.3199 REMARK 3 9 2.3300 - 2.2400 1.00 2601 138 0.2824 0.3344 REMARK 3 10 2.2400 - 2.1700 1.00 2627 138 0.3036 0.3511 REMARK 3 11 2.1700 - 2.1000 0.98 2552 135 0.3220 0.3762 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.291 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.030 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.85 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 55.42 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 : 0.008 3144 REMARK 3 ANGLE : 0.806 4270 REMARK 3 CHIRALITY : 0.053 453 REMARK 3 PLANARITY : 0.008 559 REMARK 3 DIHEDRAL : 5.715 425 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 8BS4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1292126981. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-DEC-20 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 : SLS REMARK 200 BEAMLINE : X06DA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 31056 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 45.926 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 16.13 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.7700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 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 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.55 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 M AMMONIUM CITRATE, 100 MM SODIUM REMARK 280 ACETATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 137.92667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 68.96333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 103.44500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 34.48167 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 172.40833 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 137.92667 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 68.96333 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 34.48167 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 103.44500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 172.40833 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: 3390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 4.0 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 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 B 781 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 MET A 347 REMARK 465 HIS A 348 REMARK 465 HIS A 349 REMARK 465 HIS A 350 REMARK 465 HIS A 351 REMARK 465 HIS A 352 REMARK 465 HIS A 353 REMARK 465 SER A 354 REMARK 465 SER A 355 REMARK 465 GLY A 356 REMARK 465 ARG A 357 REMARK 465 GLU A 358 REMARK 465 ASN A 359 REMARK 465 LEU A 360 REMARK 465 TYR A 361 REMARK 465 PHE A 362 REMARK 465 GLN A 363 REMARK 465 GLY A 364 REMARK 465 MET B 347 REMARK 465 HIS B 348 REMARK 465 HIS B 349 REMARK 465 HIS B 350 REMARK 465 HIS B 351 REMARK 465 HIS B 352 REMARK 465 HIS B 353 REMARK 465 SER B 354 REMARK 465 SER B 355 REMARK 465 GLY B 356 REMARK 465 ARG B 357 REMARK 465 GLU B 358 REMARK 465 ASN B 359 REMARK 465 LEU B 360 REMARK 465 TYR B 361 REMARK 465 PHE B 362 REMARK 465 GLN B 363 REMARK 465 SER B 461 REMARK 465 ALA B 462 REMARK 465 GLN B 559 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 A 369 CG CD OE1 OE2 REMARK 470 LYS A 370 CG CD CE NZ REMARK 470 SER A 376 OG REMARK 470 LYS A 380 CG CD CE NZ REMARK 470 GLU A 381 CG CD OE1 OE2 REMARK 470 GLU A 383 CG CD OE1 OE2 REMARK 470 LYS A 387 CG CD CE NZ REMARK 470 GLU A 415 CD OE1 OE2 REMARK 470 LYS A 419 CE NZ REMARK 470 SER A 429 OG REMARK 470 SER A 430 OG REMARK 470 LYS A 431 CG CD CE NZ REMARK 470 THR A 460 OG1 CG2 REMARK 470 SER A 461 OG REMARK 470 LYS A 471 CD CE NZ REMARK 470 LYS A 473 CG CD CE NZ REMARK 470 ARG A 490 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 506 NE CZ NH1 NH2 REMARK 470 LYS A 517 CG CD CE NZ REMARK 470 LYS A 521 CG CD CE NZ REMARK 470 SER A 524 OG REMARK 470 LYS A 527 CG CD CE NZ REMARK 470 LYS A 541 CG CD CE NZ REMARK 470 LYS A 551 CG CD CE NZ REMARK 470 GLN A 554 CG CD OE1 NE2 REMARK 470 LYS A 558 CG CD CE NZ REMARK 470 GLN A 559 CG CD OE1 NE2 REMARK 470 GLU B 369 CG CD OE1 OE2 REMARK 470 LYS B 380 CG CD CE NZ REMARK 470 GLU B 381 CG CD OE1 OE2 REMARK 470 GLU B 383 CG CD OE1 OE2 REMARK 470 ASN B 385 CG OD1 ND2 REMARK 470 LYS B 387 CG CD CE NZ REMARK 470 LYS B 419 CG CD CE NZ REMARK 470 SER B 429 OG REMARK 470 SER B 430 OG REMARK 470 LYS B 431 CG CD CE NZ REMARK 470 GLN B 467 CG CD OE1 NE2 REMARK 470 LYS B 469 CG CD CE NZ REMARK 470 LYS B 471 CG CD CE NZ REMARK 470 LYS B 473 CE NZ REMARK 470 ARG B 506 NE CZ NH1 NH2 REMARK 470 LYS B 521 CD CE NZ REMARK 470 LYS B 527 CG CD CE NZ REMARK 470 LYS B 541 CD CE NZ REMARK 470 LYS B 551 CG CD CE NZ REMARK 470 SER B 555 OG REMARK 470 LYS B 558 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O HOH B 772 O HOH B 782 1.97 REMARK 500 OD1 ASN A 557 O HOH A 701 2.14 REMARK 500 NZ LYS A 469 O HOH A 702 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 764 O HOH B 765 6554 2.15 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 MET A 428 31.78 -81.30 REMARK 500 SER A 429 76.39 -48.84 REMARK 500 SER A 430 -8.75 72.14 REMARK 500 SER B 376 64.97 -112.76 REMARK 500 LYS B 471 56.20 -90.72 REMARK 500 ILE B 479 -52.97 -121.17 REMARK 500 LYS B 482 141.43 -175.29 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 B 790 DISTANCE = 10.51 ANGSTROMS DBREF 8BS4 A 365 559 UNP Q9BYJ9 YTHD1_HUMAN 365 559 DBREF 8BS4 B 365 559 UNP Q9BYJ9 YTHD1_HUMAN 365 559 SEQADV 8BS4 MET A 347 UNP Q9BYJ9 INITIATING METHIONINE SEQADV 8BS4 HIS A 348 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 HIS A 349 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 HIS A 350 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 HIS A 351 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 HIS A 352 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 HIS A 353 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 SER A 354 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 SER A 355 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 GLY A 356 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 ARG A 357 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 GLU A 358 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 ASN A 359 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 LEU A 360 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 TYR A 361 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 PHE A 362 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 GLN A 363 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 GLY A 364 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 MET B 347 UNP Q9BYJ9 INITIATING METHIONINE SEQADV 8BS4 HIS B 348 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 HIS B 349 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 HIS B 350 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 HIS B 351 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 HIS B 352 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 HIS B 353 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 SER B 354 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 SER B 355 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 GLY B 356 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 ARG B 357 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 GLU B 358 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 ASN B 359 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 LEU B 360 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 TYR B 361 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 PHE B 362 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 GLN B 363 UNP Q9BYJ9 EXPRESSION TAG SEQADV 8BS4 GLY B 364 UNP Q9BYJ9 EXPRESSION TAG SEQRES 1 A 213 MET HIS HIS HIS HIS HIS HIS SER SER GLY ARG GLU ASN SEQRES 2 A 213 LEU TYR PHE GLN GLY HIS PRO VAL LEU GLU LYS LEU LYS SEQRES 3 A 213 ALA ALA HIS SER TYR ASN PRO LYS GLU PHE GLU TRP ASN SEQRES 4 A 213 LEU LYS SER GLY ARG VAL PHE ILE ILE LYS SER TYR SER SEQRES 5 A 213 GLU ASP ASP ILE HIS ARG SER ILE LYS TYR SER ILE TRP SEQRES 6 A 213 CYS SER THR GLU HIS GLY ASN LYS ARG LEU ASP SER ALA SEQRES 7 A 213 PHE ARG CYS MET SER SER LYS GLY PRO VAL TYR LEU LEU SEQRES 8 A 213 PHE SER VAL ASN GLY SER GLY HIS PHE CYS GLY VAL ALA SEQRES 9 A 213 GLU MET LYS SER PRO VAL ASP TYR GLY THR SER ALA GLY SEQRES 10 A 213 VAL TRP SER GLN ASP LYS TRP LYS GLY LYS PHE ASP VAL SEQRES 11 A 213 GLN TRP ILE PHE VAL LYS ASP VAL PRO ASN ASN GLN LEU SEQRES 12 A 213 ARG HIS ILE ARG LEU GLU ASN ASN ASP ASN LYS PRO VAL SEQRES 13 A 213 THR ASN SER ARG ASP THR GLN GLU VAL PRO LEU GLU LYS SEQRES 14 A 213 ALA LYS GLN VAL LEU LYS ILE ILE SER SER TYR LYS HIS SEQRES 15 A 213 THR THR SER ILE PHE ASP ASP PHE ALA HIS TYR GLU LYS SEQRES 16 A 213 ARG GLN GLU GLU GLU GLU VAL VAL ARG LYS GLU ARG GLN SEQRES 17 A 213 SER ARG ASN LYS GLN SEQRES 1 B 213 MET HIS HIS HIS HIS HIS HIS SER SER GLY ARG GLU ASN SEQRES 2 B 213 LEU TYR PHE GLN GLY HIS PRO VAL LEU GLU LYS LEU LYS SEQRES 3 B 213 ALA ALA HIS SER TYR ASN PRO LYS GLU PHE GLU TRP ASN SEQRES 4 B 213 LEU LYS SER GLY ARG VAL PHE ILE ILE LYS SER TYR SER SEQRES 5 B 213 GLU ASP ASP ILE HIS ARG SER ILE LYS TYR SER ILE TRP SEQRES 6 B 213 CYS SER THR GLU HIS GLY ASN LYS ARG LEU ASP SER ALA SEQRES 7 B 213 PHE ARG CYS MET SER SER LYS GLY PRO VAL TYR LEU LEU SEQRES 8 B 213 PHE SER VAL ASN GLY SER GLY HIS PHE CYS GLY VAL ALA SEQRES 9 B 213 GLU MET LYS SER PRO VAL ASP TYR GLY THR SER ALA GLY SEQRES 10 B 213 VAL TRP SER GLN ASP LYS TRP LYS GLY LYS PHE ASP VAL SEQRES 11 B 213 GLN TRP ILE PHE VAL LYS ASP VAL PRO ASN ASN GLN LEU SEQRES 12 B 213 ARG HIS ILE ARG LEU GLU ASN ASN ASP ASN LYS PRO VAL SEQRES 13 B 213 THR ASN SER ARG ASP THR GLN GLU VAL PRO LEU GLU LYS SEQRES 14 B 213 ALA LYS GLN VAL LEU LYS ILE ILE SER SER TYR LYS HIS SEQRES 15 B 213 THR THR SER ILE PHE ASP ASP PHE ALA HIS TYR GLU LYS SEQRES 16 B 213 ARG GLN GLU GLU GLU GLU VAL VAL ARG LYS GLU ARG GLN SEQRES 17 B 213 SER ARG ASN LYS GLN HET ACT A 601 4 HET GOL B 601 6 HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 ACT C2 H3 O2 1- FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *167(H2 O) HELIX 1 AA1 HIS A 365 HIS A 375 1 11 HELIX 2 AA2 SER A 398 SER A 409 1 12 HELIX 3 AA3 THR A 414 MET A 428 1 15 HELIX 4 AA4 GLY A 459 GLN A 467 5 9 HELIX 5 AA5 ASN A 487 LEU A 489 5 3 HELIX 6 AA6 PRO A 501 SER A 505 5 5 HELIX 7 AA7 PRO A 512 TYR A 526 1 15 HELIX 8 AA8 SER A 531 ASP A 534 5 4 HELIX 9 AA9 ASP A 535 ASN A 557 1 23 HELIX 10 AB1 HIS B 365 HIS B 375 1 11 HELIX 11 AB2 SER B 398 SER B 409 1 12 HELIX 12 AB3 THR B 414 MET B 428 1 15 HELIX 13 AB4 ASN B 487 LEU B 489 5 3 HELIX 14 AB5 LEU B 494 ASP B 498 5 5 HELIX 15 AB6 PRO B 501 SER B 505 5 5 HELIX 16 AB7 PRO B 512 TYR B 526 1 15 HELIX 17 AB8 SER B 531 ASP B 534 5 4 HELIX 18 AB9 ASP B 535 LYS B 558 1 24 SHEET 1 AA1 6 ILE A 410 TRP A 411 0 SHEET 2 AA1 6 PHE A 474 PRO A 485 -1 O PHE A 474 N TRP A 411 SHEET 3 AA1 6 HIS A 445 MET A 452 -1 N VAL A 449 O ILE A 479 SHEET 4 AA1 6 VAL A 434 VAL A 440 -1 N LEU A 436 O ALA A 450 SHEET 5 AA1 6 ARG A 390 SER A 396 1 N ILE A 394 O LEU A 437 SHEET 6 AA1 6 GLU A 510 VAL A 511 -1 O VAL A 511 N VAL A 391 SHEET 1 AA2 6 ILE B 410 TRP B 411 0 SHEET 2 AA2 6 PHE B 474 PRO B 485 -1 O PHE B 474 N TRP B 411 SHEET 3 AA2 6 HIS B 445 MET B 452 -1 N VAL B 449 O ILE B 479 SHEET 4 AA2 6 VAL B 434 VAL B 440 -1 N VAL B 434 O MET B 452 SHEET 5 AA2 6 ARG B 390 SER B 396 1 N ILE B 394 O LEU B 437 SHEET 6 AA2 6 GLU B 510 VAL B 511 -1 O VAL B 511 N VAL B 391 CRYST1 91.850 91.850 206.890 90.00 90.00 120.00 P 65 2 2 24 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 0.010887 0.006286 0.000000 0.00000 SCALE2 0.000000 0.012572 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004833 0.00000