HEADER RNA BINDING PROTEIN 15-OCT-24 9H35 TITLE CRYSTAL STRUCTURE OF THE YTHDC2 YTH DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3'-5' RNA HELICASE YTHDC2; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: YTH DOMAIN-CONTAINING PROTEIN 2,HYTHDC2; COMPND 5 EC: 3.6.4.13; 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: YTHDC2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS YTHDC1, INHIBITOR, COMPLEX, READER, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.K.BEDI,A.CAFLISCH REVDAT 1 30-OCT-24 9H35 0 JRNL AUTH R.K.BEDI,A.CAFLISCH JRNL TITL CRYSTAL STRUCTURE OF THE YTHDC2 YTH DOMAIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.68 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.1_5286 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) : 2.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 23678 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 1137 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 48.7900 - 5.3600 1.00 3074 126 0.2014 0.2376 REMARK 3 2 5.3600 - 4.2500 1.00 2865 141 0.1807 0.2526 REMARK 3 3 4.2500 - 3.7200 1.00 2807 164 0.1971 0.2466 REMARK 3 4 3.7200 - 3.3800 1.00 2770 156 0.2504 0.3105 REMARK 3 5 3.3800 - 3.1300 1.00 2778 122 0.2867 0.3668 REMARK 3 6 3.1300 - 2.9500 1.00 2762 135 0.2871 0.3447 REMARK 3 7 2.9500 - 2.8000 1.00 2759 153 0.3537 0.4202 REMARK 3 8 2.8000 - 2.6800 1.00 2726 140 0.4854 0.5174 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) : 0.532 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.179 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 77.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 74.44 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 : 0.009 4240 REMARK 3 ANGLE : 0.986 5752 REMARK 3 CHIRALITY : 0.055 612 REMARK 3 PLANARITY : 0.007 742 REMARK 3 DIHEDRAL : 16.052 1472 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 9H35 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1292142500. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-FEB-24 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 : ESRF REMARK 200 BEAMLINE : ID30B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96863 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43492 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.680 REMARK 200 RESOLUTION RANGE LOW (A) : 48.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.71 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.86 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 (%): 59.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM AMMONIUM SULFATE, 5 MM BIS-TRIS REMARK 280 PH 6.5, 30 % PEG 600, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 68.61567 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 137.23133 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 102.92350 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 171.53917 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 34.30783 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 68.61567 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 137.23133 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 171.53917 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 102.92350 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 34.30783 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 A1521 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 1284 REMARK 465 LEU A 1423 REMARK 465 GLY A 1424 REMARK 465 GLY B 1284 REMARK 465 GLU B 1355 REMARK 465 LYS B 1356 REMARK 465 SER B 1357 REMARK 465 GLN B 1358 REMARK 465 ASP B 1359 REMARK 465 LEU B 1423 REMARK 465 GLY B 1424 REMARK 465 GLY C 1284 REMARK 465 GLU C 1355 REMARK 465 LYS C 1356 REMARK 465 SER C 1357 REMARK 465 GLN C 1358 REMARK 465 ASP C 1359 REMARK 465 TRP C 1360 REMARK 465 GLY C 1361 REMARK 465 SER C 1362 REMARK 465 GLY C 1424 REMARK 465 GLY D 1284 REMARK 465 LYS D 1356 REMARK 465 SER D 1357 REMARK 465 GLN D 1358 REMARK 465 GLY D 1424 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 A1302 CG CD OE1 OE2 REMARK 470 GLN A1337 CG CD OE1 NE2 REMARK 470 ARG A1354 CG CD NE CZ NH1 NH2 REMARK 470 GLU A1355 CG CD OE1 OE2 REMARK 470 GLN A1358 CG CD OE1 NE2 REMARK 470 SER A1362 OG REMARK 470 GLN A1382 CG CD OE1 NE2 REMARK 470 ARG A1401 CG CD NE CZ NH1 NH2 REMARK 470 ARG A1420 CG CD NE CZ NH1 NH2 REMARK 470 ASN B1285 CG OD1 ND2 REMARK 470 GLU B1302 CG CD OE1 OE2 REMARK 470 SER B1315 OG REMARK 470 ARG B1322 CG CD NE CZ NH1 NH2 REMARK 470 SER B1328 OG REMARK 470 ARG B1354 CG CD NE CZ NH1 NH2 REMARK 470 TRP B1360 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP B1360 CZ3 CH2 REMARK 470 SER B1362 OG REMARK 470 GLN B1382 CG CD OE1 NE2 REMARK 470 HIS B1385 CG ND1 CD2 CE1 NE2 REMARK 470 ARG B1401 CG CD NE CZ NH1 NH2 REMARK 470 GLU B1412 CG CD OE1 OE2 REMARK 470 ARG B1420 CG CD NE CZ NH1 NH2 REMARK 470 LYS C1294 CG CD CE NZ REMARK 470 LEU C1298 CG CD1 CD2 REMARK 470 ARG C1318 CG CD NE CZ NH1 NH2 REMARK 470 LYS C1319 CG CD CE NZ REMARK 470 ARG C1322 CG CD NE CZ NH1 NH2 REMARK 470 SER C1328 OG REMARK 470 ARG C1354 CG CD NE CZ NH1 NH2 REMARK 470 GLN C1382 CG CD OE1 NE2 REMARK 470 LYS C1395 CG CD CE NZ REMARK 470 LYS C1396 CG CD CE NZ REMARK 470 GLN C1398 CG CD OE1 NE2 REMARK 470 ILE C1399 CG1 CG2 CD1 REMARK 470 ARG C1401 CG CD NE CZ NH1 NH2 REMARK 470 LEU C1409 CG CD1 CD2 REMARK 470 GLU C1412 CG CD OE1 OE2 REMARK 470 GLN C1413 CG CD OE1 NE2 REMARK 470 GLN C1416 CG CD OE1 NE2 REMARK 470 GLU C1419 CG CD OE1 OE2 REMARK 470 ARG C1420 CG CD NE CZ NH1 NH2 REMARK 470 LEU C1423 CG CD1 CD2 REMARK 470 ASN D1285 CG OD1 ND2 REMARK 470 LYS D1294 CG CD CE NZ REMARK 470 SER D1315 OG REMARK 470 ARG D1318 CG CD NE CZ NH1 NH2 REMARK 470 ARG D1322 CG CD NE CZ NH1 NH2 REMARK 470 GLU D1326 CG CD OE1 OE2 REMARK 470 ARG D1354 CG CD NE CZ NH1 NH2 REMARK 470 GLU D1355 CG CD OE1 OE2 REMARK 470 ASP D1359 CG OD1 OD2 REMARK 470 TRP D1360 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP D1360 CZ3 CH2 REMARK 470 SER D1362 OG REMARK 470 LEU D1379 CG CD1 CD2 REMARK 470 GLN D1382 CG CD OE1 NE2 REMARK 470 HIS D1385 CG ND1 CD2 CE1 NE2 REMARK 470 HIS D1386 CG ND1 CD2 CE1 NE2 REMARK 470 LYS D1395 CG CD CE NZ REMARK 470 LYS D1396 CG CD CE NZ REMARK 470 GLN D1398 CG CD OE1 NE2 REMARK 470 ILE D1399 CG1 CG2 CD1 REMARK 470 ARG D1401 CG CD NE CZ NH1 NH2 REMARK 470 LEU D1409 CG CD1 CD2 REMARK 470 GLU D1412 CG CD OE1 OE2 REMARK 470 GLN D1416 CG CD OE1 NE2 REMARK 470 ARG D1420 CG CD NE CZ NH1 NH2 REMARK 470 LEU D1421 CG CD1 CD2 REMARK 470 LEU D1423 CG CD1 CD2 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 N GLY B 1367 O HOH B 1501 2.12 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 GLN A1343 50.46 -90.43 REMARK 500 ARG A1354 -127.02 -150.36 REMARK 500 GLU A1355 -84.04 67.39 REMARK 500 SER A1357 37.13 -97.62 REMARK 500 TRP A1360 -66.44 -92.65 REMARK 500 ASN A1394 25.36 30.93 REMARK 500 GLN A1398 -7.15 -57.57 REMARK 500 THR B1312 -161.28 -128.06 REMARK 500 GLN B1343 36.16 -98.82 REMARK 500 PHE B1383 -17.64 -49.69 REMARK 500 TRP B1391 10.68 -66.57 REMARK 500 ASN B1392 56.81 -146.06 REMARK 500 SER C1296 -73.43 -60.80 REMARK 500 GLN C1343 37.49 -83.57 REMARK 500 ASN C1394 17.28 58.77 REMARK 500 GLN D1343 37.20 -82.82 REMARK 500 TRP D1360 -58.78 -149.08 REMARK 500 SER D1362 49.04 -76.49 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 A1521 DISTANCE = 7.18 ANGSTROMS DBREF 9H35 A 1285 1424 UNP Q9H6S0 YTDC2_HUMAN 1285 1424 DBREF 9H35 B 1285 1424 UNP Q9H6S0 YTDC2_HUMAN 1285 1424 DBREF 9H35 C 1285 1424 UNP Q9H6S0 YTDC2_HUMAN 1285 1424 DBREF 9H35 D 1285 1424 UNP Q9H6S0 YTDC2_HUMAN 1285 1424 SEQADV 9H35 GLY A 1284 UNP Q9H6S0 EXPRESSION TAG SEQADV 9H35 GLY B 1284 UNP Q9H6S0 EXPRESSION TAG SEQADV 9H35 GLY C 1284 UNP Q9H6S0 EXPRESSION TAG SEQADV 9H35 GLY D 1284 UNP Q9H6S0 EXPRESSION TAG SEQRES 1 A 141 GLY ASN MET PRO VAL ARG TYR PHE ILE MET LYS SER SER SEQRES 2 A 141 ASN LEU ARG ASN LEU GLU ILE SER GLN GLN LYS GLY ILE SEQRES 3 A 141 TRP SER THR THR PRO SER ASN GLU ARG LYS LEU ASN ARG SEQRES 4 A 141 ALA PHE TRP GLU SER SER ILE VAL TYR LEU VAL PHE SER SEQRES 5 A 141 VAL GLN GLY SER GLY HIS PHE GLN GLY PHE SER ARG MET SEQRES 6 A 141 SER SER GLU ILE GLY ARG GLU LYS SER GLN ASP TRP GLY SEQRES 7 A 141 SER ALA GLY LEU GLY GLY VAL PHE LYS VAL GLU TRP ILE SEQRES 8 A 141 ARG LYS GLU SER LEU PRO PHE GLN PHE ALA HIS HIS LEU SEQRES 9 A 141 LEU ASN PRO TRP ASN ASP ASN LYS LYS VAL GLN ILE SER SEQRES 10 A 141 ARG ASP GLY GLN GLU LEU GLU PRO LEU VAL GLY GLU GLN SEQRES 11 A 141 LEU LEU GLN LEU TRP GLU ARG LEU PRO LEU GLY SEQRES 1 B 141 GLY ASN MET PRO VAL ARG TYR PHE ILE MET LYS SER SER SEQRES 2 B 141 ASN LEU ARG ASN LEU GLU ILE SER GLN GLN LYS GLY ILE SEQRES 3 B 141 TRP SER THR THR PRO SER ASN GLU ARG LYS LEU ASN ARG SEQRES 4 B 141 ALA PHE TRP GLU SER SER ILE VAL TYR LEU VAL PHE SER SEQRES 5 B 141 VAL GLN GLY SER GLY HIS PHE GLN GLY PHE SER ARG MET SEQRES 6 B 141 SER SER GLU ILE GLY ARG GLU LYS SER GLN ASP TRP GLY SEQRES 7 B 141 SER ALA GLY LEU GLY GLY VAL PHE LYS VAL GLU TRP ILE SEQRES 8 B 141 ARG LYS GLU SER LEU PRO PHE GLN PHE ALA HIS HIS LEU SEQRES 9 B 141 LEU ASN PRO TRP ASN ASP ASN LYS LYS VAL GLN ILE SER SEQRES 10 B 141 ARG ASP GLY GLN GLU LEU GLU PRO LEU VAL GLY GLU GLN SEQRES 11 B 141 LEU LEU GLN LEU TRP GLU ARG LEU PRO LEU GLY SEQRES 1 C 141 GLY ASN MET PRO VAL ARG TYR PHE ILE MET LYS SER SER SEQRES 2 C 141 ASN LEU ARG ASN LEU GLU ILE SER GLN GLN LYS GLY ILE SEQRES 3 C 141 TRP SER THR THR PRO SER ASN GLU ARG LYS LEU ASN ARG SEQRES 4 C 141 ALA PHE TRP GLU SER SER ILE VAL TYR LEU VAL PHE SER SEQRES 5 C 141 VAL GLN GLY SER GLY HIS PHE GLN GLY PHE SER ARG MET SEQRES 6 C 141 SER SER GLU ILE GLY ARG GLU LYS SER GLN ASP TRP GLY SEQRES 7 C 141 SER ALA GLY LEU GLY GLY VAL PHE LYS VAL GLU TRP ILE SEQRES 8 C 141 ARG LYS GLU SER LEU PRO PHE GLN PHE ALA HIS HIS LEU SEQRES 9 C 141 LEU ASN PRO TRP ASN ASP ASN LYS LYS VAL GLN ILE SER SEQRES 10 C 141 ARG ASP GLY GLN GLU LEU GLU PRO LEU VAL GLY GLU GLN SEQRES 11 C 141 LEU LEU GLN LEU TRP GLU ARG LEU PRO LEU GLY SEQRES 1 D 141 GLY ASN MET PRO VAL ARG TYR PHE ILE MET LYS SER SER SEQRES 2 D 141 ASN LEU ARG ASN LEU GLU ILE SER GLN GLN LYS GLY ILE SEQRES 3 D 141 TRP SER THR THR PRO SER ASN GLU ARG LYS LEU ASN ARG SEQRES 4 D 141 ALA PHE TRP GLU SER SER ILE VAL TYR LEU VAL PHE SER SEQRES 5 D 141 VAL GLN GLY SER GLY HIS PHE GLN GLY PHE SER ARG MET SEQRES 6 D 141 SER SER GLU ILE GLY ARG GLU LYS SER GLN ASP TRP GLY SEQRES 7 D 141 SER ALA GLY LEU GLY GLY VAL PHE LYS VAL GLU TRP ILE SEQRES 8 D 141 ARG LYS GLU SER LEU PRO PHE GLN PHE ALA HIS HIS LEU SEQRES 9 D 141 LEU ASN PRO TRP ASN ASP ASN LYS LYS VAL GLN ILE SER SEQRES 10 D 141 ARG ASP GLY GLN GLU LEU GLU PRO LEU VAL GLY GLU GLN SEQRES 11 D 141 LEU LEU GLN LEU TRP GLU ARG LEU PRO LEU GLY FORMUL 5 HOH *38(H2 O) HELIX 1 AA1 ASN A 1297 GLY A 1308 1 12 HELIX 2 AA2 THR A 1313 SER A 1327 1 15 HELIX 3 AA3 ARG A 1354 GLN A 1358 5 5 HELIX 4 AA4 GLN A 1382 HIS A 1385 5 4 HELIX 5 AA5 PRO A 1390 ASP A 1393 5 4 HELIX 6 AA6 GLU A 1407 LEU A 1417 1 11 HELIX 7 AA7 TRP A 1418 LEU A 1421 5 4 HELIX 8 AA8 ASN B 1297 GLY B 1308 1 12 HELIX 9 AA9 THR B 1313 SER B 1327 1 15 HELIX 10 AB1 SER B 1362 GLY B 1366 5 5 HELIX 11 AB2 GLN B 1382 HIS B 1385 5 4 HELIX 12 AB3 ASN B 1389 ASP B 1393 5 5 HELIX 13 AB4 GLU B 1407 LEU B 1417 1 11 HELIX 14 AB5 TRP B 1418 LEU B 1421 5 4 HELIX 15 AB6 ASN C 1297 GLY C 1308 1 12 HELIX 16 AB7 THR C 1313 SER C 1327 1 15 HELIX 17 AB8 GLN C 1382 HIS C 1385 5 4 HELIX 18 AB9 GLU C 1407 GLN C 1416 1 10 HELIX 19 AC1 LEU C 1417 ARG C 1420 5 4 HELIX 20 AC2 ASN D 1297 GLY D 1308 1 12 HELIX 21 AC3 THR D 1313 SER D 1327 1 15 HELIX 22 AC4 GLN D 1382 HIS D 1385 5 4 HELIX 23 AC5 ASN D 1389 ASP D 1393 5 5 HELIX 24 AC6 GLU D 1407 TRP D 1418 1 12 SHEET 1 AA1 6 ILE A1309 TRP A1310 0 SHEET 2 AA1 6 PHE A1369 ARG A1375 -1 O PHE A1369 N TRP A1310 SHEET 3 AA1 6 PHE A1345 MET A1348 -1 N ARG A1347 O GLU A1372 SHEET 4 AA1 6 ILE A1329 VAL A1336 -1 N LEU A1332 O SER A1346 SHEET 5 AA1 6 VAL A1288 SER A1295 1 N MET A1293 O VAL A1333 SHEET 6 AA1 6 GLU A1405 LEU A1406 -1 O LEU A1406 N TYR A1290 SHEET 1 AA2 2 HIS A1341 PHE A1342 0 SHEET 2 AA2 2 LEU A1379 PRO A1380 -1 O LEU A1379 N PHE A1342 SHEET 1 AA3 2 LEU A1388 ASN A1389 0 SHEET 2 AA3 2 LYS A1395 LYS A1396 -1 O LYS A1395 N ASN A1389 SHEET 1 AA4 6 ILE B1309 TRP B1310 0 SHEET 2 AA4 6 PHE B1369 ARG B1375 -1 O PHE B1369 N TRP B1310 SHEET 3 AA4 6 PHE B1345 MET B1348 -1 N ARG B1347 O GLU B1372 SHEET 4 AA4 6 ILE B1329 VAL B1336 -1 N LEU B1332 O SER B1346 SHEET 5 AA4 6 VAL B1288 SER B1295 1 N PHE B1291 O VAL B1333 SHEET 6 AA4 6 GLU B1405 LEU B1406 -1 O LEU B1406 N TYR B1290 SHEET 1 AA5 2 HIS B1341 PHE B1342 0 SHEET 2 AA5 2 LEU B1379 PRO B1380 -1 O LEU B1379 N PHE B1342 SHEET 1 AA6 6 ILE C1309 TRP C1310 0 SHEET 2 AA6 6 PHE C1369 ARG C1375 -1 O PHE C1369 N TRP C1310 SHEET 3 AA6 6 PHE C1345 MET C1348 -1 N ARG C1347 O GLU C1372 SHEET 4 AA6 6 ILE C1329 VAL C1336 -1 N VAL C1330 O MET C1348 SHEET 5 AA6 6 VAL C1288 SER C1295 1 N PHE C1291 O VAL C1333 SHEET 6 AA6 6 GLN C1404 LEU C1406 -1 O GLN C1404 N ILE C1292 SHEET 1 AA7 2 HIS C1341 PHE C1342 0 SHEET 2 AA7 2 LEU C1379 PRO C1380 -1 O LEU C1379 N PHE C1342 SHEET 1 AA8 6 ILE D1309 TRP D1310 0 SHEET 2 AA8 6 PHE D1369 ARG D1375 -1 O PHE D1369 N TRP D1310 SHEET 3 AA8 6 PHE D1345 MET D1348 -1 N ARG D1347 O GLU D1372 SHEET 4 AA8 6 ILE D1329 VAL D1336 -1 N LEU D1332 O SER D1346 SHEET 5 AA8 6 VAL D1288 SER D1295 1 N MET D1293 O VAL D1333 SHEET 6 AA8 6 GLN D1404 LEU D1406 -1 O LEU D1406 N TYR D1290 SHEET 1 AA9 2 HIS D1341 PHE D1342 0 SHEET 2 AA9 2 LEU D1379 PRO D1380 -1 O LEU D1379 N PHE D1342 CRYST1 115.972 115.972 205.847 90.00 90.00 120.00 P 61 2 2 48 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 0.008623 0.004978 0.000000 0.00000 SCALE2 0.000000 0.009957 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004858 0.00000