HEADER RNA BINDING PROTEIN 08-SEP-21 7PO6 TITLE XIST (M6A)UCG TETRALOOP RNA BOUND TO THE YTH DOMAIN OF YTHDC1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (5'-R(*(6MZ)P*UP*C)-3'); COMPND 3 CHAIN: D, E, F; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: ISOFORM 2 OF YTH DOMAIN-CONTAINING PROTEIN 1; COMPND 7 CHAIN: B, A, C; COMPND 8 SYNONYM: SPLICING FACTOR YT521,YT521-B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 8 ORGANISM_COMMON: HUMAN; SOURCE 9 ORGANISM_TAXID: 9606; SOURCE 10 GENE: YTHDC1, KIAA1966, YT521; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS M6A, YTHDC1, XIST, COMPLEX, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.N.JONES,A.MOURAO,M.SATTLER REVDAT 2 31-JAN-24 7PO6 1 COMPND SOURCE REMARK HET REVDAT 2 2 1 HETNAM FORMUL ATOM REVDAT 1 16-MAR-22 7PO6 0 JRNL AUTH A.N.JONES,E.TIKHAIA,A.MOURAO,M.SATTLER JRNL TITL STRUCTURAL EFFECTS OF M6A MODIFICATION OF THE XIST A-REPEAT JRNL TITL 2 AUCG TETRALOOP AND ITS RECOGNITION BY YTHDC1. JRNL REF NUCLEIC ACIDS RES. V. 50 2350 2022 JRNL REFN ESSN 1362-4962 JRNL PMID 35166835 JRNL DOI 10.1093/NAR/GKAC080 REMARK 2 REMARK 2 RESOLUTION. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 57964 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2894 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 48.3400 - 4.8700 1.00 2865 151 0.1953 0.2041 REMARK 3 2 4.8700 - 3.8700 1.00 2733 142 0.1462 0.1602 REMARK 3 3 3.8700 - 3.3800 1.00 2719 144 0.1770 0.2154 REMARK 3 4 3.3800 - 3.0700 1.00 2676 141 0.1826 0.2160 REMARK 3 5 3.0700 - 2.8500 1.00 2681 141 0.2019 0.2574 REMARK 3 6 2.8500 - 2.6800 1.00 2674 141 0.1997 0.2945 REMARK 3 7 2.6800 - 2.5500 1.00 2662 140 0.2039 0.2377 REMARK 3 8 2.5500 - 2.4400 1.00 2646 140 0.1889 0.2346 REMARK 3 9 2.4400 - 2.3400 1.00 2660 139 0.1814 0.2148 REMARK 3 10 2.3400 - 2.2600 1.00 2649 139 0.1825 0.2550 REMARK 3 11 2.2600 - 2.1900 1.00 2641 138 0.2174 0.2407 REMARK 3 12 2.1900 - 2.1300 1.00 2641 140 0.2053 0.2491 REMARK 3 13 2.1300 - 2.0700 1.00 2633 138 0.2165 0.2328 REMARK 3 14 2.0700 - 2.0200 1.00 2653 140 0.2189 0.2581 REMARK 3 15 2.0200 - 1.9800 1.00 2617 138 0.2340 0.3180 REMARK 3 16 1.9800 - 1.9300 1.00 2648 138 0.2630 0.2706 REMARK 3 17 1.9300 - 1.8900 1.00 2600 138 0.3104 0.3612 REMARK 3 18 1.8900 - 1.8600 1.00 2647 139 0.3453 0.3807 REMARK 3 19 1.8600 - 1.8300 0.99 2593 136 0.3927 0.4618 REMARK 3 20 1.8300 - 1.7900 0.90 2356 123 0.4695 0.4401 REMARK 3 21 1.7900 - 1.7700 0.79 2076 108 0.4820 0.4963 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) : 0.295 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.303 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.22 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.87 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 : 0.011 4303 REMARK 3 ANGLE : 1.317 5848 REMARK 3 CHIRALITY : 0.063 644 REMARK 3 PLANARITY : 0.009 699 REMARK 3 DIHEDRAL : 10.914 630 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 7PO6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1292118001. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57964 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 48.340 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.0800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 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 : 1.460 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: 4R3I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS HCL, 0.2M LITHIUM SULFATE, REMARK 280 30% (W/V) PEG 4000, PH 8.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 39.21900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.30850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.55950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 44.30850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.21900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.55950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: 2540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, 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: 2 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: 1510 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -5.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, F 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 G D -2 REMARK 465 G D -1 REMARK 465 C D 0 REMARK 465 G D 1 REMARK 465 C D 2 REMARK 465 G D 6 REMARK 465 G D 7 REMARK 465 C D 8 REMARK 465 G D 9 REMARK 465 C D 10 REMARK 465 C D 11 REMARK 465 GLY B 341 REMARK 465 GLY B 342 REMARK 465 HIS B 509 REMARK 465 GLY A 341 REMARK 465 GLY A 342 REMARK 465 GLY A 343 REMARK 465 GLY A 344 REMARK 465 ARG A 508 REMARK 465 HIS A 509 REMARK 465 GLY C 341 REMARK 465 GLY C 342 REMARK 465 GLY C 343 REMARK 465 G E -2 REMARK 465 G E -1 REMARK 465 C E 0 REMARK 465 G E 1 REMARK 465 C E 2 REMARK 465 G E 6 REMARK 465 G E 7 REMARK 465 C E 8 REMARK 465 G E 9 REMARK 465 C E 10 REMARK 465 C E 11 REMARK 465 G F -2 REMARK 465 G F -1 REMARK 465 C F 0 REMARK 465 G F 1 REMARK 465 C F 2 REMARK 465 G F 7 REMARK 465 C F 8 REMARK 465 G F 9 REMARK 465 C F 10 REMARK 465 C F 11 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 6MZ D 3 O1P O2P P REMARK 470 SER B 424 OG REMARK 470 MET B 434 CG SD CE REMARK 470 HIS B 505 CG ND1 CD2 CE1 NE2 REMARK 470 LYS B 506 CG CD CE NZ REMARK 470 ARG B 508 CD NE CZ NH1 NH2 REMARK 470 LYS A 347 NZ REMARK 470 LYS A 437 NZ REMARK 470 TYR A 501 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN A 502 CG CD OE1 NE2 REMARK 470 HIS A 505 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 506 CG CD CE NZ REMARK 470 SER C 346 OG REMARK 470 ARG C 392 CG CD NE CZ NH1 NH2 REMARK 470 SER C 424 OG REMARK 470 HIS C 427 CG ND1 CD2 CE1 NE2 REMARK 470 LYS C 437 CE REMARK 470 6MZ F 3 O1P O2P O5' P REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 SER A 369 CA CB REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 U D 4 O5' - P - OP1 ANGL. DEV. = -30.8 DEGREES REMARK 500 U D 4 O5' - P - OP2 ANGL. DEV. = 11.0 DEGREES 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 PRO A 470 139.51 -39.71 REMARK 500 LYS A 506 -2.81 -57.35 REMARK 500 SER C 424 98.64 -55.65 REMARK 500 PRO C 431 151.87 -49.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 GTP D 101 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 NA C 605 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR C 379 O REMARK 620 2 GLU C 384 OE1 114.4 REMARK 620 3 MET C 438 O 80.0 162.4 REMARK 620 4 LEU C 439 O 66.9 110.4 84.0 REMARK 620 5 HOH C 733 O 152.1 91.6 72.7 115.0 REMARK 620 N 1 2 3 4 DBREF 7PO6 D -2 11 PDB 7PO6 7PO6 -2 11 DBREF 7PO6 B 345 509 UNP Q96MU7 YTDC1_HUMAN 327 491 DBREF 7PO6 A 345 509 UNP Q96MU7 YTDC1_HUMAN 327 491 DBREF 7PO6 C 345 509 UNP Q96MU7 YTDC1_HUMAN 327 491 DBREF 7PO6 E -2 11 PDB 7PO6 7PO6 -2 11 DBREF 7PO6 F -2 11 PDB 7PO6 7PO6 -2 11 SEQADV 7PO6 GLY B 341 UNP Q96MU7 EXPRESSION TAG SEQADV 7PO6 GLY B 342 UNP Q96MU7 EXPRESSION TAG SEQADV 7PO6 GLY B 343 UNP Q96MU7 EXPRESSION TAG SEQADV 7PO6 GLY B 344 UNP Q96MU7 EXPRESSION TAG SEQADV 7PO6 GLY A 341 UNP Q96MU7 EXPRESSION TAG SEQADV 7PO6 GLY A 342 UNP Q96MU7 EXPRESSION TAG SEQADV 7PO6 GLY A 343 UNP Q96MU7 EXPRESSION TAG SEQADV 7PO6 GLY A 344 UNP Q96MU7 EXPRESSION TAG SEQADV 7PO6 GLY C 341 UNP Q96MU7 EXPRESSION TAG SEQADV 7PO6 GLY C 342 UNP Q96MU7 EXPRESSION TAG SEQADV 7PO6 GLY C 343 UNP Q96MU7 EXPRESSION TAG SEQADV 7PO6 GLY C 344 UNP Q96MU7 EXPRESSION TAG SEQRES 1 D 14 G G C G C 6MZ U C G G C G C SEQRES 2 D 14 C SEQRES 1 B 169 GLY GLY GLY GLY THR SER LYS LEU LYS TYR VAL LEU GLN SEQRES 2 B 169 ASP ALA ARG PHE PHE LEU ILE LYS SER ASN ASN HIS GLU SEQRES 3 B 169 ASN VAL SER LEU ALA LYS ALA LYS GLY VAL TRP SER THR SEQRES 4 B 169 LEU PRO VAL ASN GLU LYS LYS LEU ASN LEU ALA PHE ARG SEQRES 5 B 169 SER ALA ARG SER VAL ILE LEU ILE PHE SER VAL ARG GLU SEQRES 6 B 169 SER GLY LYS PHE GLN GLY PHE ALA ARG LEU SER SER GLU SEQRES 7 B 169 SER HIS HIS GLY GLY SER PRO ILE HIS TRP VAL LEU PRO SEQRES 8 B 169 ALA GLY MET SER ALA LYS MET LEU GLY GLY VAL PHE LYS SEQRES 9 B 169 ILE ASP TRP ILE CYS ARG ARG GLU LEU PRO PHE THR LYS SEQRES 10 B 169 SER ALA HIS LEU THR ASN PRO TRP ASN GLU HIS LYS PRO SEQRES 11 B 169 VAL LYS ILE GLY ARG ASP GLY GLN GLU ILE GLU LEU GLU SEQRES 12 B 169 CYS GLY THR GLN LEU CYS LEU LEU PHE PRO PRO ASP GLU SEQRES 13 B 169 SER ILE ASP LEU TYR GLN VAL ILE HIS LYS MET ARG HIS SEQRES 1 A 169 GLY GLY GLY GLY THR SER LYS LEU LYS TYR VAL LEU GLN SEQRES 2 A 169 ASP ALA ARG PHE PHE LEU ILE LYS SER ASN ASN HIS GLU SEQRES 3 A 169 ASN VAL SER LEU ALA LYS ALA LYS GLY VAL TRP SER THR SEQRES 4 A 169 LEU PRO VAL ASN GLU LYS LYS LEU ASN LEU ALA PHE ARG SEQRES 5 A 169 SER ALA ARG SER VAL ILE LEU ILE PHE SER VAL ARG GLU SEQRES 6 A 169 SER GLY LYS PHE GLN GLY PHE ALA ARG LEU SER SER GLU SEQRES 7 A 169 SER HIS HIS GLY GLY SER PRO ILE HIS TRP VAL LEU PRO SEQRES 8 A 169 ALA GLY MET SER ALA LYS MET LEU GLY GLY VAL PHE LYS SEQRES 9 A 169 ILE ASP TRP ILE CYS ARG ARG GLU LEU PRO PHE THR LYS SEQRES 10 A 169 SER ALA HIS LEU THR ASN PRO TRP ASN GLU HIS LYS PRO SEQRES 11 A 169 VAL LYS ILE GLY ARG ASP GLY GLN GLU ILE GLU LEU GLU SEQRES 12 A 169 CYS GLY THR GLN LEU CYS LEU LEU PHE PRO PRO ASP GLU SEQRES 13 A 169 SER ILE ASP LEU TYR GLN VAL ILE HIS LYS MET ARG HIS SEQRES 1 C 169 GLY GLY GLY GLY THR SER LYS LEU LYS TYR VAL LEU GLN SEQRES 2 C 169 ASP ALA ARG PHE PHE LEU ILE LYS SER ASN ASN HIS GLU SEQRES 3 C 169 ASN VAL SER LEU ALA LYS ALA LYS GLY VAL TRP SER THR SEQRES 4 C 169 LEU PRO VAL ASN GLU LYS LYS LEU ASN LEU ALA PHE ARG SEQRES 5 C 169 SER ALA ARG SER VAL ILE LEU ILE PHE SER VAL ARG GLU SEQRES 6 C 169 SER GLY LYS PHE GLN GLY PHE ALA ARG LEU SER SER GLU SEQRES 7 C 169 SER HIS HIS GLY GLY SER PRO ILE HIS TRP VAL LEU PRO SEQRES 8 C 169 ALA GLY MET SER ALA LYS MET LEU GLY GLY VAL PHE LYS SEQRES 9 C 169 ILE ASP TRP ILE CYS ARG ARG GLU LEU PRO PHE THR LYS SEQRES 10 C 169 SER ALA HIS LEU THR ASN PRO TRP ASN GLU HIS LYS PRO SEQRES 11 C 169 VAL LYS ILE GLY ARG ASP GLY GLN GLU ILE GLU LEU GLU SEQRES 12 C 169 CYS GLY THR GLN LEU CYS LEU LEU PHE PRO PRO ASP GLU SEQRES 13 C 169 SER ILE ASP LEU TYR GLN VAL ILE HIS LYS MET ARG HIS SEQRES 1 E 14 G G C G C 6MZ U C G G C G C SEQRES 2 E 14 C SEQRES 1 F 14 G G C G C 6MZ U C G G C G C SEQRES 2 F 14 C HET 6MZ D 3 32 HET 6MZ E 3 37 HET 6MZ F 3 30 HET GTP D 101 35 HET EDO B 601 10 HET SO4 B 602 5 HET EDO B 603 10 HET SO4 B 604 5 HET EDO B 605 10 HET SO4 B 606 5 HET EDO B 607 10 HET EDO A 601 10 HET EDO A 602 10 HET SO4 A 603 5 HET SO4 C 601 5 HET EDO C 602 10 HET SO4 C 603 5 HET SO4 C 604 5 HET NA C 605 1 HETNAM 6MZ N6-METHYLADENOSINE-5'-MONOPHOSPHATE HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETNAM NA SODIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 1 6MZ 3(C11 H16 N5 O7 P) FORMUL 7 GTP C10 H16 N5 O14 P3 FORMUL 8 EDO 7(C2 H6 O2) FORMUL 9 SO4 7(O4 S 2-) FORMUL 22 NA NA 1+ FORMUL 23 HOH *192(H2 O) HELIX 1 AA1 GLY B 343 GLN B 353 1 11 HELIX 2 AA2 ASN B 364 GLY B 375 1 12 HELIX 3 AA3 LEU B 380 ALA B 394 1 15 HELIX 4 AA4 SER B 435 GLY B 440 5 6 HELIX 5 AA5 THR B 456 ALA B 459 5 4 HELIX 6 AA6 ASN B 463 GLU B 467 5 5 HELIX 7 AA7 GLU B 481 PHE B 492 1 12 HELIX 8 AA8 ASP B 499 LYS B 506 1 8 HELIX 9 AA9 SER A 346 GLN A 353 1 8 HELIX 10 AB1 ASN A 364 GLY A 375 1 12 HELIX 11 AB2 LEU A 380 ALA A 394 1 15 HELIX 12 AB3 ALA A 436 GLY A 440 5 5 HELIX 13 AB4 THR A 456 ALA A 459 5 4 HELIX 14 AB5 ASN A 463 GLU A 467 5 5 HELIX 15 AB6 GLU A 481 PHE A 492 1 12 HELIX 16 AB7 ASP A 499 LYS A 506 1 8 HELIX 17 AB8 THR C 345 GLN C 353 1 9 HELIX 18 AB9 ASN C 364 GLY C 375 1 12 HELIX 19 AC1 LEU C 380 ALA C 394 1 15 HELIX 20 AC2 SER C 435 GLY C 440 1 6 HELIX 21 AC3 PHE C 455 ALA C 459 1 5 HELIX 22 AC4 ASN C 463 GLU C 467 5 5 HELIX 23 AC5 GLU C 481 PHE C 492 1 12 HELIX 24 AC6 ASP C 499 MET C 507 1 9 SHEET 1 AA1 6 VAL B 376 TRP B 377 0 SHEET 2 AA1 6 PHE B 443 CYS B 449 -1 O PHE B 443 N TRP B 377 SHEET 3 AA1 6 GLY B 411 LEU B 415 -1 N ARG B 414 O ASP B 446 SHEET 4 AA1 6 VAL B 397 VAL B 403 -1 N VAL B 397 O LEU B 415 SHEET 5 AA1 6 ARG B 356 SER B 362 1 N ILE B 360 O ILE B 400 SHEET 6 AA1 6 GLU B 479 ILE B 480 -1 O ILE B 480 N PHE B 357 SHEET 1 AA2 2 LYS B 408 PHE B 409 0 SHEET 2 AA2 2 LEU B 453 PRO B 454 -1 O LEU B 453 N PHE B 409 SHEET 1 AA3 6 VAL A 376 TRP A 377 0 SHEET 2 AA3 6 PHE A 443 CYS A 449 -1 O PHE A 443 N TRP A 377 SHEET 3 AA3 6 GLY A 411 LEU A 415 -1 N ARG A 414 O ASP A 446 SHEET 4 AA3 6 SER A 396 VAL A 403 -1 N LEU A 399 O ALA A 413 SHEET 5 AA3 6 ALA A 355 SER A 362 1 N ILE A 360 O ILE A 400 SHEET 6 AA3 6 GLU A 479 ILE A 480 -1 O ILE A 480 N PHE A 357 SHEET 1 AA4 2 LYS A 408 PHE A 409 0 SHEET 2 AA4 2 LEU A 453 PRO A 454 -1 O LEU A 453 N PHE A 409 SHEET 1 AA5 6 VAL C 376 TRP C 377 0 SHEET 2 AA5 6 PHE C 443 CYS C 449 -1 O PHE C 443 N TRP C 377 SHEET 3 AA5 6 GLY C 411 LEU C 415 -1 N ARG C 414 O ASP C 446 SHEET 4 AA5 6 VAL C 397 VAL C 403 -1 N LEU C 399 O ALA C 413 SHEET 5 AA5 6 ARG C 356 SER C 362 1 N ILE C 360 O ILE C 400 SHEET 6 AA5 6 GLU C 479 ILE C 480 -1 O ILE C 480 N PHE C 357 SHEET 1 AA6 2 LYS C 408 PHE C 409 0 SHEET 2 AA6 2 LEU C 453 PRO C 454 -1 O LEU C 453 N PHE C 409 LINK O3' 6MZ D 3 P U D 4 1555 1555 1.60 LINK O3' 6MZ E 3 P U E 4 1555 1555 1.63 LINK O3' 6MZ F 3 P U F 4 1555 1555 1.60 LINK O THR C 379 NA NA C 605 1555 1555 2.88 LINK OE1 GLU C 384 NA NA C 605 1555 1555 2.54 LINK O MET C 438 NA NA C 605 1555 1555 2.75 LINK O LEU C 439 NA NA C 605 1555 1555 3.11 LINK NA NA C 605 O HOH C 733 1555 1555 2.66 CRYST1 78.438 85.119 88.617 90.00 90.00 90.00 P 21 21 21 12 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 0.012749 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011748 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011285 0.00000 HETATM 1 C2 6MZ D 3 -3.066 5.301 -3.027 1.00 49.05 C HETATM 2 C4 6MZ D 3 -2.205 3.110 -3.135 1.00 49.33 C HETATM 3 C5 6MZ D 3 -3.467 2.659 -3.158 1.00 50.01 C HETATM 4 N9 6MZ D 3 -1.459 1.999 -3.190 1.00 52.42 N HETATM 5 N3 6MZ D 3 -2.014 4.468 -3.069 1.00 48.58 N HETATM 6 N1 6MZ D 3 -4.317 4.810 -3.055 1.00 48.78 N HETATM 7 C6 6MZ D 3 -4.508 3.518 -3.119 1.00 46.86 C HETATM 8 N6 6MZ D 3 -5.919 3.199 -3.137 1.00 48.31 N HETATM 9 C9 6MZ D 3 -6.976 4.165 -3.203 1.00 50.33 C HETATM 10 N7 6MZ D 3 -3.518 1.319 -3.227 1.00 51.12 N HETATM 11 C8 6MZ D 3 -2.272 0.926 -3.268 1.00 52.05 C HETATM 12 O5' 6MZ D 3 2.674 1.252 -6.484 1.00 64.82 O HETATM 13 C5' 6MZ D 3 2.287 0.471 -5.362 1.00 56.31 C HETATM 14 C4' 6MZ D 3 1.827 1.363 -4.235 1.00 48.35 C HETATM 15 O4' 6MZ D 3 0.456 1.728 -4.431 1.00 54.15 O HETATM 16 C1' 6MZ D 3 -0.019 2.289 -3.213 1.00 51.00 C HETATM 17 C2' 6MZ D 3 0.715 1.557 -2.082 1.00 59.26 C HETATM 18 O2' 6MZ D 3 1.270 2.511 -1.174 1.00 54.33 O HETATM 19 C3' 6MZ D 3 1.818 0.761 -2.818 1.00 48.88 C HETATM 20 O3' 6MZ D 3 3.093 0.833 -2.199 1.00 54.89 O HETATM 21 H2 6MZ D 3 -2.906 6.370 -2.970 1.00 58.86 H HETATM 22 H8 6MZ D 3 -1.944 -0.103 -3.352 1.00 62.46 H HETATM 23 H1' 6MZ D 3 0.181 3.353 -3.147 1.00 61.19 H HETATM 24 H9C1 6MZ D 3 -7.907 3.706 -2.880 1.00 60.39 H HETATM 25 H9C2 6MZ D 3 -6.741 5.004 -2.553 1.00 60.39 H HETATM 26 H5'1 6MZ D 3 1.477 -0.191 -5.648 1.00 67.57 H HETATM 27 H5'2 6MZ D 3 3.135 -0.119 -5.028 1.00 67.57 H HETATM 28 H4' 6MZ D 3 2.452 2.250 -4.233 1.00 58.02 H HETATM 29 H2' 6MZ D 3 0.033 0.877 -1.585 1.00 71.11 H HETATM 30 HA 6MZ D 3 1.688 2.059 -0.453 1.00 65.20 H HETATM 31 H6 6MZ D 3 -6.177 2.232 -3.100 1.00 57.97 H HETATM 32 H9 6MZ D 3 -7.081 4.517 -4.225 1.00 60.39 H