HEADER OXIDOREDUCTASE 08-NOV-19 6L94 TITLE THE STRUCTURE OF THE DIOXYGENASE ABH1 FROM MOUSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEIC ACID DIOXYGENASE ALKBH1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ALKYLATED DNA REPAIR PROTEIN ALKB HOMOLOG 1,ALPHA- COMPND 5 KETOGLUTARATE-DEPENDENT DIOXYGENASE ABH1,DNA 6MA DEMETHYLASE,DNA N6- COMPND 6 METHYL ADENINE DEMETHYLASE ALKBH1,DNA LYASE ABH1,DNA OXIDATIVE COMPND 7 DEMETHYLASE ALKBH1,MRNA N(3)-METHYLCYTIDINE DEMETHYLASE,TRNA N1- COMPND 8 METHYL ADENINE DEMETHYLASE; COMPND 9 EC: 1.14.11.-,1.14.11.51,4.2.99.18,1.14.11.33; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: ALKBH1, ABH, ALKBH; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DIOXYGENASE, ABH1, DEMETHYLATION, RNA BINDING PROTEIN, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR W.XIE,C.WANG,H.LI,Y.ZHANG REVDAT 4 22-NOV-23 6L94 1 REMARK REVDAT 3 16-JUN-21 6L94 1 JRNL REVDAT 2 26-MAY-21 6L94 1 JRNL REVDAT 1 11-NOV-20 6L94 0 JRNL AUTH H.LI,Y.ZHANG,Y.GUO,R.LIU,Q.YU,L.GONG,Z.LIU,W.XIE,C.WANG JRNL TITL ALKBH1 PROMOTES LUNG CANCER BY REGULATING M6A RNA JRNL TITL 2 DEMETHYLATION. JRNL REF BIOCHEM PHARMACOL V. 189 14284 2021 JRNL REFN ISSN 1873-2968 JRNL PMID 33068553 JRNL DOI 10.1016/J.BCP.2020.114284 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.338 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 8256 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.279 REMARK 3 R VALUE (WORKING SET) : 0.278 REMARK 3 FREE R VALUE : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.111 REMARK 3 FREE R VALUE TEST SET COUNT : 422 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 21.1780 - 4.4618 1.00 2596 173 0.2443 0.2675 REMARK 3 2 4.4618 - 3.5469 1.00 2623 122 0.2843 0.3164 REMARK 3 3 3.5469 - 3.1002 1.00 2615 127 0.3398 0.3600 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) : 0.521 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 38.503 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 54.55 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.89 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 : 0.004 2428 REMARK 3 ANGLE : 0.660 3307 REMARK 3 CHIRALITY : 0.042 357 REMARK 3 PLANARITY : 0.005 435 REMARK 3 DIHEDRAL : 15.812 1417 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 21 THROUGH 70 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.1859 50.6080 -13.3744 REMARK 3 T TENSOR REMARK 3 T11: 0.7080 T22: 0.7831 REMARK 3 T33: 1.2936 T12: 0.0090 REMARK 3 T13: -0.5963 T23: 0.2673 REMARK 3 L TENSOR REMARK 3 L11: 0.3758 L22: 0.2189 REMARK 3 L33: 0.4360 L12: -0.2862 REMARK 3 L13: 0.1484 L23: -0.1675 REMARK 3 S TENSOR REMARK 3 S11: -0.0924 S12: -0.0069 S13: 0.0745 REMARK 3 S21: -0.1320 S22: -0.0653 S23: 0.0166 REMARK 3 S31: -0.0025 S32: 0.0001 S33: -0.1138 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 71 THROUGH 110 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.7646 35.7878 -1.3800 REMARK 3 T TENSOR REMARK 3 T11: 0.5459 T22: 0.6526 REMARK 3 T33: 1.2143 T12: -0.2996 REMARK 3 T13: -0.3374 T23: 0.3986 REMARK 3 L TENSOR REMARK 3 L11: 1.4187 L22: 1.3846 REMARK 3 L33: 1.9251 L12: -0.1037 REMARK 3 L13: -0.8555 L23: 0.2684 REMARK 3 S TENSOR REMARK 3 S11: -0.3678 S12: 0.2445 S13: -0.1303 REMARK 3 S21: 0.1332 S22: -0.2693 S23: 0.2776 REMARK 3 S31: 0.0423 S32: -0.1003 S33: 0.1982 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 111 THROUGH 129 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.6028 45.5615 11.7291 REMARK 3 T TENSOR REMARK 3 T11: 0.5505 T22: 0.5194 REMARK 3 T33: 0.6028 T12: 0.0009 REMARK 3 T13: 0.4432 T23: 0.2710 REMARK 3 L TENSOR REMARK 3 L11: 0.9998 L22: 1.7614 REMARK 3 L33: 2.3368 L12: 0.0429 REMARK 3 L13: -1.3422 L23: -0.2987 REMARK 3 S TENSOR REMARK 3 S11: 0.0339 S12: -0.3300 S13: -0.0659 REMARK 3 S21: 0.1933 S22: -0.0331 S23: 0.2250 REMARK 3 S31: -0.0757 S32: 0.0612 S33: 0.0079 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 130 THROUGH 179 ) REMARK 3 ORIGIN FOR THE GROUP (A): 32.1206 53.8646 10.3479 REMARK 3 T TENSOR REMARK 3 T11: 0.4889 T22: 0.3932 REMARK 3 T33: 0.1312 T12: 0.0229 REMARK 3 T13: 0.1020 T23: 0.1585 REMARK 3 L TENSOR REMARK 3 L11: 1.3739 L22: 1.0268 REMARK 3 L33: 0.9504 L12: 0.2300 REMARK 3 L13: -0.2045 L23: -0.0321 REMARK 3 S TENSOR REMARK 3 S11: 0.0005 S12: -0.2764 S13: 0.3811 REMARK 3 S21: 0.3487 S22: 0.2997 S23: 0.2652 REMARK 3 S31: -0.2695 S32: 0.1208 S33: -0.1229 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 180 THROUGH 241 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.3203 39.5182 -1.4309 REMARK 3 T TENSOR REMARK 3 T11: 0.2769 T22: 0.3482 REMARK 3 T33: 0.3809 T12: -0.1254 REMARK 3 T13: -0.0808 T23: 0.1238 REMARK 3 L TENSOR REMARK 3 L11: 0.9495 L22: 0.8432 REMARK 3 L33: 0.6107 L12: -0.4664 REMARK 3 L13: 0.0168 L23: 0.1758 REMARK 3 S TENSOR REMARK 3 S11: -0.2944 S12: 0.3038 S13: 0.0496 REMARK 3 S21: -0.0118 S22: 0.3405 S23: 0.6364 REMARK 3 S31: 0.0122 S32: 0.1415 S33: -0.0144 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 242 THROUGH 302 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.9925 47.4260 -8.2020 REMARK 3 T TENSOR REMARK 3 T11: 0.2353 T22: 0.5611 REMARK 3 T33: 1.0289 T12: -0.0560 REMARK 3 T13: -0.5896 T23: 0.3612 REMARK 3 L TENSOR REMARK 3 L11: 1.6561 L22: 0.9365 REMARK 3 L33: 0.7740 L12: -0.5223 REMARK 3 L13: 0.7992 L23: -0.3417 REMARK 3 S TENSOR REMARK 3 S11: 0.0519 S12: 0.2635 S13: 0.1144 REMARK 3 S21: -0.1996 S22: 0.2418 S23: 0.4211 REMARK 3 S31: 0.0370 S32: -0.1597 S33: 0.1210 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 303 THROUGH 323 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.8088 41.2475 14.8403 REMARK 3 T TENSOR REMARK 3 T11: 0.8926 T22: 0.8313 REMARK 3 T33: 1.0225 T12: 0.0460 REMARK 3 T13: 0.6017 T23: 0.3429 REMARK 3 L TENSOR REMARK 3 L11: 0.9772 L22: 0.5164 REMARK 3 L33: 0.5015 L12: -0.3755 REMARK 3 L13: 0.0832 L23: 0.3267 REMARK 3 S TENSOR REMARK 3 S11: 0.0333 S12: -0.0183 S13: 0.2200 REMARK 3 S21: 0.2197 S22: -0.0805 S23: 0.0199 REMARK 3 S31: -0.1792 S32: -0.1183 S33: -0.1843 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 324 THROUGH 356 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.8109 43.8579 3.7206 REMARK 3 T TENSOR REMARK 3 T11: 0.1764 T22: 0.3352 REMARK 3 T33: 0.7739 T12: 0.0267 REMARK 3 T13: 0.0814 T23: -0.0006 REMARK 3 L TENSOR REMARK 3 L11: 0.9399 L22: 0.5347 REMARK 3 L33: 0.9491 L12: -0.1260 REMARK 3 L13: 0.4748 L23: -0.4875 REMARK 3 S TENSOR REMARK 3 S11: 0.2859 S12: -0.0759 S13: 0.2243 REMARK 3 S21: 0.2580 S22: 0.2215 S23: 0.5171 REMARK 3 S31: -0.0281 S32: -0.0326 S33: -0.1905 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 6L94 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1300014351. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSALISPRO REMARK 200 DATA SCALING SOFTWARE : CRYSALISPRO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8262 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 21.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.18800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.60 REMARK 200 R MERGE FOR SHELL (I) : 0.80000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: 5XEG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15-19% PEG 3350, 0.1 M NA-CITRATE PH REMARK 280 5.5, 0.1 M NACL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 51.60100 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.60100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 43.05400 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 51.60100 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.60100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 43.05400 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 51.60100 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 51.60100 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 43.05400 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 51.60100 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 51.60100 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 43.05400 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -13.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -12 REMARK 465 GLY A -11 REMARK 465 SER A -10 REMARK 465 HIS A -9 REMARK 465 HIS A -8 REMARK 465 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 SER A 0 REMARK 465 GLY A 1 REMARK 465 HIS A 2 REMARK 465 MET A 3 REMARK 465 MET A 4 REMARK 465 ALA A 5 REMARK 465 ALA A 6 REMARK 465 ALA A 7 REMARK 465 VAL A 8 REMARK 465 ALA A 9 REMARK 465 SER A 10 REMARK 465 LEU A 11 REMARK 465 ALA A 12 REMARK 465 THR A 13 REMARK 465 LEU A 14 REMARK 465 ALA A 15 REMARK 465 ALA A 16 REMARK 465 GLU A 17 REMARK 465 PRO A 18 REMARK 465 ARG A 19 REMARK 465 GLU A 20 REMARK 465 SER A 47 REMARK 465 GLU A 48 REMARK 465 ALA A 49 REMARK 465 HIS A 50 REMARK 465 LEU A 51 REMARK 465 ALA A 52 REMARK 465 ARG A 53 REMARK 465 SER A 54 REMARK 465 PRO A 55 REMARK 465 LYS A 56 REMARK 465 PRO A 57 REMARK 465 GLY A 58 REMARK 465 VAL A 59 REMARK 465 PRO A 60 REMARK 465 GLU A 155 REMARK 465 VAL A 156 REMARK 465 THR A 157 REMARK 465 LYS A 158 REMARK 465 ARG A 159 REMARK 465 ARG A 160 REMARK 465 PRO A 161 REMARK 465 ASP A 297 REMARK 465 GLY A 298 REMARK 465 GLU A 299 REMARK 465 CYS A 300 REMARK 465 PRO A 357 REMARK 465 VAL A 358 REMARK 465 GLU A 359 REMARK 465 GLU A 360 REMARK 465 THR A 361 REMARK 465 LYS A 362 REMARK 465 ARG A 363 REMARK 465 ASP A 364 REMARK 465 ILE A 365 REMARK 465 ALA A 366 REMARK 465 ALA A 367 REMARK 465 ASP A 368 REMARK 465 GLY A 369 REMARK 465 LEU A 370 REMARK 465 CYS A 371 REMARK 465 HIS A 372 REMARK 465 LEU A 373 REMARK 465 HIS A 374 REMARK 465 ASP A 375 REMARK 465 PRO A 376 REMARK 465 ASN A 377 REMARK 465 SER A 378 REMARK 465 PRO A 379 REMARK 465 VAL A 380 REMARK 465 LYS A 381 REMARK 465 ARG A 382 REMARK 465 LYS A 383 REMARK 465 ARG A 384 REMARK 465 LEU A 385 REMARK 465 ASN A 386 REMARK 465 PRO A 387 REMARK 465 ASN A 388 REMARK 465 SER A 389 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 ARG A 24 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 25 CG CD CE NZ REMARK 470 LEU A 26 CG CD1 CD2 REMARK 470 ARG A 28 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 39 CG OD1 OD2 REMARK 470 LEU A 40 CG CD1 CD2 REMARK 470 ARG A 64 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 69 CG1 CG2 REMARK 470 VAL A 72 CG1 CG2 REMARK 470 GLU A 74 CG CD OE1 OE2 REMARK 470 ARG A 75 CG CD NE CZ NH1 NH2 REMARK 470 SER A 86 OG REMARK 470 LYS A 87 CG CD CE NZ REMARK 470 GLU A 94 CG CD OE1 OE2 REMARK 470 LYS A 120 CG CD CE NZ REMARK 470 GLU A 145 CG CD OE1 OE2 REMARK 470 GLN A 146 CG CD OE1 NE2 REMARK 470 LYS A 148 CG CD CE NZ REMARK 470 VAL A 150 CG1 CG2 REMARK 470 LEU A 151 CG CD1 CD2 REMARK 470 ARG A 152 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 154 CG CD CE NZ REMARK 470 LYS A 241 CG CD CE NZ REMARK 470 LEU A 243 CG CD1 CD2 REMARK 470 SER A 251 OG REMARK 470 LEU A 255 CG CD1 CD2 REMARK 470 LEU A 256 CG CD1 CD2 REMARK 470 LEU A 259 CG CD1 CD2 REMARK 470 LYS A 260 CG CD CE NZ REMARK 470 ARG A 261 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 263 CG CD OE1 OE2 REMARK 470 LEU A 284 CG CD1 CD2 REMARK 470 LEU A 285 CG CD1 CD2 REMARK 470 ASN A 286 CG OD1 ND2 REMARK 470 LEU A 305 CG CD1 CD2 REMARK 470 THR A 307 OG1 CG2 REMARK 470 VAL A 312 CG1 CG2 REMARK 470 LEU A 313 CG CD1 CD2 REMARK 470 CYS A 322 SG REMARK 470 GLN A 328 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 THR A 37 -157.44 -144.72 REMARK 500 ASP A 233 73.57 -103.06 REMARK 500 MET A 270 88.68 -150.55 REMARK 500 PRO A 302 -168.49 -73.50 REMARK 500 REMARK 500 REMARK: NULL 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 FE2 A 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 231 NE2 REMARK 620 2 ASP A 233 OD1 97.6 REMARK 620 3 HIS A 287 NE2 99.5 67.5 REMARK 620 4 HOH A 501 O 131.8 92.2 127.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE2 A 401 DBREF 6L94 A 4 389 UNP P0CB42 ALKB1_MOUSE 4 389 SEQADV 6L94 MET A -12 UNP P0CB42 EXPRESSION TAG SEQADV 6L94 GLY A -11 UNP P0CB42 EXPRESSION TAG SEQADV 6L94 SER A -10 UNP P0CB42 EXPRESSION TAG SEQADV 6L94 HIS A -9 UNP P0CB42 EXPRESSION TAG SEQADV 6L94 HIS A -8 UNP P0CB42 EXPRESSION TAG SEQADV 6L94 HIS A -7 UNP P0CB42 EXPRESSION TAG SEQADV 6L94 HIS A -6 UNP P0CB42 EXPRESSION TAG SEQADV 6L94 HIS A -5 UNP P0CB42 EXPRESSION TAG SEQADV 6L94 HIS A -4 UNP P0CB42 EXPRESSION TAG SEQADV 6L94 HIS A -3 UNP P0CB42 EXPRESSION TAG SEQADV 6L94 HIS A -2 UNP P0CB42 EXPRESSION TAG SEQADV 6L94 HIS A -1 UNP P0CB42 EXPRESSION TAG SEQADV 6L94 SER A 0 UNP P0CB42 EXPRESSION TAG SEQADV 6L94 GLY A 1 UNP P0CB42 EXPRESSION TAG SEQADV 6L94 HIS A 2 UNP P0CB42 EXPRESSION TAG SEQADV 6L94 MET A 3 UNP P0CB42 EXPRESSION TAG SEQRES 1 A 402 MET GLY SER HIS HIS HIS HIS HIS HIS HIS HIS HIS SER SEQRES 2 A 402 GLY HIS MET MET ALA ALA ALA VAL ALA SER LEU ALA THR SEQRES 3 A 402 LEU ALA ALA GLU PRO ARG GLU ASP ALA PHE ARG LYS LEU SEQRES 4 A 402 PHE ARG PHE TYR ARG GLN SER ARG PRO GLY THR ALA ASP SEQRES 5 A 402 LEU GLY ALA VAL ILE ASP PHE SER GLU ALA HIS LEU ALA SEQRES 6 A 402 ARG SER PRO LYS PRO GLY VAL PRO GLN VAL VAL ARG PHE SEQRES 7 A 402 PRO LEU ASN VAL SER SER VAL THR GLU ARG ASP ALA GLU SEQRES 8 A 402 ARG VAL GLY LEU GLU PRO VAL SER LYS TRP ARG ALA TYR SEQRES 9 A 402 GLY LEU GLU GLY TYR PRO GLY PHE ILE PHE ILE PRO ASN SEQRES 10 A 402 PRO PHE LEU PRO GLY CYS GLN ARG HIS TRP VAL LYS GLN SEQRES 11 A 402 CYS LEU LYS LEU TYR SER GLN LYS PRO ASN VAL CYS ASN SEQRES 12 A 402 LEU ASP LYS HIS MET THR LYS GLU GLU THR GLN GLY LEU SEQRES 13 A 402 TRP GLU GLN SER LYS GLU VAL LEU ARG SER LYS GLU VAL SEQRES 14 A 402 THR LYS ARG ARG PRO ARG SER LEU LEU GLU ARG LEU ARG SEQRES 15 A 402 TRP VAL THR LEU GLY TYR HIS TYR ASN TRP ASP SER LYS SEQRES 16 A 402 LYS TYR SER ALA ASP HIS TYR THR PRO PHE PRO SER ASP SEQRES 17 A 402 LEU ALA PHE LEU SER GLU GLN VAL ALA THR ALA CYS GLY SEQRES 18 A 402 PHE GLN GLY PHE GLN ALA GLU ALA GLY ILE LEU ASN TYR SEQRES 19 A 402 TYR ARG LEU ASP SER THR LEU GLY ILE HIS VAL ASP ARG SEQRES 20 A 402 SER GLU LEU ASP HIS SER LYS PRO LEU LEU SER PHE SER SEQRES 21 A 402 PHE GLY GLN SER ALA ILE PHE LEU LEU GLY GLY LEU LYS SEQRES 22 A 402 ARG ASP GLU ALA PRO THR ALA MET PHE MET HIS SER GLY SEQRES 23 A 402 ASP ILE MET VAL MET SER GLY PHE SER ARG LEU LEU ASN SEQRES 24 A 402 HIS ALA VAL PRO ARG VAL LEU PRO HIS PRO ASP GLY GLU SEQRES 25 A 402 CYS LEU PRO HIS CYS LEU GLU THR PRO LEU PRO ALA VAL SEQRES 26 A 402 LEU PRO SER ASN SER LEU VAL GLU PRO CYS SER VAL GLU SEQRES 27 A 402 ASP TRP GLN VAL CYS ALA THR TYR LEU ARG THR ALA ARG SEQRES 28 A 402 VAL ASN MET THR VAL ARG GLN VAL LEU ALA THR GLY GLN SEQRES 29 A 402 ASP PHE PRO LEU GLU PRO VAL GLU GLU THR LYS ARG ASP SEQRES 30 A 402 ILE ALA ALA ASP GLY LEU CYS HIS LEU HIS ASP PRO ASN SEQRES 31 A 402 SER PRO VAL LYS ARG LYS ARG LEU ASN PRO ASN SER HET FE2 A 401 1 HETNAM FE2 FE (II) ION FORMUL 2 FE2 FE 2+ FORMUL 3 HOH *(H2 O) HELIX 1 AA1 ASP A 21 GLN A 32 1 12 HELIX 2 AA2 ASP A 39 VAL A 43 5 5 HELIX 3 AA3 THR A 73 GLY A 81 1 9 HELIX 4 AA4 PRO A 84 TRP A 88 5 5 HELIX 5 AA5 GLY A 109 LYS A 120 1 12 HELIX 6 AA6 LEU A 131 LYS A 133 5 3 HELIX 7 AA7 THR A 136 GLY A 142 1 7 HELIX 8 AA8 GLY A 142 LYS A 154 1 13 HELIX 9 AA9 SER A 163 LEU A 168 1 6 HELIX 10 AB1 PRO A 193 CYS A 207 1 15 HELIX 11 AB2 SER A 323 ALA A 337 1 15 SHEET 1 AA1 9 VAL A 62 ARG A 64 0 SHEET 2 AA1 9 TYR A 91 LEU A 93 -1 O GLY A 92 N VAL A 63 SHEET 3 AA1 9 TYR A 96 ILE A 102 -1 O PHE A 101 N TYR A 91 SHEET 4 AA1 9 ILE A 275 MET A 278 -1 O ILE A 275 N ILE A 102 SHEET 5 AA1 9 LEU A 243 SER A 247 -1 N SER A 245 O MET A 276 SHEET 6 AA1 9 VAL A 339 ARG A 344 -1 O VAL A 343 N LEU A 244 SHEET 7 AA1 9 ALA A 216 TYR A 221 -1 N ALA A 216 O ARG A 344 SHEET 8 AA1 9 TRP A 170 GLY A 174 -1 N VAL A 171 O LEU A 219 SHEET 9 AA1 9 VAL A 128 CYS A 129 -1 N VAL A 128 O THR A 172 SHEET 1 AA2 3 LEU A 228 HIS A 231 0 SHEET 2 AA2 3 ASN A 286 VAL A 289 -1 O HIS A 287 N HIS A 231 SHEET 3 AA2 3 LEU A 256 GLY A 257 -1 N GLY A 257 O ASN A 286 SHEET 1 AA3 3 PHE A 269 MET A 270 0 SHEET 2 AA3 3 ALA A 252 ILE A 253 -1 N ALA A 252 O MET A 270 SHEET 3 AA3 3 ARG A 291 VAL A 292 -1 O ARG A 291 N ILE A 253 LINK NE2 HIS A 231 FE FE2 A 401 1555 1555 2.10 LINK OD1 ASP A 233 FE FE2 A 401 1555 1555 2.02 LINK NE2 HIS A 287 FE FE2 A 401 1555 1555 2.05 LINK FE FE2 A 401 O HOH A 501 1555 1555 2.03 SITE 1 AC1 4 HIS A 231 ASP A 233 HIS A 287 HOH A 501 CRYST1 103.202 103.202 86.108 90.00 90.00 90.00 I 4 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 0.009690 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009690 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011613 0.00000