PDB Short entry for 3THP HEADER OXIDOREDUCTASE 19-AUG-11 3THP TITLE CRYSTAL STRUCTURE AND RNA BINDING PROPERTIES OF THE RRM/ALKB DOMAINS TITLE 2 IN HUMAN ABH8, AN ENZYME CATALYZING TRNA HYPERMODIFICATION, NORTHEAST TITLE 3 STRUCTURAL GENOMICS CONSORTIUM TARGET HR5601B COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALKYLATED DNA REPAIR PROTEIN ALKB HOMOLOG 8; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RRM AND ALKB DOMAINS OF ABH8; COMPND 5 SYNONYM: PROBABLE ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE ABH8; COMPND 6 EC: 1.14.11.-; COMPND 7 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: ABH8, ALKBH8; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: B834(LAMBDA)(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PET26 KEYWDS STRUCTURAL GENOMICS, PSI-BIOLOGY, NORTHEAST STRUCTURAL GENOMICS KEYWDS 2 CONSORTIUM, NESG, ALPHA-BETA TWO DOMAIN-PROTEIN CONTAINING A ZINC KEYWDS 3 STRUCTURE MOTIF, TRNA MODIFYING ENZYME, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR C.PASTORE,I.TOPALIDOU,F.FOROUHAR,A.C.YAN,M.LEVY,J.F.HUNT,NORTHEAST AUTHOR 2 STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 5 06-DEC-23 3THP 1 REMARK REVDAT 4 13-SEP-23 3THP 1 REMARK SEQADV LINK REVDAT 3 25-OCT-17 3THP 1 REMARK REVDAT 2 10-OCT-12 3THP 1 JRNL REVDAT 1 02-NOV-11 3THP 0 JRNL AUTH C.PASTORE,I.TOPALIDOU,F.FOROUHAR,A.C.YAN,M.LEVY,J.F.HUNT JRNL TITL CRYSTAL STRUCTURE AND RNA BINDING PROPERTIES OF THE RNA JRNL TITL 2 RECOGNITION MOTIF (RRM) AND ALKB DOMAINS IN HUMAN ALKB JRNL TITL 3 HOMOLOG 8 (ABH8), AN ENZYME CATALYZING TRNA JRNL TITL 4 HYPERMODIFICATION. JRNL REF J.BIOL.CHEM. V. 287 2130 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22065580 JRNL DOI 10.1074/JBC.M111.286187 REMARK 2 REMARK 2 RESOLUTION. 3.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 & XTALVIEW REMARK 3 AUTHORS : NULL REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 296587.360 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 12202 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1210 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.31 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 79.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 950 REMARK 3 BIN R VALUE (WORKING SET) : 0.3070 REMARK 3 BIN FREE R VALUE : 0.3850 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 88 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.041 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2413 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -12.99000 REMARK 3 B22 (A**2) : 24.43000 REMARK 3 B33 (A**2) : -11.44000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.35 REMARK 3 ESD FROM SIGMAA (A) : 0.48 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.50 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.59 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.760 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 24.03 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3THP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-AUG-11. REMARK 100 THE DEPOSITION ID IS D_1000067490. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97885 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12770 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.200 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.15400 REMARK 200 R SYM (I) : 0.12400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.31 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.40 REMARK 200 R MERGE FOR SHELL (I) : 0.43700 REMARK 200 R SYM FOR SHELL (I) : 0.39300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.700 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: PDB ENTRY 2CQ2 FOR RRM DOMAIN, PDB ENTRY 2FDI FOR REMARK 200 ALKB DOMAIN. REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.54 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 3350 AND 0.15 M D/L MALIC REMARK 280 ACID, 2.8 MM MNCL2, AND 8.6 MM 2-OXYGLUTARATE., PH 7, MICROBATCH REMARK 280 UNDER OIL, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-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 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 34.13800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.83750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 72.36000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 34.13800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.83750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 72.36000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 34.13800 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 40.83750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 72.36000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 34.13800 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 40.83750 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 72.36000 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 300 REMARK: THE LIGHT SCATTERING DATA OF THIS CONSTRUCT WITHOUT C-TAG REMARK 300 SHOWS MAINLY MONOMERIC PROTEIN IN THE SOLUTION, WHILE THE SAME REMARK 300 CONSTRUCT WITH C-TAG APPEARS TO HAVE POPULATION OF MONOMER AND REMARK 300 TETRAMERIC SPECIES. CONSISTENT WITH THE LATTER OBSERVATION, THE REMARK 300 CRYSTAL STRUCTURE REVEALS THAT A FEW RESIDUES OF THE C-TAG PLAY AN REMARK 300 IMPORTANT ROLE IN PROTEIN TETRAMERIZATION, WHICH IS POSSIBLY NOT A REMARK 300 PHYSIOLOGICAL PHENOMENON 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 57380 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 68.27600 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 81.67500 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 68.27600 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 81.67500 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 81.67500 REMARK 350 BIOMT3 2 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 ALA A 25 REMARK 465 LYS A 26 REMARK 465 HIS A 27 REMARK 465 ASP A 157 REMARK 465 TRP A 158 REMARK 465 THR A 159 REMARK 465 GLU A 160 REMARK 465 ASP A 161 REMARK 465 THR A 162 REMARK 465 ASP A 163 REMARK 465 ASN A 164 REMARK 465 GLN A 165 REMARK 465 ASN A 166 REMARK 465 SER A 167 REMARK 465 GLN A 168 REMARK 465 LYS A 169 REMARK 465 SER A 170 REMARK 465 LEU A 171 REMARK 465 LYS A 172 REMARK 465 HIS A 173 REMARK 465 GLU A 182 REMARK 465 PHE A 183 REMARK 465 HIS A 184 REMARK 465 TYR A 185 REMARK 465 GLU A 186 REMARK 465 ASN A 187 REMARK 465 ASN A 188 REMARK 465 ASN A 189 REMARK 465 VAL A 190 REMARK 465 ASP A 191 REMARK 465 SER A 307 REMARK 465 LEU A 308 REMARK 465 GLY A 361 REMARK 465 LEU A 362 REMARK 465 GLU A 363 REMARK 465 HIS A 364 REMARK 465 HIS A 365 REMARK 465 HIS A 366 REMARK 465 HIS A 367 REMARK 465 HIS A 368 REMARK 465 HIS A 369 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 LEU A 29 -17.97 -46.33 REMARK 500 LEU A 30 -1.75 -166.96 REMARK 500 LYS A 214 -80.95 -75.28 REMARK 500 ASP A 222 -2.77 -153.34 REMARK 500 PRO A 231 91.93 -41.88 REMARK 500 ALA A 244 -81.94 -106.39 REMARK 500 GLU A 246 -169.15 -54.35 REMARK 500 ASP A 247 -77.32 -69.27 REMARK 500 ARG A 297 166.64 172.33 REMARK 500 ALA A 304 33.46 -75.55 REMARK 500 SER A 305 -121.39 -134.58 REMARK 500 ASN A 342 41.73 -145.05 REMARK 500 CYS A 343 -173.74 -58.46 REMARK 500 ASN A 356 117.31 -169.18 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 MN A 402 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 238 NE2 REMARK 620 2 ASP A 240 OD2 86.7 REMARK 620 3 HIS A 292 NE2 101.9 100.2 REMARK 620 4 AKG A 403 O2 82.5 107.0 152.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 242 ND1 REMARK 620 2 CYS A 341 SG 145.8 REMARK 620 3 CYS A 343 SG 107.2 86.0 REMARK 620 4 CYS A 349 SG 96.5 109.0 109.2 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 ZN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKG A 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HR5601B RELATED DB: TARGETDB REMARK 900 RELATED ID: 3THT RELATED DB: PDB DBREF 3THP A 25 355 UNP Q96BT7 ALKB8_HUMAN 25 355 SEQADV 3THP ASN A 356 UNP Q96BT7 EXPRESSION TAG SEQADV 3THP LEU A 357 UNP Q96BT7 EXPRESSION TAG SEQADV 3THP TYR A 358 UNP Q96BT7 EXPRESSION TAG SEQADV 3THP PHE A 359 UNP Q96BT7 EXPRESSION TAG SEQADV 3THP GLN A 360 UNP Q96BT7 EXPRESSION TAG SEQADV 3THP GLY A 361 UNP Q96BT7 EXPRESSION TAG SEQADV 3THP LEU A 362 UNP Q96BT7 EXPRESSION TAG SEQADV 3THP GLU A 363 UNP Q96BT7 EXPRESSION TAG SEQADV 3THP HIS A 364 UNP Q96BT7 EXPRESSION TAG SEQADV 3THP HIS A 365 UNP Q96BT7 EXPRESSION TAG SEQADV 3THP HIS A 366 UNP Q96BT7 EXPRESSION TAG SEQADV 3THP HIS A 367 UNP Q96BT7 EXPRESSION TAG SEQADV 3THP HIS A 368 UNP Q96BT7 EXPRESSION TAG SEQADV 3THP HIS A 369 UNP Q96BT7 EXPRESSION TAG SEQRES 1 A 345 ALA LYS HIS THR LEU LEU ARG HIS GLU GLY ILE GLU THR SEQRES 2 A 345 VAL SER TYR ALA THR GLN SER LEU VAL VAL ALA ASN GLY SEQRES 3 A 345 GLY LEU GLY ASN GLY VAL SER ARG ASN GLN LEU LEU PRO SEQRES 4 A 345 VAL LEU GLU LYS CYS GLY LEU VAL ASP ALA LEU LEU MSE SEQRES 5 A 345 PRO PRO ASN LYS PRO TYR SER PHE ALA ARG TYR ARG THR SEQRES 6 A 345 THR GLU GLU SER LYS ARG ALA TYR VAL THR LEU ASN GLY SEQRES 7 A 345 LYS GLU VAL VAL ASP ASP LEU GLY GLN LYS ILE THR LEU SEQRES 8 A 345 TYR LEU ASN PHE VAL GLU LYS VAL GLN TRP LYS GLU LEU SEQRES 9 A 345 ARG PRO GLN ALA LEU PRO PRO GLY LEU MSE VAL VAL GLU SEQRES 10 A 345 GLU ILE ILE SER SER GLU GLU GLU LYS MSE LEU LEU GLU SEQRES 11 A 345 SER VAL ASP TRP THR GLU ASP THR ASP ASN GLN ASN SER SEQRES 12 A 345 GLN LYS SER LEU LYS HIS ARG ARG VAL LYS HIS PHE GLY SEQRES 13 A 345 TYR GLU PHE HIS TYR GLU ASN ASN ASN VAL ASP LYS ASP SEQRES 14 A 345 LYS PRO LEU SER GLY GLY LEU PRO ASP ILE CYS GLU SER SEQRES 15 A 345 PHE LEU GLU LYS TRP LEU ARG LYS GLY TYR ILE LYS HIS SEQRES 16 A 345 LYS PRO ASP GLN MSE THR ILE ASN GLN TYR GLU PRO GLY SEQRES 17 A 345 GLN GLY ILE PRO ALA HIS ILE ASP THR HIS SER ALA PHE SEQRES 18 A 345 GLU ASP GLU ILE VAL SER LEU SER LEU GLY SER GLU ILE SEQRES 19 A 345 VAL MSE ASP PHE LYS HIS PRO ASP GLY ILE ALA VAL PRO SEQRES 20 A 345 VAL MSE LEU PRO ARG ARG SER LEU LEU VAL MSE THR GLY SEQRES 21 A 345 GLU SER ARG TYR LEU TRP THR HIS GLY ILE THR CYS ARG SEQRES 22 A 345 LYS PHE ASP THR VAL GLN ALA SER GLU SER LEU LYS SER SEQRES 23 A 345 GLY ILE ILE THR SER ASP VAL GLY ASP LEU THR LEU SER SEQRES 24 A 345 LYS ARG GLY LEU ARG THR SER PHE THR PHE ARG LYS VAL SEQRES 25 A 345 ARG GLN THR PRO CYS ASN CYS SER TYR PRO LEU VAL CYS SEQRES 26 A 345 ASP SER GLN ARG LYS GLU ASN LEU TYR PHE GLN GLY LEU SEQRES 27 A 345 GLU HIS HIS HIS HIS HIS HIS MODRES 3THP MSE A 76 MET SELENOMETHIONINE MODRES 3THP MSE A 138 MET SELENOMETHIONINE MODRES 3THP MSE A 151 MET SELENOMETHIONINE MODRES 3THP MSE A 224 MET SELENOMETHIONINE MODRES 3THP MSE A 260 MET SELENOMETHIONINE MODRES 3THP MSE A 273 MET SELENOMETHIONINE MODRES 3THP MSE A 282 MET SELENOMETHIONINE HET MSE A 76 8 HET MSE A 138 8 HET MSE A 151 8 HET MSE A 224 8 HET MSE A 260 8 HET MSE A 273 8 HET MSE A 282 8 HET ZN A 401 1 HET MN A 402 1 HET AKG A 403 10 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION HETNAM MN MANGANESE (II) ION HETNAM AKG 2-OXOGLUTARIC ACID FORMUL 1 MSE 7(C5 H11 N O2 SE) FORMUL 2 ZN ZN 2+ FORMUL 3 MN MN 2+ FORMUL 4 AKG C5 H6 O5 HELIX 1 1 GLY A 51 GLY A 55 5 5 HELIX 2 2 SER A 57 GLU A 66 1 10 HELIX 3 3 THR A 89 LEU A 100 1 12 HELIX 4 4 SER A 145 GLU A 154 1 10 HELIX 5 5 PRO A 201 GLY A 215 1 15 HELIX 6 6 GLY A 284 LEU A 289 1 6 HELIX 7 7 TYR A 345 CYS A 349 5 5 SHEET 1 A 3 VAL A 47 ALA A 48 0 SHEET 2 A 3 TYR A 82 TYR A 87 -1 O SER A 83 N VAL A 47 SHEET 3 A 3 VAL A 71 LEU A 75 -1 N LEU A 75 O PHE A 84 SHEET 1 B 2 GLU A 104 VAL A 106 0 SHEET 2 B 2 LYS A 112 THR A 114 -1 O ILE A 113 N VAL A 105 SHEET 1 C 6 LEU A 137 VAL A 140 0 SHEET 2 C 6 SER A 278 MSE A 282 -1 O LEU A 279 N VAL A 140 SHEET 3 C 6 ILE A 249 LEU A 254 -1 N SER A 251 O LEU A 280 SHEET 4 C 6 ARG A 328 ARG A 334 -1 O THR A 329 N LEU A 254 SHEET 5 C 6 GLN A 223 TYR A 229 -1 N TYR A 229 O ARG A 328 SHEET 6 C 6 ARG A 175 PHE A 179 -1 N LYS A 177 O ILE A 226 SHEET 1 D 2 ILE A 258 LYS A 263 0 SHEET 2 D 2 ALA A 269 LEU A 274 -1 O VAL A 270 N PHE A 262 SHEET 1 E 2 PHE A 299 GLN A 303 0 SHEET 2 E 2 LEU A 320 LYS A 324 -1 O THR A 321 N VAL A 302 LINK C LEU A 75 N MSE A 76 1555 1555 1.33 LINK C MSE A 76 N PRO A 77 1555 1555 1.34 LINK C LEU A 137 N MSE A 138 1555 1555 1.33 LINK C MSE A 138 N VAL A 139 1555 1555 1.33 LINK C LYS A 150 N MSE A 151 1555 1555 1.33 LINK C MSE A 151 N LEU A 152 1555 1555 1.33 LINK C GLN A 223 N MSE A 224 1555 1555 1.33 LINK C MSE A 224 N THR A 225 1555 1555 1.34 LINK C VAL A 259 N MSE A 260 1555 1555 1.33 LINK C MSE A 260 N ASP A 261 1555 1555 1.33 LINK C VAL A 272 N MSE A 273 1555 1555 1.33 LINK C MSE A 273 N LEU A 274 1555 1555 1.33 LINK C VAL A 281 N MSE A 282 1555 1555 1.33 LINK C MSE A 282 N THR A 283 1555 1555 1.33 LINK NE2 HIS A 238 MN MN A 402 1555 1555 2.34 LINK OD2 ASP A 240 MN MN A 402 1555 1555 2.38 LINK ND1 HIS A 242 ZN ZN A 401 1555 1555 2.41 LINK NE2 HIS A 292 MN MN A 402 1555 1555 2.56 LINK SG CYS A 341 ZN ZN A 401 1555 1555 2.45 LINK SG CYS A 343 ZN ZN A 401 1555 1555 2.29 LINK SG CYS A 349 ZN ZN A 401 1555 1555 2.56 LINK MN MN A 402 O2 AKG A 403 1555 1555 2.41 SITE 1 AC1 4 HIS A 242 CYS A 341 CYS A 343 CYS A 349 SITE 1 AC2 4 HIS A 238 ASP A 240 HIS A 292 AKG A 403 SITE 1 AC3 11 ASN A 227 TYR A 229 HIS A 238 SER A 251 SITE 2 AC3 11 MSE A 260 HIS A 292 ARG A 328 SER A 330 SITE 3 AC3 11 THR A 332 ARG A 334 MN A 402 CRYST1 68.276 81.675 144.720 90.00 90.00 90.00 I 2 2 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 0.014646 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012244 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006910 0.00000