HEADER OXIDOREDUCTASE 09-JAN-14 4OCT TITLE CRYSTAL STRUCTURE OF HUMAN ALKBH5 CRYSTALLIZED IN THE PRESENCE OF TITLE 2 MN^{2+} AND 2-OXOGLUTARATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA DEMETHYLASE ALKBH5; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 74-294; COMPND 5 SYNONYM: ALKYLATED DNA REPAIR PROTEIN ALKB HOMOLOG 5, ALPHA- COMPND 6 KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB HOMOLOG 5; COMPND 7 EC: 1.14.11.-; COMPND 8 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: ALKBH5, ABH5, OFOXD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-V2R-PRARE2; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28-MHL KEYWDS STRUCTURAL GENOMICS, STRUCTURAL GENOMICS CONSORTIUM, SGC, RNA KEYWDS 2 DEMETHYLASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR W.TEMPEL,X.CHAO,K.LIU,A.DONG,T.CEROVINA,H.HE,C.BOUNTRA, AUTHOR 2 C.H.ARROWSMITH,A.M.EDWARDS,J.MIN,STRUCTURAL GENOMICS CONSORTIUM AUTHOR 3 (SGC) REVDAT 4 20-SEP-23 4OCT 1 REMARK SEQADV LINK REVDAT 3 24-DEC-14 4OCT 1 JRNL REVDAT 2 04-JUN-14 4OCT 1 JRNL REVDAT 1 16-APR-14 4OCT 0 JRNL AUTH C.XU,K.LIU,W.TEMPEL,M.DEMETRIADES,W.AIK,C.J.SCHOFIELD,J.MIN JRNL TITL STRUCTURES OF HUMAN ALKBH5 DEMETHYLASE REVEAL A UNIQUE JRNL TITL 2 BINDING MODE FOR SPECIFIC SINGLE-STRANDED N6-METHYLADENOSINE JRNL TITL 3 RNA DEMETHYLATION. JRNL REF J.BIOL.CHEM. V. 289 17299 2014 JRNL REFN ISSN 0021-9258 JRNL PMID 24778178 JRNL DOI 10.1074/JBC.M114.550350 REMARK 2 REMARK 2 RESOLUTION. 2.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 18790 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : THIN SHELLS (SFTOOLS) REMARK 3 R VALUE (WORKING + TEST SET) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 934 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.28 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1326 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3010 REMARK 3 BIN FREE R VALUE SET COUNT : 53 REMARK 3 BIN FREE R VALUE : 0.3770 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3248 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 23 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 45.22 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.05000 REMARK 3 B22 (A**2) : 1.87000 REMARK 3 B33 (A**2) : -0.15000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.85000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.472 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.285 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.305 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 27.978 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.934 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.910 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3360 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3154 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4547 ; 1.401 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7239 ; 0.878 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 418 ; 6.479 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 151 ;27.915 ;23.113 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 541 ;14.775 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 29 ;18.784 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 505 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3795 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 758 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1677 ; 0.935 ; 1.232 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1676 ; 0.935 ; 1.232 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2091 ; 1.559 ; 1.842 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 77 293 B 77 293 12076 0.080 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 77 A 502 REMARK 3 ORIGIN FOR THE GROUP (A): 16.1047 5.0288 6.1494 REMARK 3 T TENSOR REMARK 3 T11: 0.4033 T22: 0.4219 REMARK 3 T33: 0.0608 T12: 0.0092 REMARK 3 T13: -0.1343 T23: 0.0338 REMARK 3 L TENSOR REMARK 3 L11: 0.8112 L22: 3.0783 REMARK 3 L33: 3.1389 L12: 0.0409 REMARK 3 L13: 1.0722 L23: 0.5869 REMARK 3 S TENSOR REMARK 3 S11: 0.0197 S12: -0.1553 S13: -0.0739 REMARK 3 S21: -0.2635 S22: 0.0206 S23: -0.0275 REMARK 3 S31: 0.0127 S32: -0.3809 S33: -0.0402 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 76 B 502 REMARK 3 ORIGIN FOR THE GROUP (A): 29.5905 0.6668 39.3732 REMARK 3 T TENSOR REMARK 3 T11: 0.3904 T22: 0.4360 REMARK 3 T33: 0.0645 T12: 0.0077 REMARK 3 T13: -0.1357 T23: 0.0061 REMARK 3 L TENSOR REMARK 3 L11: 1.6238 L22: 3.2358 REMARK 3 L33: 1.3874 L12: 0.5611 REMARK 3 L13: 1.0438 L23: 0.3652 REMARK 3 S TENSOR REMARK 3 S11: -0.0484 S12: -0.0980 S13: 0.0648 REMARK 3 S21: 0.1802 S22: 0.0838 S23: -0.1413 REMARK 3 S31: -0.0495 S32: 0.1132 S33: -0.0354 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: PDB ENTRY 2IUW AIDED IN THE REMARK 3 INTERPRETATION OF THE MANGANESE CATION BINDING SITE. COOT WAS REMARK 3 USED FOR INTERACTIVE MODEL ADJUSTMENTS. MOLPROBITY WAS USED FOR REMARK 3 VALIDATION OF MODEL GEOMETRY. REMARK 4 REMARK 4 4OCT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000084330. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 FR-E REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.2.14 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18808 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.280 REMARK 200 RESOLUTION RANGE LOW (A) : 38.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.300 REMARK 200 R MERGE (I) : 0.12700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.36 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.10 REMARK 200 R MERGE FOR SHELL (I) : 0.01100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: DIRECT PLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: RELATED TO PDB ENTRY 4O61 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.005 M OF EACH MANGANOUS SULFATE AND REMARK 280 2-OXYGLUTARATE WERE ADDED TO THE PROTEIN STOCK SOLUTION. REMARK 280 RESERVOIR: 20% PEG-3350, 0.2 M DIAMMONIUM PHOSPHATE, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 28.61700 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 73 REMARK 465 GLN A 74 REMARK 465 GLN A 75 REMARK 465 LEU A 76 REMARK 465 TYR A 141 REMARK 465 GLY A 142 REMARK 465 ALA A 143 REMARK 465 GLN A 144 REMARK 465 LEU A 145 REMARK 465 GLN A 146 REMARK 465 LYS A 147 REMARK 465 THR A 294 REMARK 465 GLY B 73 REMARK 465 GLN B 74 REMARK 465 GLN B 75 REMARK 465 TYR B 141 REMARK 465 GLY B 142 REMARK 465 ALA B 143 REMARK 465 GLN B 144 REMARK 465 LEU B 145 REMARK 465 GLN B 146 REMARK 465 LYS B 147 REMARK 465 ARG B 148 REMARK 465 THR B 294 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 GLN A 77 CG CD OE1 NE2 REMARK 470 LYS A 78 CG CD CE NZ REMARK 470 GLU A 79 CG CD OE1 OE2 REMARK 470 GLU A 80 CG CD OE1 OE2 REMARK 470 LYS A 84 CE NZ REMARK 470 LYS A 86 NZ REMARK 470 ARG A 93 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 97 CG CD OE1 NE2 REMARK 470 LYS A 102 NZ REMARK 470 THR A 140 OG1 CG2 REMARK 470 ARG A 148 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 180 NE CZ NH1 NH2 REMARK 470 LYS A 231 CE NZ REMARK 470 ARG A 238 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 241 OE1 OE2 REMARK 470 ARG A 249 CD NE CZ NH1 NH2 REMARK 470 GLU A 263 CD OE1 OE2 REMARK 470 LYS A 274 CD CE NZ REMARK 470 ASP A 288 OD1 OD2 REMARK 470 ARG A 291 NE CZ NH1 NH2 REMARK 470 GLU A 293 CA C O CB CG CD OE1 REMARK 470 GLU A 293 OE2 REMARK 470 LEU B 76 CG CD1 CD2 REMARK 470 GLN B 77 CG CD OE1 NE2 REMARK 470 LYS B 78 CG CD CE NZ REMARK 470 GLU B 80 CD OE1 OE2 REMARK 470 ARG B 83 NE CZ NH1 NH2 REMARK 470 LYS B 84 NZ REMARK 470 LYS B 86 CD CE NZ REMARK 470 ARG B 93 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 102 CE NZ REMARK 470 ARG B 180 NE CZ NH1 NH2 REMARK 470 LYS B 231 CE NZ REMARK 470 LYS B 235 NZ REMARK 470 ILE B 237 CG1 CG2 CD1 REMARK 470 ARG B 238 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 274 CE NZ REMARK 470 GLU B 293 CG CD OE1 OE2 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 PHE A 221 -46.58 68.57 REMARK 500 SER A 224 -154.93 -161.16 REMARK 500 LYS A 235 65.06 -116.90 REMARK 500 PHE B 221 -45.20 67.50 REMARK 500 SER B 224 -155.36 -160.75 REMARK 500 LYS B 235 64.65 -116.33 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 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 204 NE2 REMARK 620 2 ASP A 206 OD1 99.9 REMARK 620 3 HIS A 266 NE2 84.2 106.1 REMARK 620 4 AKG A 502 O5 94.7 163.8 82.4 REMARK 620 5 AKG A 502 O1 100.5 81.5 170.5 88.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 501 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 204 NE2 REMARK 620 2 ASP B 206 OD1 99.7 REMARK 620 3 HIS B 266 NE2 85.9 107.0 REMARK 620 4 AKG B 502 O1 107.4 78.8 164.7 REMARK 620 5 AKG B 502 O5 88.9 165.3 85.3 87.3 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKG B 502 DBREF 4OCT A 74 294 UNP Q6P6C2 ALKB5_HUMAN 74 294 DBREF 4OCT B 74 294 UNP Q6P6C2 ALKB5_HUMAN 74 294 SEQADV 4OCT GLY A 73 UNP Q6P6C2 EXPRESSION TAG SEQADV 4OCT GLY B 73 UNP Q6P6C2 EXPRESSION TAG SEQRES 1 A 222 GLY GLN GLN LEU GLN LYS GLU GLU GLU ALA ARG LYS VAL SEQRES 2 A 222 LYS SER GLY ILE ARG GLN MET ARG LEU PHE SER GLN ASP SEQRES 3 A 222 GLU CYS ALA LYS ILE GLU ALA ARG ILE ASP GLU VAL VAL SEQRES 4 A 222 SER ARG ALA GLU LYS GLY LEU TYR ASN GLU HIS THR VAL SEQRES 5 A 222 ASP ARG ALA PRO LEU ARG ASN LYS TYR PHE PHE GLY GLU SEQRES 6 A 222 GLY TYR THR TYR GLY ALA GLN LEU GLN LYS ARG GLY PRO SEQRES 7 A 222 GLY GLN GLU ARG LEU TYR PRO PRO GLY ASP VAL ASP GLU SEQRES 8 A 222 ILE PRO GLU TRP VAL HIS GLN LEU VAL ILE GLN LYS LEU SEQRES 9 A 222 VAL GLU HIS ARG VAL ILE PRO GLU GLY PHE VAL ASN SER SEQRES 10 A 222 ALA VAL ILE ASN ASP TYR GLN PRO GLY GLY CYS ILE VAL SEQRES 11 A 222 SER HIS VAL ASP PRO ILE HIS ILE PHE GLU ARG PRO ILE SEQRES 12 A 222 VAL SER VAL SER PHE PHE SER ASP SER ALA LEU CYS PHE SEQRES 13 A 222 GLY CYS LYS PHE GLN PHE LYS PRO ILE ARG VAL SER GLU SEQRES 14 A 222 PRO VAL LEU SER LEU PRO VAL ARG ARG GLY SER VAL THR SEQRES 15 A 222 VAL LEU SER GLY TYR ALA ALA ASP GLU ILE THR HIS CYS SEQRES 16 A 222 ILE ARG PRO GLN ASP ILE LYS GLU ARG ARG ALA VAL ILE SEQRES 17 A 222 ILE LEU ARG LYS THR ARG LEU ASP ALA PRO ARG LEU GLU SEQRES 18 A 222 THR SEQRES 1 B 222 GLY GLN GLN LEU GLN LYS GLU GLU GLU ALA ARG LYS VAL SEQRES 2 B 222 LYS SER GLY ILE ARG GLN MET ARG LEU PHE SER GLN ASP SEQRES 3 B 222 GLU CYS ALA LYS ILE GLU ALA ARG ILE ASP GLU VAL VAL SEQRES 4 B 222 SER ARG ALA GLU LYS GLY LEU TYR ASN GLU HIS THR VAL SEQRES 5 B 222 ASP ARG ALA PRO LEU ARG ASN LYS TYR PHE PHE GLY GLU SEQRES 6 B 222 GLY TYR THR TYR GLY ALA GLN LEU GLN LYS ARG GLY PRO SEQRES 7 B 222 GLY GLN GLU ARG LEU TYR PRO PRO GLY ASP VAL ASP GLU SEQRES 8 B 222 ILE PRO GLU TRP VAL HIS GLN LEU VAL ILE GLN LYS LEU SEQRES 9 B 222 VAL GLU HIS ARG VAL ILE PRO GLU GLY PHE VAL ASN SER SEQRES 10 B 222 ALA VAL ILE ASN ASP TYR GLN PRO GLY GLY CYS ILE VAL SEQRES 11 B 222 SER HIS VAL ASP PRO ILE HIS ILE PHE GLU ARG PRO ILE SEQRES 12 B 222 VAL SER VAL SER PHE PHE SER ASP SER ALA LEU CYS PHE SEQRES 13 B 222 GLY CYS LYS PHE GLN PHE LYS PRO ILE ARG VAL SER GLU SEQRES 14 B 222 PRO VAL LEU SER LEU PRO VAL ARG ARG GLY SER VAL THR SEQRES 15 B 222 VAL LEU SER GLY TYR ALA ALA ASP GLU ILE THR HIS CYS SEQRES 16 B 222 ILE ARG PRO GLN ASP ILE LYS GLU ARG ARG ALA VAL ILE SEQRES 17 B 222 ILE LEU ARG LYS THR ARG LEU ASP ALA PRO ARG LEU GLU SEQRES 18 B 222 THR HET MN A 501 1 HET AKG A 502 10 HET UNX A 503 1 HET UNX A 504 1 HET UNX A 505 1 HET UNX A 506 1 HET UNX A 507 1 HET UNX A 508 1 HET UNX A 509 1 HET UNX A 510 1 HET UNX A 511 1 HET MN B 501 1 HET AKG B 502 10 HET UNX B 503 1 HET UNX B 504 1 HET UNX B 505 1 HET UNX B 506 1 HET UNX B 507 1 HET UNX B 508 1 HET UNX B 509 1 HET UNX B 510 1 HET UNX B 511 1 HET UNX B 512 1 HET UNX B 513 1 HET UNX B 514 1 HET UNX B 515 1 HET UNX B 516 1 HETNAM MN MANGANESE (II) ION HETNAM AKG 2-OXOGLUTARIC ACID HETNAM UNX UNKNOWN ATOM OR ION FORMUL 3 MN 2(MN 2+) FORMUL 4 AKG 2(C5 H6 O5) FORMUL 5 UNX 23(X) FORMUL 30 HOH *23(H2 O) HELIX 1 1 GLN A 77 GLY A 88 1 12 HELIX 2 2 SER A 96 LYS A 116 1 21 HELIX 3 3 ASN A 120 HIS A 122 5 3 HELIX 4 4 PRO A 165 VAL A 172 1 8 HELIX 5 5 VAL A 172 HIS A 179 1 8 HELIX 6 6 CYS A 230 PHE A 234 5 5 HELIX 7 7 GLY A 258 GLU A 263 1 6 HELIX 8 8 ARG A 269 ILE A 273 5 5 HELIX 9 9 GLN B 77 GLY B 88 1 12 HELIX 10 10 SER B 96 LYS B 116 1 21 HELIX 11 11 ASN B 120 HIS B 122 5 3 HELIX 12 12 PRO B 165 VAL B 172 1 8 HELIX 13 13 VAL B 172 HIS B 179 1 8 HELIX 14 14 CYS B 230 PHE B 234 5 5 HELIX 15 15 GLY B 258 GLU B 263 1 6 HELIX 16 16 ARG B 269 ILE B 273 5 5 SHEET 1 A 7 ILE A 89 ARG A 93 0 SHEET 2 A 7 SER A 252 LEU A 256 -1 O VAL A 255 N ARG A 90 SHEET 3 A 7 ILE A 215 PHE A 220 -1 N SER A 217 O THR A 254 SHEET 4 A 7 ARG A 277 ARG A 283 -1 O ALA A 278 N PHE A 220 SHEET 5 A 7 SER A 189 TYR A 195 -1 N TYR A 195 O ARG A 277 SHEET 6 A 7 ARG A 130 PHE A 135 -1 N ASN A 131 O ASP A 194 SHEET 7 A 7 VAL A 124 ALA A 127 -1 N ASP A 125 O LYS A 132 SHEET 1 B 4 ILE A 201 HIS A 204 0 SHEET 2 B 4 HIS A 266 ILE A 268 -1 O HIS A 266 N HIS A 204 SHEET 3 B 4 SER A 224 PHE A 228 -1 N CYS A 227 O CYS A 267 SHEET 4 B 4 LEU A 244 VAL A 248 -1 O LEU A 244 N PHE A 228 SHEET 1 C 7 ILE B 89 ARG B 93 0 SHEET 2 C 7 SER B 252 LEU B 256 -1 O VAL B 255 N ARG B 90 SHEET 3 C 7 ILE B 215 PHE B 220 -1 N SER B 217 O THR B 254 SHEET 4 C 7 ARG B 277 ARG B 283 -1 O ALA B 278 N PHE B 220 SHEET 5 C 7 SER B 189 TYR B 195 -1 N TYR B 195 O ARG B 277 SHEET 6 C 7 ARG B 130 PHE B 135 -1 N ASN B 131 O ASP B 194 SHEET 7 C 7 VAL B 124 ALA B 127 -1 N ASP B 125 O LYS B 132 SHEET 1 D 4 ILE B 201 HIS B 204 0 SHEET 2 D 4 HIS B 266 ILE B 268 -1 O HIS B 266 N HIS B 204 SHEET 3 D 4 SER B 224 PHE B 228 -1 N CYS B 227 O CYS B 267 SHEET 4 D 4 LEU B 244 VAL B 248 -1 O LEU B 244 N PHE B 228 SSBOND 1 CYS A 230 CYS A 267 1555 1555 2.09 SSBOND 2 CYS B 230 CYS B 267 1555 1555 2.08 LINK NE2 HIS A 204 MN MN A 501 1555 1555 2.06 LINK OD1 ASP A 206 MN MN A 501 1555 1555 1.91 LINK NE2 HIS A 266 MN MN A 501 1555 1555 2.05 LINK MN MN A 501 O5 AKG A 502 1555 1555 1.91 LINK MN MN A 501 O1 AKG A 502 1555 1555 1.92 LINK NE2 HIS B 204 MN MN B 501 1555 1555 2.06 LINK OD1 ASP B 206 MN MN B 501 1555 1555 1.90 LINK NE2 HIS B 266 MN MN B 501 1555 1555 2.07 LINK MN MN B 501 O1 AKG B 502 1555 1555 1.92 LINK MN MN B 501 O5 AKG B 502 1555 1555 1.93 CISPEP 1 ARG A 213 PRO A 214 0 6.55 CISPEP 2 ARG B 213 PRO B 214 0 5.37 SITE 1 AC1 4 HIS A 204 ASP A 206 HIS A 266 AKG A 502 SITE 1 AC2 10 ASN A 193 TYR A 195 HIS A 204 ASP A 206 SITE 2 AC2 10 HIS A 266 ILE A 268 ARG A 277 VAL A 279 SITE 3 AC2 10 ILE A 281 MN A 501 SITE 1 AC3 4 HIS B 204 ASP B 206 HIS B 266 AKG B 502 SITE 1 AC4 11 ASN B 193 TYR B 195 HIS B 204 ASP B 206 SITE 2 AC4 11 HIS B 266 ILE B 268 ARG B 277 VAL B 279 SITE 3 AC4 11 ILE B 281 ARG B 283 MN B 501 CRYST1 46.930 57.234 78.407 90.00 101.07 90.00 P 1 21 1 4 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 0.021309 0.000000 0.004170 0.00000 SCALE2 0.000000 0.017472 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012996 0.00000