HEADER OXIDOREDUCTASE/DNA 11-MAY-11 3RZJ TITLE DUPLEX INTERROGATION BY A DIRECT DNA REPAIR PROTEIN IN THE SEARCH OF TITLE 2 DAMAGE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB HOMOLOG 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 56-261; COMPND 5 SYNONYM: ALKYLATED DNA REPAIR PROTEIN ALKB HOMOLOG 2, OXY DC1; COMPND 6 EC: 1.14.11.-; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: 5'-D(*CP*TP*GP*TP*CP*TP*(ME6)P*AP*CP*TP*GP*CP*G)-3'; COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: 5'-D(*TP*CP*GP*CP*AP*GP*TP*GP*AP*GP*AP*CP*A)-3'; COMPND 15 CHAIN: C; COMPND 16 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: ALKBH2, ABH2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 MOL_ID: 3; SOURCE 11 SYNTHETIC: YES KEYWDS PROTEIN-DNA COMPLEX, JELLY-ROLL, DEMETHYLASE, NUCLEUS, KEYWDS 2 OXIDOREDUCTASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR C.YI,B.CHEN,B.QI,W.ZHANG,G.JIA,L.ZHANG,C.LI,A.DINNER,C.YANG,C.HE REVDAT 3 01-NOV-23 3RZJ 1 REMARK SEQADV LINK REVDAT 2 03-JUL-13 3RZJ 1 JRNL REVDAT 1 06-JUN-12 3RZJ 0 JRNL AUTH C.YI,B.CHEN,B.QI,W.ZHANG,G.JIA,L.ZHANG,C.J.LI,A.R.DINNER, JRNL AUTH 2 C.G.YANG,C.HE JRNL TITL DUPLEX INTERROGATION BY A DIRECT DNA REPAIR PROTEIN IN JRNL TITL 2 SEARCH OF BASE DAMAGE JRNL REF NAT.STRUCT.MOL.BIOL. V. 19 671 2012 JRNL REFN ISSN 1545-9993 JRNL PMID 22659876 JRNL DOI 10.1038/NSMB.2320 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0110 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.200 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 14048 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 + TEST SET) : 0.229 REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 749 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.57 REMARK 3 REFLECTION IN BIN (WORKING SET) : 950 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.68 REMARK 3 BIN R VALUE (WORKING SET) : 0.3580 REMARK 3 BIN FREE R VALUE SET COUNT : 68 REMARK 3 BIN FREE R VALUE : 0.4540 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1636 REMARK 3 NUCLEIC ACID ATOMS : 526 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 44 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.09 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.07000 REMARK 3 B22 (A**2) : -1.07000 REMARK 3 B33 (A**2) : 1.61000 REMARK 3 B12 (A**2) : -0.54000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.264 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.196 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.062 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.931 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.916 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2281 ; 0.006 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3192 ; 1.112 ; 2.241 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 201 ; 5.185 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 80 ;30.152 ;21.500 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 277 ;13.184 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;15.062 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 345 ; 0.068 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1569 ; 0.003 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 1011 ; 0.434 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1632 ; 0.794 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1270 ; 0.858 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1560 ; 1.557 ; 4.500 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 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 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 55 A 258 REMARK 3 ORIGIN FOR THE GROUP (A): 18.8800 -27.1500 3.4900 REMARK 3 T TENSOR REMARK 3 T11: 0.0734 T22: 0.0579 REMARK 3 T33: 0.1820 T12: -0.0403 REMARK 3 T13: -0.0487 T23: 0.0178 REMARK 3 L TENSOR REMARK 3 L11: 4.9844 L22: 2.6122 REMARK 3 L33: 1.2497 L12: -1.4531 REMARK 3 L13: -0.3799 L23: 0.2535 REMARK 3 S TENSOR REMARK 3 S11: 0.2826 S12: -0.2496 S13: -0.0652 REMARK 3 S21: 0.1073 S22: -0.0777 S23: -0.1265 REMARK 3 S31: -0.0326 S32: 0.0611 S33: -0.2049 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 259 B 271 REMARK 3 ORIGIN FOR THE GROUP (A): 3.5400 -10.0000 3.9080 REMARK 3 T TENSOR REMARK 3 T11: 0.2977 T22: 0.3198 REMARK 3 T33: 0.2314 T12: 0.0354 REMARK 3 T13: 0.1801 T23: 0.1329 REMARK 3 L TENSOR REMARK 3 L11: 0.1597 L22: 2.3434 REMARK 3 L33: 0.1562 L12: 0.1795 REMARK 3 L13: 0.1545 L23: 0.1699 REMARK 3 S TENSOR REMARK 3 S11: 0.1174 S12: 0.0316 S13: 0.0690 REMARK 3 S21: -0.0976 S22: -0.1673 S23: -0.0750 REMARK 3 S31: 0.0675 S32: 0.0268 S33: 0.0499 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : C 272 C 284 REMARK 3 ORIGIN FOR THE GROUP (A): 2.6530 -12.2220 3.7770 REMARK 3 T TENSOR REMARK 3 T11: 0.2643 T22: 0.1185 REMARK 3 T33: 0.1808 T12: 0.0262 REMARK 3 T13: 0.1266 T23: 0.0067 REMARK 3 L TENSOR REMARK 3 L11: 3.4698 L22: 1.3993 REMARK 3 L33: 11.1847 L12: -1.0452 REMARK 3 L13: -3.7998 L23: 0.1383 REMARK 3 S TENSOR REMARK 3 S11: 0.6094 S12: 0.3066 S13: 0.4067 REMARK 3 S21: -0.0529 S22: -0.2408 S23: -0.0083 REMARK 3 S31: -0.4460 S32: -0.8319 S33: -0.3686 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3RZJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-JUN-11. REMARK 100 THE DEPOSITION ID IS D_1000065571. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-10 REMARK 200 TEMPERATURE (KELVIN) : 200.0 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL 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 : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14950 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 67.360 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: 3BTX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% PEG 5000, 0.1M SODIUM CHLORIDE, REMARK 280 0.05M MAGNESIUM CHLORIDE, 0.1M CACODYLATE, PH 6.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+1/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+5/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 152.67733 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 76.33867 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 114.50800 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 38.16933 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 190.84667 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 152.67733 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 76.33867 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 38.16933 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 114.50800 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 190.84667 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 204 REMARK 465 LYS A 205 REMARK 465 SER A 206 REMARK 465 THR A 259 REMARK 465 LYS A 260 REMARK 465 LYS A 261 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 DT B 262 O4' - C1' - N1 ANGL. DEV. = 3.3 DEGREES REMARK 500 DC B 263 O4' - C1' - N1 ANGL. DEV. = 2.6 DEGREES REMARK 500 DA B 266 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DC B 267 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT C 278 O4' - C1' - N1 ANGL. DEV. = 3.8 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 SER A 54 76.96 41.64 REMARK 500 ARG A 110 -172.65 169.49 REMARK 500 ASP A 163 -169.57 -163.71 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 1 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 171 NE2 REMARK 620 2 ASP A 173 OD2 104.3 REMARK 620 3 HIS A 236 NE2 100.0 84.5 REMARK 620 4 AKG A 262 O2 98.3 103.3 157.6 REMARK 620 5 AKG A 262 O5 95.6 159.9 95.0 70.5 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 1 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKG A 262 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE XL3 A 263 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3RZG RELATED DB: PDB REMARK 900 RELATED ID: 3RZH RELATED DB: PDB REMARK 900 RELATED ID: 3RZK RELATED DB: PDB REMARK 900 RELATED ID: 3RZL RELATED DB: PDB REMARK 900 RELATED ID: 3RZM RELATED DB: PDB DBREF 3RZJ A 56 261 UNP Q6NS38 ALKB2_HUMAN 56 261 DBREF 3RZJ B 259 271 PDB 3RZJ 3RZJ 259 271 DBREF 3RZJ C 272 284 PDB 3RZJ 3RZJ 272 284 SEQADV 3RZJ GLY A 53 UNP Q6NS38 EXPRESSION TAG SEQADV 3RZJ SER A 54 UNP Q6NS38 EXPRESSION TAG SEQADV 3RZJ HIS A 55 UNP Q6NS38 EXPRESSION TAG SEQADV 3RZJ SER A 67 UNP Q6NS38 CYS 67 ENGINEERED MUTATION SEQADV 3RZJ SER A 165 UNP Q6NS38 CYS 165 ENGINEERED MUTATION SEQADV 3RZJ CYS A 169 UNP Q6NS38 GLY 169 ENGINEERED MUTATION SEQADV 3RZJ SER A 192 UNP Q6NS38 CYS 192 ENGINEERED MUTATION SEQRES 1 A 209 GLY SER HIS SER TRP ARG HIS ILE ARG ALA GLU GLY LEU SEQRES 2 A 209 ASP SER SER TYR THR VAL LEU PHE GLY LYS ALA GLU ALA SEQRES 3 A 209 ASP GLU ILE PHE GLN GLU LEU GLU LYS GLU VAL GLU TYR SEQRES 4 A 209 PHE THR GLY ALA LEU ALA ARG VAL GLN VAL PHE GLY LYS SEQRES 5 A 209 TRP HIS SER VAL PRO ARG LYS GLN ALA THR TYR GLY ASP SEQRES 6 A 209 ALA GLY LEU THR TYR THR PHE SER GLY LEU THR LEU SER SEQRES 7 A 209 PRO LYS PRO TRP ILE PRO VAL LEU GLU ARG ILE ARG ASP SEQRES 8 A 209 HIS VAL SER GLY VAL THR GLY GLN THR PHE ASN PHE VAL SEQRES 9 A 209 LEU ILE ASN ARG TYR LYS ASP GLY SER ASP HIS ILE CYS SEQRES 10 A 209 GLU HIS ARG ASP ASP GLU ARG GLU LEU ALA PRO GLY SER SEQRES 11 A 209 PRO ILE ALA SER VAL SER PHE GLY ALA SER ARG ASP PHE SEQRES 12 A 209 VAL PHE ARG HIS LYS ASP SER ARG GLY LYS SER PRO SER SEQRES 13 A 209 ARG ARG VAL ALA VAL VAL ARG LEU PRO LEU ALA HIS GLY SEQRES 14 A 209 SER LEU LEU MET MET ASN HIS PRO THR ASN THR HIS TRP SEQRES 15 A 209 TYR HIS SER LEU PRO VAL ARG LYS LYS VAL LEU ALA PRO SEQRES 16 A 209 ARG VAL ASN LEU THR PHE ARG LYS ILE LEU LEU THR LYS SEQRES 17 A 209 LYS SEQRES 1 B 13 DC DT DG DT DC DT ME6 DA DC DT DG DC DG SEQRES 1 C 13 DT DC DG DC DA DG DT DG DA DG DA DC DA MODRES 3RZJ ME6 B 265 DC HET ME6 B 265 20 HET MN A 1 1 HET AKG A 262 10 HET XL3 A 263 4 HETNAM ME6 [(2R,3S,5R)-5-(4-AZANYL-3-METHYL-2-OXO-PYRIMIDIN-3-IUM- HETNAM 2 ME6 1-YL)-3-HYDROXY-OXOLAN-2-YL]METHYL DIHYDROGEN HETNAM 3 ME6 PHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM AKG 2-OXOGLUTARIC ACID HETNAM XL3 PROPANE-1-THIOL FORMUL 2 ME6 C10 H17 N3 O7 P 1+ FORMUL 4 MN MN 2+ FORMUL 5 AKG C5 H6 O5 FORMUL 6 XL3 C3 H8 S FORMUL 7 HOH *44(H2 O) HELIX 1 1 GLY A 74 VAL A 89 1 16 HELIX 2 2 THR A 93 LEU A 96 5 4 HELIX 3 3 ILE A 135 GLY A 150 1 16 HELIX 4 4 ASP A 201 ARG A 203 5 3 HELIX 5 5 PRO A 229 HIS A 233 1 5 SHEET 1 A 7 ARG A 58 ALA A 62 0 SHEET 2 A 7 LEU A 65 VAL A 71 -1 O SER A 67 N ILE A 60 SHEET 3 A 7 SER A 222 MET A 226 -1 O LEU A 223 N THR A 70 SHEET 4 A 7 ILE A 184 GLY A 190 -1 N SER A 186 O LEU A 224 SHEET 5 A 7 ARG A 248 ARG A 254 -1 O LEU A 251 N VAL A 187 SHEET 6 A 7 PHE A 155 TYR A 161 -1 N ASN A 159 O ASN A 250 SHEET 7 A 7 LYS A 111 GLY A 116 -1 N ALA A 113 O ILE A 158 SHEET 1 B 2 ARG A 98 VAL A 101 0 SHEET 2 B 2 LYS A 104 SER A 107 -1 O HIS A 106 N VAL A 99 SHEET 1 C 2 TYR A 122 PHE A 124 0 SHEET 2 C 2 LEU A 127 LEU A 129 -1 O LEU A 129 N TYR A 122 SHEET 1 D 4 ILE A 168 HIS A 171 0 SHEET 2 D 4 TRP A 234 LEU A 238 -1 O HIS A 236 N HIS A 171 SHEET 3 D 4 ARG A 193 HIS A 199 -1 N ARG A 198 O TYR A 235 SHEET 4 D 4 VAL A 214 LEU A 218 -1 O VAL A 214 N PHE A 197 LINK O3' DT B 264 P ME6 B 265 1555 1555 1.60 LINK O3' ME6 B 265 P DA B 266 1555 1555 1.59 LINK MN MN A 1 NE2 HIS A 171 1555 1555 2.25 LINK MN MN A 1 OD2 ASP A 173 1555 1555 2.18 LINK MN MN A 1 NE2 HIS A 236 1555 1555 2.23 LINK MN MN A 1 O2 AKG A 262 1555 1555 2.07 LINK MN MN A 1 O5 AKG A 262 1555 1555 2.44 CISPEP 1 HIS A 228 PRO A 229 0 3.05 SITE 1 AC1 4 HIS A 171 ASP A 173 HIS A 236 AKG A 262 SITE 1 AC2 12 MN A 1 LEU A 157 ASN A 159 TYR A 161 SITE 2 AC2 12 HIS A 171 ASP A 173 HIS A 236 ARG A 248 SITE 3 AC2 12 ASN A 250 THR A 252 ARG A 254 ME6 B 265 SITE 1 AC3 2 CYS A 169 DC B 267 CRYST1 77.779 77.779 229.016 90.00 90.00 120.00 P 65 2 2 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 0.012857 0.007423 0.000000 0.00000 SCALE2 0.000000 0.014846 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004367 0.00000