HEADER OXIDOREDUCTASE/DNA 29-APR-09 3H8R TITLE STRUCTURE DETERMINATION OF DNA METHYLATION LESIONS N1-MEA AND N3-MEC TITLE 2 IN DUPLEX DNA USING A CROSS-LINKED HOST-GUEST SYSTEM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-KETOGLUTARATE-DEPENDENT DIOXYGENASE ALKB HOMOLOG 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TRUNCATION WITH N-TERMINAL 55 AMINO ACID DELETED; 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*AP*TP*(2YR)P*AP*TP*(6MA)P*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*TP*AP*TP*AP*AP*TP*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: ABH2, ALKB HUMAN HOMOLOG 2(ABH2), ALKBH2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 18 ORGANISM_TAXID: 32630 KEYWDS PROTEIN-DNA COMPLEX, DIOXYGENASE, DNA DAMAGE, DNA REPAIR, IRON, KEYWDS 2 METAL-BINDING, NUCLEUS, OXIDOREDUCTASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR L.LU,C.YI,X.JIAN,G.ZHENG,C.HE REVDAT 7 20-NOV-24 3H8R 1 REMARK REVDAT 6 13-OCT-21 3H8R 1 REMARK SEQADV LINK REVDAT 5 24-JAN-18 3H8R 1 AUTHOR REVDAT 4 04-JUN-14 3H8R 1 ATOM COMPND FORMUL HET REVDAT 4 2 1 HETATM HETNAM LINK REMARK REVDAT 4 3 1 SEQRES SITE SOURCE REVDAT 3 13-JUL-11 3H8R 1 VERSN REVDAT 2 11-AUG-10 3H8R 1 JRNL REVDAT 1 31-MAR-10 3H8R 0 JRNL AUTH L.LU,C.YI,X.JIAN,G.ZHENG,C.HE JRNL TITL STRUCTURE DETERMINATION OF DNA METHYLATION LESIONS N1-MEA JRNL TITL 2 AND N3-MEC IN DUPLEX DNA USING A CROSS-LINKED PROTEIN-DNA JRNL TITL 3 SYSTEM. JRNL REF NUCLEIC ACIDS RES. V. 38 4415 2010 JRNL REFN ISSN 0305-1048 JRNL PMID 20223766 JRNL DOI 10.1093/NAR/GKQ129 REMARK 2 REMARK 2 RESOLUTION. 1.77 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0088 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) : 1.77 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 38371 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) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1993 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) : 1.77 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2180 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3480 REMARK 3 BIN FREE R VALUE SET COUNT : 118 REMARK 3 BIN FREE R VALUE : 0.3650 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1640 REMARK 3 NUCLEIC ACID ATOMS : 528 REMARK 3 HETEROGEN ATOMS : 14 REMARK 3 SOLVENT ATOMS : 218 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.55000 REMARK 3 B22 (A**2) : 0.55000 REMARK 3 B33 (A**2) : -0.83000 REMARK 3 B12 (A**2) : 0.28000 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): 0.110 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.106 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.079 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.760 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2303 ; 0.010 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3227 ; 1.534 ; 2.244 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 207 ; 6.288 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 79 ;26.448 ;21.392 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 282 ;13.761 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;14.219 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 349 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1584 ; 0.007 ; 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): 1031 ; 0.678 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1668 ; 1.233 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1272 ; 1.724 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1558 ; 2.719 ; 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 : 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 53 A 258 REMARK 3 ORIGIN FOR THE GROUP (A): -18.2340 -26.8880 -3.6930 REMARK 3 T TENSOR REMARK 3 T11: 0.0076 T22: -0.0418 REMARK 3 T33: 0.0664 T12: 0.0212 REMARK 3 T13: -0.0471 T23: -0.0180 REMARK 3 L TENSOR REMARK 3 L11: 5.4312 L22: 1.8900 REMARK 3 L33: 1.0048 L12: 1.2366 REMARK 3 L13: -0.8538 L23: -0.4424 REMARK 3 S TENSOR REMARK 3 S11: 0.3192 S12: 0.3125 S13: -0.1147 REMARK 3 S21: -0.1313 S22: -0.0907 S23: 0.1755 REMARK 3 S31: 0.0122 S32: -0.1005 S33: -0.2285 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 259 B 271 REMARK 3 RESIDUE RANGE : C 272 C 284 REMARK 3 ORIGIN FOR THE GROUP (A): -2.4410 -10.9660 -3.7570 REMARK 3 T TENSOR REMARK 3 T11: 0.0912 T22: 0.0292 REMARK 3 T33: 0.1163 T12: -0.0106 REMARK 3 T13: 0.1053 T23: -0.0521 REMARK 3 L TENSOR REMARK 3 L11: 0.5628 L22: 0.7649 REMARK 3 L33: 0.5836 L12: 0.3840 REMARK 3 L13: 0.2947 L23: -0.2636 REMARK 3 S TENSOR REMARK 3 S11: 0.2766 S12: -0.0721 S13: 0.2189 REMARK 3 S21: -0.0043 S22: -0.1470 S23: -0.0122 REMARK 3 S31: -0.1339 S32: 0.0568 S33: -0.1296 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3H8R COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-MAY-09. REMARK 100 THE DEPOSITION ID IS D_1000052834. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-AUG-08 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : 23-ID-B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38371 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 20.30 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) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 5000, NACL, MGCL2, CACODYLATE REMARK 280 BUFFER, PH 6.5, VAPOR 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 152.47333 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 76.23667 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 114.35500 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 38.11833 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 190.59167 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 152.47333 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 76.23667 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 38.11833 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 114.35500 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 190.59167 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: 5100 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 3.0 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 53 REMARK 465 SER A 54 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 LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 DT B 260 O3' DG B 261 P -0.079 REMARK 500 REMARK 500 REMARK: NULL 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' - C4' - C3' ANGL. DEV. = -2.9 DEGREES REMARK 500 DG C 274 C3' - C2' - C1' ANGL. DEV. = -4.8 DEGREES REMARK 500 DT C 276 C4 - C5 - C7 ANGL. DEV. = 3.9 DEGREES REMARK 500 DT C 278 O4' - C4' - C3' ANGL. DEV. = 4.2 DEGREES REMARK 500 DT C 278 C1' - O4' - C4' ANGL. DEV. = -7.8 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 ARG A 110 -174.66 175.50 REMARK 500 LYS A 205 -67.55 69.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 2YR B 265 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS C 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3H8O RELATED DB: PDB REMARK 900 RELATED ID: 3H8X RELATED DB: PDB DBREF 3H8R A 56 261 UNP Q6NS38 ALKB2_HUMAN 56 261 DBREF 3H8R B 259 271 PDB 3H8R 3H8R 259 271 DBREF 3H8R C 272 284 PDB 3H8R 3H8R 272 284 SEQADV 3H8R GLY A 53 UNP Q6NS38 EXPRESSION TAG SEQADV 3H8R SER A 54 UNP Q6NS38 EXPRESSION TAG SEQADV 3H8R HIS A 55 UNP Q6NS38 EXPRESSION TAG SEQADV 3H8R SER A 67 UNP Q6NS38 CYS 67 ENGINEERED MUTATION SEQADV 3H8R SER A 165 UNP Q6NS38 CYS 165 ENGINEERED MUTATION SEQADV 3H8R CYS A 175 UNP Q6NS38 GLU 175 ENGINEERED MUTATION SEQADV 3H8R 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 GLY SEQRES 10 A 209 GLU HIS ARG ASP ASP CYS 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 DA DT 2YR DA DT 6MA DG DC DG SEQRES 1 C 13 DT DC DG DC DT DA DT DA DA DT DA DC DA MODRES 3H8R 6MA B 268 A HET 2YR B 265 22 HET 6MA B 268 22 HET GOL A 301 6 HET TRS C 301 8 HETNAM 2YR 2'-DEOXY-N-(2-SULFANYLETHYL)CYTIDINE 5'-(DIHYDROGEN HETNAM 2 2YR PHOSPHATE) HETNAM 6MA N6-METHYL-DEOXY-ADENOSINE-5'-MONOPHOSPHATE HETNAM GOL GLYCEROL HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN TRS TRIS BUFFER FORMUL 2 2YR C11 H18 N3 O7 P S FORMUL 2 6MA C11 H16 N5 O6 P FORMUL 4 GOL C3 H8 O3 FORMUL 5 TRS C4 H12 N O3 1+ FORMUL 6 HOH *218(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 ILE A 184 O MET A 226 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 LYS A 104 N VAL A 101 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 LEU A 216 N PHE A 195 LINK SG CYS A 175 S 2YR B 265 1555 1555 1.87 LINK O3' DT B 264 P 2YR B 265 1555 1555 1.59 LINK O3' 2YR B 265 P DA B 266 1555 1555 1.58 LINK O3' DT B 267 P 6MA B 268 1555 1555 1.60 LINK O3' 6MA B 268 P DG B 269 1555 1555 1.61 CISPEP 1 HIS A 228 PRO A 229 0 -3.83 SITE 1 AC1 14 VAL A 101 TYR A 122 PHE A 124 SER A 125 SITE 2 AC1 14 ILE A 168 GLY A 169 HIS A 171 CYS A 175 SITE 3 AC1 14 HOH A 403 DT B 264 DA B 266 HOH B 305 SITE 4 AC1 14 HOH B 309 HOH B 311 SITE 1 AC2 7 GLU A 77 ILE A 81 ARG A 98 ARG A 140 SITE 2 AC2 7 HOH A 425 HOH A 459 HOH A 468 SITE 1 AC3 7 6MA B 268 DG B 269 HOH B 312 DA C 277 SITE 2 AC3 7 DT C 278 HOH C 416 HOH C 430 CRYST1 78.080 78.080 228.710 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 0.012807 0.007394 0.000000 0.00000 SCALE2 0.000000 0.014789 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004372 0.00000