HEADER OXIDOREDUCTASE 13-SEP-18 6IE3 TITLE CRYSTAL STRUCTURE OF METHYLADENINE DEMETHYLASE 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,DNA LYASE ABH1,DNA OXIDATIVE DEMETHYLASE COMPND 7 ALKBH1,TRNA N1-METHYL ADENINE DEMETHYLASE; COMPND 8 EC: 1.14.11.51; COMPND 9 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: ALKBH1, ABH, ABH1, ALKBH; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS DEMETHYLASE, DNA BINDING PROTEIN, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR L.F.TIAN,Q.TANG,Z.Z.CHEN,X.X.YAN REVDAT 3 27-MAR-24 6IE3 1 REMARK REVDAT 2 08-JUL-20 6IE3 1 JRNL REVDAT 1 18-SEP-19 6IE3 0 JRNL AUTH L.F.TIAN,Y.P.LIU,L.CHEN,Q.TANG,W.WU,W.SUN,Z.CHEN,X.X.YAN JRNL TITL STRUCTURAL BASIS OF NUCLEIC ACID RECOGNITION AND 6MA JRNL TITL 2 DEMETHYLATION BY HUMAN ALKBH1. JRNL REF CELL RES. V. 30 272 2020 JRNL REFN ISSN 1001-0602 JRNL PMID 32051559 JRNL DOI 10.1038/S41422-019-0233-9 REMARK 2 REMARK 2 RESOLUTION. 1.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.13 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 86.1 REMARK 3 NUMBER OF REFLECTIONS : 20188 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.600 REMARK 3 FREE R VALUE TEST SET COUNT : 978 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) : 1.97 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 REFLECTION IN BIN (WORKING SET) : 621 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 35.72 REMARK 3 BIN R VALUE (WORKING SET) : 0.2260 REMARK 3 BIN FREE R VALUE SET COUNT : 27 REMARK 3 BIN FREE R VALUE : 0.1860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2419 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 283 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.32 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.15000 REMARK 3 B22 (A**2) : 0.15000 REMARK 3 B33 (A**2) : -0.48000 REMARK 3 B12 (A**2) : 0.07000 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): 0.230 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.180 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.118 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.163 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.929 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2502 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2233 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3396 ; 1.181 ; 1.952 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5167 ; 0.871 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 312 ; 6.011 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 110 ;33.978 ;23.182 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 384 ;13.717 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 15 ;11.970 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 357 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2813 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 546 ; 0.001 ; 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): 1251 ; 1.547 ; 3.185 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1250 ; 1.545 ; 3.184 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1559 ; 2.769 ; 4.752 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1560 ; 2.768 ; 4.753 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1251 ; 1.169 ; 3.234 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1252 ; 1.168 ; 3.235 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1837 ; 2.123 ; 4.811 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2791 ; 5.336 ;37.150 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2750 ; 5.174 ;36.734 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 6IE3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1300009008. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JAN-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97929 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24558 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.970 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 15.30 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.74600 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: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.35 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% ETHANOL, 5% MPD, 100 MM NAF, 100 MM REMARK 280 HEPESPH7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 286K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 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 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 127.79067 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 63.89533 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 95.84300 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 31.94767 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 159.73833 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 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 1 REMARK 465 GLY A 2 REMARK 465 LYS 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 GLY A 9 REMARK 465 SER A 10 REMARK 465 VAL A 11 REMARK 465 ALA A 12 REMARK 465 THR A 13 REMARK 465 LEU A 14 REMARK 465 ALA A 15 REMARK 465 THR A 16 REMARK 465 GLU A 17 REMARK 465 PRO A 18 REMARK 465 HIS A 50 REMARK 465 ALA A 51 REMARK 465 ALA A 52 REMARK 465 ARG A 53 REMARK 465 LYS A 133 REMARK 465 HIS A 134 REMARK 465 MET A 135 REMARK 465 SER A 136 REMARK 465 LYS A 137 REMARK 465 GLU A 138 REMARK 465 GLU A 139 REMARK 465 ALA 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 ALA A 348 REMARK 465 THR A 349 REMARK 465 ASP A 350 REMARK 465 GLN A 351 REMARK 465 ASN A 352 REMARK 465 PHE A 353 REMARK 465 PRO A 354 REMARK 465 LEU A 355 REMARK 465 GLU A 356 REMARK 465 PRO A 357 REMARK 465 ILE A 358 REMARK 465 GLU A 359 REMARK 465 ASP A 360 REMARK 465 GLU A 361 REMARK 465 LYS A 362 REMARK 465 ARG A 363 REMARK 465 ASP A 364 REMARK 465 ILE A 365 REMARK 465 SER A 366 REMARK 465 THR A 367 REMARK 465 GLU A 368 REMARK 465 GLY A 369 REMARK 465 PHE A 370 REMARK 465 CYS A 371 REMARK 465 HIS A 372 REMARK 465 LEU A 373 REMARK 465 ASP A 374 REMARK 465 ASP A 375 REMARK 465 GLN A 376 REMARK 465 ASN A 377 REMARK 465 SER A 378 REMARK 465 GLU A 379 REMARK 465 VAL A 380 REMARK 465 LYS A 381 REMARK 465 ARG A 382 REMARK 465 ALA A 383 REMARK 465 ARG A 384 REMARK 465 ILE A 385 REMARK 465 ASN A 386 REMARK 465 PRO A 387 REMARK 465 ASP 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 GLU A 20 CG CD OE1 OE2 REMARK 470 LYS A 25 CG CD CE NZ REMARK 470 GLN A 60 CD OE1 NE2 REMARK 470 GLU A 74 CD OE1 OE2 REMARK 470 GLN A 75 CD OE1 NE2 REMARK 470 LYS A 87 CE NZ REMARK 470 THR A 140 OG1 CG2 REMARK 470 GLU A 149 CG CD OE1 OE2 REMARK 470 ARG A 152 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 153 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS A 154 CG CD CE NZ REMARK 470 GLU A 155 CG CD OE1 OE2 REMARK 470 ASN A 178 CG OD1 ND2 REMARK 470 LYS A 182 CD CE NZ REMARK 470 ASP A 211 CG OD1 OD2 REMARK 470 SER A 235 OG REMARK 470 GLU A 236 CG CD OE1 OE2 REMARK 470 LEU A 237 CG CD1 CD2 REMARK 470 VAL A 312 CG1 CG2 REMARK 470 ARG A 315 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 347 CD1 CD2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O ASN A 104 O HOH A 501 2.18 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 ILE A 102 CB - CA - C ANGL. DEV. = 19.5 DEGREES REMARK 500 ILE A 102 N - CA - C ANGL. DEV. = -20.1 DEGREES REMARK 500 PRO A 103 C - N - CD ANGL. DEV. = -19.2 DEGREES REMARK 500 PRO A 103 CB - CA - C ANGL. DEV. = 12.8 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 GLU A 20 -62.10 -145.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 765 DISTANCE = 5.85 ANGSTROMS REMARK 525 HOH A 766 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH A 767 DISTANCE = 5.98 ANGSTROMS REMARK 525 HOH A 768 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A 769 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A 770 DISTANCE = 6.21 ANGSTROMS REMARK 525 HOH A 771 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH A 772 DISTANCE = 6.44 ANGSTROMS REMARK 525 HOH A 773 DISTANCE = 6.48 ANGSTROMS REMARK 525 HOH A 774 DISTANCE = 6.67 ANGSTROMS REMARK 525 HOH A 775 DISTANCE = 6.68 ANGSTROMS REMARK 525 HOH A 776 DISTANCE = 6.75 ANGSTROMS REMARK 525 HOH A 777 DISTANCE = 6.89 ANGSTROMS REMARK 525 HOH A 778 DISTANCE = 6.93 ANGSTROMS REMARK 525 HOH A 779 DISTANCE = 7.05 ANGSTROMS REMARK 525 HOH A 780 DISTANCE = 7.06 ANGSTROMS REMARK 525 HOH A 781 DISTANCE = 7.16 ANGSTROMS REMARK 525 HOH A 782 DISTANCE = 7.24 ANGSTROMS REMARK 525 HOH A 783 DISTANCE = 7.60 ANGSTROMS 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 401 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 231 NE2 REMARK 620 2 ASP A 233 OD1 79.7 REMARK 620 3 HIS A 287 NE2 86.3 86.8 REMARK 620 4 HOH A 619 O 176.6 103.4 95.2 REMARK 620 5 HOH A 661 O 80.3 91.9 166.5 98.2 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EOH A 402 DBREF 6IE3 A 1 389 UNP Q13686 ALKB1_HUMAN 1 389 SEQRES 1 A 389 MET GLY LYS MET ALA ALA ALA VAL GLY SER VAL ALA THR SEQRES 2 A 389 LEU ALA THR GLU PRO GLY GLU ASP ALA PHE ARG LYS LEU SEQRES 3 A 389 PHE ARG PHE TYR ARG GLN SER ARG PRO GLY THR ALA ASP SEQRES 4 A 389 LEU GLU GLY VAL ILE ASP PHE SER ALA ALA HIS ALA ALA SEQRES 5 A 389 ARG GLY LYS GLY PRO GLY ALA GLN LYS VAL ILE LYS SER SEQRES 6 A 389 GLN LEU ASN VAL SER SER VAL SER GLU GLN ASN ALA TYR SEQRES 7 A 389 ARG ALA GLY LEU GLN PRO VAL SER LYS TRP GLN ALA TYR SEQRES 8 A 389 GLY LEU LYS GLY TYR PRO GLY PHE ILE PHE ILE PRO ASN SEQRES 9 A 389 PRO PHE LEU PRO GLY TYR GLN TRP HIS TRP VAL LYS GLN SEQRES 10 A 389 CYS LEU LYS LEU TYR SER GLN LYS PRO ASN VAL CYS ASN SEQRES 11 A 389 LEU ASP LYS HIS MET SER LYS GLU GLU THR GLN ASP LEU SEQRES 12 A 389 TRP GLU GLN SER LYS GLU PHE LEU ARG TYR LYS GLU ALA SEQRES 13 A 389 THR LYS ARG ARG PRO ARG SER LEU LEU GLU LYS LEU ARG SEQRES 14 A 389 TRP VAL THR VAL GLY TYR HIS TYR ASN TRP ASP SER LYS SEQRES 15 A 389 LYS TYR SER ALA ASP HIS TYR THR PRO PHE PRO SER ASP SEQRES 16 A 389 LEU GLY PHE LEU SER GLU GLN VAL ALA ALA ALA CYS GLY SEQRES 17 A 389 PHE GLU ASP PHE ARG ALA GLU ALA GLY ILE LEU ASN TYR SEQRES 18 A 389 TYR ARG LEU ASP SER THR LEU GLY ILE HIS VAL ASP ARG SEQRES 19 A 389 SER GLU LEU ASP HIS SER LYS PRO LEU LEU SER PHE SER SEQRES 20 A 389 PHE GLY GLN SER ALA ILE PHE LEU LEU GLY GLY LEU GLN SEQRES 21 A 389 ARG ASP GLU ALA PRO THR ALA MET PHE MET HIS SER GLY SEQRES 22 A 389 ASP ILE MET ILE MET SER GLY PHE SER ARG LEU LEU ASN SEQRES 23 A 389 HIS ALA VAL PRO ARG VAL LEU PRO ASN PRO GLU GLY GLU SEQRES 24 A 389 GLY LEU PRO HIS CYS LEU GLU ALA PRO LEU PRO ALA VAL SEQRES 25 A 389 LEU PRO ARG ASP SER MET VAL GLU PRO CYS SER MET GLU SEQRES 26 A 389 ASP TRP GLN VAL CYS ALA SER TYR LEU LYS THR ALA ARG SEQRES 27 A 389 VAL ASN MET THR VAL ARG GLN VAL LEU ALA THR ASP GLN SEQRES 28 A 389 ASN PHE PRO LEU GLU PRO ILE GLU ASP GLU LYS ARG ASP SEQRES 29 A 389 ILE SER THR GLU GLY PHE CYS HIS LEU ASP ASP GLN ASN SEQRES 30 A 389 SER GLU VAL LYS ARG ALA ARG ILE ASN PRO ASP SER HET MN A 401 1 HET EOH A 402 3 HETNAM MN MANGANESE (II) ION HETNAM EOH ETHANOL FORMUL 2 MN MN 2+ FORMUL 3 EOH C2 H6 O FORMUL 4 HOH *283(H2 O) HELIX 1 AA1 ASP A 21 SER A 33 1 13 HELIX 2 AA2 THR A 37 GLU A 41 5 5 HELIX 3 AA3 GLY A 56 LYS A 61 1 6 HELIX 4 AA4 ASN A 68 VAL A 72 5 5 HELIX 5 AA5 SER A 73 GLY A 81 1 9 HELIX 6 AA6 PRO A 84 TRP A 88 5 5 HELIX 7 AA7 TYR A 110 LEU A 121 1 12 HELIX 8 AA8 ASP A 142 TYR A 153 1 12 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 GLY A 280 LEU A 285 5 6 HELIX 12 AB3 PRO A 302 GLU A 306 5 5 HELIX 13 AB4 SER A 323 LYS A 335 1 13 SHEET 1 AA1 2 VAL A 62 LYS A 64 0 SHEET 2 AA1 2 TYR A 91 LEU A 93 -1 O GLY A 92 N ILE A 63 SHEET 1 AA2 7 PHE A 99 ILE A 102 0 SHEET 2 AA2 7 ILE A 275 MET A 278 -1 O ILE A 275 N ILE A 102 SHEET 3 AA2 7 LEU A 243 GLY A 249 -1 N SER A 245 O MET A 276 SHEET 4 AA2 7 ALA A 337 ARG A 344 -1 O MET A 341 N PHE A 246 SHEET 5 AA2 7 ALA A 216 ARG A 223 -1 N TYR A 222 O ARG A 338 SHEET 6 AA2 7 TRP A 170 GLY A 174 -1 N VAL A 171 O LEU A 219 SHEET 7 AA2 7 VAL A 128 CYS A 129 -1 N VAL A 128 O THR A 172 SHEET 1 AA3 4 LEU A 228 HIS A 231 0 SHEET 2 AA3 4 HIS A 287 VAL A 292 -1 O VAL A 289 N LEU A 228 SHEET 3 AA3 4 ALA A 252 LEU A 256 -1 N LEU A 255 O ALA A 288 SHEET 4 AA3 4 THR A 266 MET A 270 -1 O MET A 268 N PHE A 254 LINK NE2 HIS A 231 MN MN A 401 1555 1555 2.31 LINK OD1 ASP A 233 MN MN A 401 1555 1555 2.25 LINK NE2 HIS A 287 MN MN A 401 1555 1555 2.17 LINK MN MN A 401 O HOH A 619 1555 1555 2.47 LINK MN MN A 401 O HOH A 661 1555 1555 2.53 SITE 1 AC1 5 HIS A 231 ASP A 233 HIS A 287 HOH A 619 SITE 2 AC1 5 HOH A 661 SITE 1 AC2 2 TRP A 179 HOH A 578 CRYST1 56.732 56.732 191.686 90.00 90.00 120.00 P 65 6 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 0.017627 0.010177 0.000000 0.00000 SCALE2 0.000000 0.020354 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005217 0.00000