HEADER OXIDOREDUCTASE 21-NOV-13 4NPM TITLE CRYSTAL STRUCTURE OF ZEBRAFISH ALKBH5 IN COMPLEX WITH SUCCINIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA DEMETHYLASE ALKBH5; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 38-287; 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: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: LEOPARD DANIO,ZEBRA DANIO,ZEBRA FISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: ALKBH5; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR C.HE,W.CHEN,L.ZHANG REVDAT 3 28-FEB-24 4NPM 1 REMARK LINK REVDAT 2 02-APR-14 4NPM 1 JRNL REVDAT 1 19-FEB-14 4NPM 0 JRNL AUTH W.CHEN,L.ZHANG,G.ZHENG,Y.FU,Q.JI,F.LIU,H.CHEN,C.HE JRNL TITL CRYSTAL STRUCTURE OF THE RNA DEMETHYLASE ALKBH5 FROM JRNL TITL 2 ZEBRAFISH. JRNL REF FEBS LETT. V. 588 892 2014 JRNL REFN ISSN 0014-5793 JRNL PMID 24561204 JRNL DOI 10.1016/J.FEBSLET.2014.02.021 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 49614 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 2512 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 47.9962 - 4.7251 1.00 2820 147 0.1910 0.2164 REMARK 3 2 4.7251 - 3.7509 0.99 2669 151 0.1462 0.1354 REMARK 3 3 3.7509 - 3.2769 1.00 2642 156 0.1504 0.1618 REMARK 3 4 3.2769 - 2.9773 1.00 2669 130 0.1661 0.1678 REMARK 3 5 2.9773 - 2.7639 1.00 2595 158 0.1754 0.1552 REMARK 3 6 2.7639 - 2.6010 1.00 2629 131 0.1804 0.2020 REMARK 3 7 2.6010 - 2.4707 1.00 2628 128 0.1750 0.1901 REMARK 3 8 2.4707 - 2.3632 1.00 2591 160 0.1715 0.1975 REMARK 3 9 2.3632 - 2.2722 1.00 2602 141 0.1668 0.1760 REMARK 3 10 2.2722 - 2.1938 1.00 2599 143 0.1710 0.2033 REMARK 3 11 2.1938 - 2.1252 1.00 2606 130 0.1764 0.2235 REMARK 3 12 2.1252 - 2.0645 1.00 2561 149 0.1773 0.2050 REMARK 3 13 2.0645 - 2.0101 1.00 2615 114 0.1782 0.1953 REMARK 3 14 2.0101 - 1.9611 1.00 2593 138 0.1754 0.2061 REMARK 3 15 1.9611 - 1.9165 1.00 2599 141 0.1829 0.1855 REMARK 3 16 1.9165 - 1.8757 1.00 2568 140 0.1960 0.2087 REMARK 3 17 1.8757 - 1.8382 1.00 2570 135 0.2170 0.2398 REMARK 3 18 1.8382 - 1.8030 0.97 2546 120 0.2521 0.2420 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.020 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.009 3464 REMARK 3 ANGLE : 1.161 4701 REMARK 3 CHIRALITY : 0.086 525 REMARK 3 PLANARITY : 0.005 617 REMARK 3 DIHEDRAL : 14.047 1321 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -5.4265 1.7759 -9.5206 REMARK 3 T TENSOR REMARK 3 T11: 0.1772 T22: 0.1812 REMARK 3 T33: 0.1388 T12: 0.0113 REMARK 3 T13: 0.0129 T23: -0.0197 REMARK 3 L TENSOR REMARK 3 L11: 1.2095 L22: 0.7209 REMARK 3 L33: 0.0938 L12: 0.6749 REMARK 3 L13: 0.0140 L23: -0.0994 REMARK 3 S TENSOR REMARK 3 S11: -0.0858 S12: 0.1843 S13: -0.1288 REMARK 3 S21: -0.0839 S22: 0.0805 S23: -0.0680 REMARK 3 S31: 0.0288 S32: -0.0074 S33: 0.0021 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4NPM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-DEC-13. REMARK 100 THE DEPOSITION ID IS D_1000083497. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-AUG-13 REMARK 200 TEMPERATURE (KELVIN) : 180 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9676 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49614 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM IODIDE, PH 7.0, 20% W/V REMARK 280 POLYETHYLENE GLYCOL 3350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 33.03350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 57.52500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.89600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 57.52500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.03350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.89600 REMARK 290 SMTRY3 4 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 ASP A 1 REMARK 465 GLU A 2 REMARK 465 SER A 3 REMARK 465 TYR A 72 REMARK 465 GLY A 73 REMARK 465 ALA A 74 REMARK 465 GLN A 75 REMARK 465 LEU A 76 REMARK 465 GLU A 77 REMARK 465 LYS A 78 REMARK 465 ARG A 79 REMARK 465 GLY A 80 REMARK 465 PRO A 81 REMARK 465 GLY A 82 REMARK 465 SER A 225 REMARK 465 ASN A 226 REMARK 465 SER A 227 REMARK 465 LEU A 228 REMARK 465 SER A 229 REMARK 465 PRO A 230 REMARK 465 SER A 231 REMARK 465 ILE A 232 REMARK 465 VAL A 233 REMARK 465 SER A 234 REMARK 465 PRO A 235 REMARK 465 LYS A 236 REMARK 465 ARG A 237 REMARK 465 ARG A 238 REMARK 465 HIS A 239 REMARK 465 ILE A 240 REMARK 465 LEU A 241 REMARK 465 LYS A 242 REMARK 465 ALA A 243 REMARK 465 LYS A 244 REMARK 465 ARG A 245 REMARK 465 SER A 246 REMARK 465 HIS A 247 REMARK 465 ARG A 248 REMARK 465 LYS A 249 REMARK 465 ALA A 250 REMARK 465 ASP B 1 REMARK 465 GLU B 2 REMARK 465 SER B 3 REMARK 465 GLU B 4 REMARK 465 TYR B 5 REMARK 465 GLU B 6 REMARK 465 GLU B 7 REMARK 465 ARG B 8 REMARK 465 TYR B 72 REMARK 465 GLY B 73 REMARK 465 ALA B 74 REMARK 465 GLN B 75 REMARK 465 LEU B 76 REMARK 465 GLU B 77 REMARK 465 LYS B 78 REMARK 465 ARG B 79 REMARK 465 GLY B 80 REMARK 465 PRO B 81 REMARK 465 GLY B 82 REMARK 465 ASP B 224 REMARK 465 SER B 225 REMARK 465 ASN B 226 REMARK 465 SER B 227 REMARK 465 LEU B 228 REMARK 465 SER B 229 REMARK 465 PRO B 230 REMARK 465 SER B 231 REMARK 465 ILE B 232 REMARK 465 VAL B 233 REMARK 465 SER B 234 REMARK 465 PRO B 235 REMARK 465 LYS B 236 REMARK 465 ARG B 237 REMARK 465 ARG B 238 REMARK 465 HIS B 239 REMARK 465 ILE B 240 REMARK 465 LEU B 241 REMARK 465 LYS B 242 REMARK 465 ALA B 243 REMARK 465 LYS B 244 REMARK 465 ARG B 245 REMARK 465 SER B 246 REMARK 465 HIS B 247 REMARK 465 ARG B 248 REMARK 465 LYS B 249 REMARK 465 ALA B 250 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 HOH B 402 O HOH B 631 1.86 REMARK 500 O HOH B 430 O HOH B 594 2.11 REMARK 500 O HOH B 606 O HOH B 634 2.17 REMARK 500 O HOH A 472 O HOH B 568 2.18 REMARK 500 O HOH B 550 O HOH B 556 2.19 REMARK 500 O HOH B 514 O HOH B 594 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 633 O HOH B 475 4455 2.19 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 TYR A 5 -60.99 68.17 REMARK 500 SER A 24 -76.79 -109.26 REMARK 500 ILE A 25 -60.40 71.27 REMARK 500 PHE A 152 -48.13 77.13 REMARK 500 SER A 155 -152.70 -156.22 REMARK 500 SER B 24 -78.31 -112.98 REMARK 500 ILE B 25 -59.78 73.28 REMARK 500 VAL B 103 -68.60 -120.61 REMARK 500 SER B 134 131.80 -36.98 REMARK 500 PHE B 152 -49.37 76.20 REMARK 500 SER B 155 -155.98 -154.86 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 300 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 135 NE2 REMARK 620 2 ASP A 137 OD1 91.1 REMARK 620 3 HIS A 197 NE2 87.1 90.7 REMARK 620 4 SIN A 301 O1 94.2 174.2 91.7 REMARK 620 5 HOH A 414 O 173.2 85.8 98.9 88.7 REMARK 620 6 HOH A 634 O 90.6 90.1 177.6 87.8 83.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 300 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 135 NE2 REMARK 620 2 ASP B 137 OD1 89.7 REMARK 620 3 HIS B 197 NE2 87.9 94.3 REMARK 620 4 SIN B 301 O1 94.7 173.9 90.1 REMARK 620 5 HOH B 417 O 177.6 89.8 94.5 85.6 REMARK 620 6 HOH B 632 O 90.6 89.2 176.2 86.5 87.1 REMARK 620 N 1 2 3 4 5 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 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SIN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN B 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SIN B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NPL RELATED DB: PDB DBREF 4NPM A 1 250 UNP Q08BA6 ALKB5_DANRE 38 287 DBREF 4NPM B 1 250 UNP Q08BA6 ALKB5_DANRE 38 287 SEQRES 1 A 250 ASP GLU SER GLU TYR GLU GLU ARG ARG ASP ALA GLU ALA SEQRES 2 A 250 ARG ARG VAL LYS SER GLY ILE LYS GLN ALA SER ILE PHE SEQRES 3 A 250 THR LEU GLU GLU CYS ALA ARG ILE GLU ALA LYS ILE ASP SEQRES 4 A 250 GLU VAL VAL ALA LYS ALA ASP LYS GLY LEU TYR ARG GLU SEQRES 5 A 250 HIS THR VAL ASP ARG ALA PRO LEU ARG ASN LYS TYR PHE SEQRES 6 A 250 PHE GLY GLU GLY TYR THR TYR GLY ALA GLN LEU GLU LYS SEQRES 7 A 250 ARG GLY PRO GLY GLN GLU ARG LEU TYR SER LYS GLY GLU SEQRES 8 A 250 VAL ASP ASP ILE PRO ASP TRP VAL HIS GLU LEU VAL ILE SEQRES 9 A 250 ASP ARG LEU VAL THR HIS GLY VAL ILE PRO GLU GLY PHE SEQRES 10 A 250 VAL ASN SER ALA VAL ILE ASN ASP TYR GLN PRO GLY GLY SEQRES 11 A 250 CYS ILE VAL SER HIS VAL ASP PRO ILE HIS ILE PHE GLU SEQRES 12 A 250 ARG PRO ILE VAL SER VAL SER PHE PHE SER ASP SER ALA SEQRES 13 A 250 LEU CYS PHE GLY CYS LYS PHE LEU PHE LYS PRO ILE ARG SEQRES 14 A 250 VAL SER GLU PRO VAL LEU HIS LEU PRO VAL ARG ARG GLY SEQRES 15 A 250 SER VAL THR VAL LEU SER GLY TYR ALA ALA ASP ASP ILE SEQRES 16 A 250 THR HIS CYS ILE ARG PRO GLN ASP ILE LYS GLU ARG ARG SEQRES 17 A 250 ALA VAL ILE ILE LEU ARG LYS THR ARG ALA ASP ALA PRO SEQRES 18 A 250 ARG LEU ASP SER ASN SER LEU SER PRO SER ILE VAL SER SEQRES 19 A 250 PRO LYS ARG ARG HIS ILE LEU LYS ALA LYS ARG SER HIS SEQRES 20 A 250 ARG LYS ALA SEQRES 1 B 250 ASP GLU SER GLU TYR GLU GLU ARG ARG ASP ALA GLU ALA SEQRES 2 B 250 ARG ARG VAL LYS SER GLY ILE LYS GLN ALA SER ILE PHE SEQRES 3 B 250 THR LEU GLU GLU CYS ALA ARG ILE GLU ALA LYS ILE ASP SEQRES 4 B 250 GLU VAL VAL ALA LYS ALA ASP LYS GLY LEU TYR ARG GLU SEQRES 5 B 250 HIS THR VAL ASP ARG ALA PRO LEU ARG ASN LYS TYR PHE SEQRES 6 B 250 PHE GLY GLU GLY TYR THR TYR GLY ALA GLN LEU GLU LYS SEQRES 7 B 250 ARG GLY PRO GLY GLN GLU ARG LEU TYR SER LYS GLY GLU SEQRES 8 B 250 VAL ASP ASP ILE PRO ASP TRP VAL HIS GLU LEU VAL ILE SEQRES 9 B 250 ASP ARG LEU VAL THR HIS GLY VAL ILE PRO GLU GLY PHE SEQRES 10 B 250 VAL ASN SER ALA VAL ILE ASN ASP TYR GLN PRO GLY GLY SEQRES 11 B 250 CYS ILE VAL SER HIS VAL ASP PRO ILE HIS ILE PHE GLU SEQRES 12 B 250 ARG PRO ILE VAL SER VAL SER PHE PHE SER ASP SER ALA SEQRES 13 B 250 LEU CYS PHE GLY CYS LYS PHE LEU PHE LYS PRO ILE ARG SEQRES 14 B 250 VAL SER GLU PRO VAL LEU HIS LEU PRO VAL ARG ARG GLY SEQRES 15 B 250 SER VAL THR VAL LEU SER GLY TYR ALA ALA ASP ASP ILE SEQRES 16 B 250 THR HIS CYS ILE ARG PRO GLN ASP ILE LYS GLU ARG ARG SEQRES 17 B 250 ALA VAL ILE ILE LEU ARG LYS THR ARG ALA ASP ALA PRO SEQRES 18 B 250 ARG LEU ASP SER ASN SER LEU SER PRO SER ILE VAL SER SEQRES 19 B 250 PRO LYS ARG ARG HIS ILE LEU LYS ALA LYS ARG SER HIS SEQRES 20 B 250 ARG LYS ALA HET MN A 300 1 HET SIN A 301 8 HET MN B 300 1 HET SIN B 301 8 HETNAM MN MANGANESE (II) ION HETNAM SIN SUCCINIC ACID FORMUL 3 MN 2(MN 2+) FORMUL 4 SIN 2(C4 H6 O4) FORMUL 7 HOH *471(H2 O) HELIX 1 1 TYR A 5 SER A 18 1 14 HELIX 2 2 THR A 27 LYS A 47 1 21 HELIX 3 3 ARG A 51 HIS A 53 5 3 HELIX 4 4 PRO A 96 VAL A 103 1 8 HELIX 5 5 VAL A 103 HIS A 110 1 8 HELIX 6 6 SER A 188 ASP A 194 1 7 HELIX 7 7 ARG A 200 ILE A 204 5 5 HELIX 8 8 ASP B 10 GLY B 19 1 10 HELIX 9 9 THR B 27 LYS B 47 1 21 HELIX 10 10 ARG B 51 HIS B 53 5 3 HELIX 11 11 PRO B 96 VAL B 103 1 8 HELIX 12 12 VAL B 103 HIS B 110 1 8 HELIX 13 13 SER B 188 ASP B 194 1 7 HELIX 14 14 ARG B 200 ILE B 204 5 5 SHEET 1 A 7 ILE A 20 ALA A 23 0 SHEET 2 A 7 VAL A 184 LEU A 187 -1 O VAL A 184 N ALA A 23 SHEET 3 A 7 ILE A 146 PHE A 151 -1 N SER A 148 O THR A 185 SHEET 4 A 7 ARG A 208 ARG A 214 -1 O LEU A 213 N VAL A 147 SHEET 5 A 7 SER A 120 TYR A 126 -1 N TYR A 126 O ARG A 208 SHEET 6 A 7 ARG A 61 PHE A 66 -1 N ASN A 62 O ASP A 125 SHEET 7 A 7 VAL A 55 ALA A 58 -1 N ASP A 56 O LYS A 63 SHEET 1 B 2 TYR A 70 THR A 71 0 SHEET 2 B 2 ARG A 85 LEU A 86 -1 O ARG A 85 N THR A 71 SHEET 1 C 4 ILE A 132 HIS A 135 0 SHEET 2 C 4 HIS A 197 ILE A 199 -1 O HIS A 197 N HIS A 135 SHEET 3 C 4 SER A 155 PHE A 159 -1 N CYS A 158 O CYS A 198 SHEET 4 C 4 LEU A 175 VAL A 179 -1 O LEU A 177 N LEU A 157 SHEET 1 D 2 PHE A 163 LEU A 164 0 SHEET 2 D 2 ARG A 169 VAL A 170 -1 O ARG A 169 N LEU A 164 SHEET 1 E 7 ILE B 20 ALA B 23 0 SHEET 2 E 7 VAL B 184 LEU B 187 -1 O VAL B 186 N LYS B 21 SHEET 3 E 7 ILE B 146 PHE B 151 -1 N ILE B 146 O LEU B 187 SHEET 4 E 7 ARG B 208 ARG B 214 -1 O LEU B 213 N VAL B 147 SHEET 5 E 7 SER B 120 TYR B 126 -1 N TYR B 126 O ARG B 208 SHEET 6 E 7 ARG B 61 PHE B 66 -1 N ASN B 62 O ASP B 125 SHEET 7 E 7 VAL B 55 ALA B 58 -1 N ASP B 56 O LYS B 63 SHEET 1 F 2 TYR B 70 THR B 71 0 SHEET 2 F 2 ARG B 85 LEU B 86 -1 O ARG B 85 N THR B 71 SHEET 1 G 4 ILE B 132 HIS B 135 0 SHEET 2 G 4 HIS B 197 ILE B 199 -1 O HIS B 197 N HIS B 135 SHEET 3 G 4 SER B 155 PHE B 159 -1 N CYS B 158 O CYS B 198 SHEET 4 G 4 LEU B 175 VAL B 179 -1 O LEU B 177 N LEU B 157 SHEET 1 H 2 PHE B 163 LEU B 164 0 SHEET 2 H 2 ARG B 169 VAL B 170 -1 O ARG B 169 N LEU B 164 LINK NE2 HIS A 135 MN MN A 300 1555 1555 2.21 LINK OD1 ASP A 137 MN MN A 300 1555 1555 2.20 LINK NE2 HIS A 197 MN MN A 300 1555 1555 2.25 LINK MN MN A 300 O1 SIN A 301 1555 1555 2.15 LINK MN MN A 300 O HOH A 414 1555 1555 2.11 LINK MN MN A 300 O HOH A 634 1555 1555 2.13 LINK NE2 HIS B 135 MN MN B 300 1555 1555 2.24 LINK OD1 ASP B 137 MN MN B 300 1555 1555 2.24 LINK NE2 HIS B 197 MN MN B 300 1555 1555 2.24 LINK MN MN B 300 O1 SIN B 301 1555 1555 2.25 LINK MN MN B 300 O HOH B 417 1555 1555 2.11 LINK MN MN B 300 O HOH B 632 1555 1555 2.21 CISPEP 1 ARG A 144 PRO A 145 0 2.03 CISPEP 2 LYS A 166 PRO A 167 0 -0.41 CISPEP 3 ARG B 144 PRO B 145 0 4.44 CISPEP 4 LYS B 166 PRO B 167 0 -24.31 SITE 1 AC1 6 HIS A 135 ASP A 137 HIS A 197 SIN A 301 SITE 2 AC1 6 HOH A 414 HOH A 634 SITE 1 AC2 13 ASN A 124 TYR A 126 ILE A 132 HIS A 135 SITE 2 AC2 13 HIS A 197 ILE A 199 ARG A 208 VAL A 210 SITE 3 AC2 13 ILE A 212 MN A 300 HOH A 414 HOH A 455 SITE 4 AC2 13 HOH A 634 SITE 1 AC3 6 HIS B 135 ASP B 137 HIS B 197 SIN B 301 SITE 2 AC3 6 HOH B 417 HOH B 632 SITE 1 AC4 14 ASN B 124 TYR B 126 ILE B 132 HIS B 135 SITE 2 AC4 14 HIS B 197 ILE B 199 ARG B 208 VAL B 210 SITE 3 AC4 14 ILE B 212 MN B 300 HOH B 417 HOH B 443 SITE 4 AC4 14 HOH B 488 HOH B 632 CRYST1 66.067 69.792 115.050 90.00 90.00 90.00 P 21 21 21 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 0.015136 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014328 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008692 0.00000