PDB Short entry for 4NRO HEADER OXIDOREDUCTASE 27-NOV-13 4NRO TITLE CRYSTAL STRUCTURE OF HUMAN ALKBH5 IN COMPLEX WITH ALPHA-KETOGLUTARATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA DEMETHYLASE ALKBH5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 66-292; 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_TAXID: 9606; SOURCE 4 GENE: ABH5, ALKBH5, OFOXD1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET-28A KEYWDS ALKBH5, 6-METHYL ADENOSINE, PROTEIN/DNA INTERACTION, HUMAN KEYWDS 2 DIOXYGENASE, METAL-BINDING, NUCLEUS, DEMETHYLATION, RNA REPAIR, KEYWDS 3 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR C.FENG,Z.CHEN,Y.LIU REVDAT 3 08-NOV-23 4NRO 1 REMARK SEQADV LINK REVDAT 2 21-OCT-15 4NRO 1 JRNL REVDAT 1 19-MAR-14 4NRO 0 JRNL AUTH C.FENG,Y.LIU,G.WANG,Z.DENG,Q.ZHANG,W.WU,Y.TONG,C.CHENG, JRNL AUTH 2 Z.CHEN JRNL TITL CRYSTAL STRUCTURES OF THE HUMAN RNA DEMETHYLASE ALKBH5 JRNL TITL 2 REVEAL BASIS FOR SUBSTRATE RECOGNITION JRNL REF J.BIOL.CHEM. V. 289 11571 2014 JRNL REFN ISSN 0021-9258 JRNL PMID 24616105 JRNL DOI 10.1074/JBC.M113.546168 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 89.7 REMARK 3 NUMBER OF REFLECTIONS : 9363 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) : 0.238 REMARK 3 R VALUE (WORKING SET) : 0.237 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 473 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 693 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.18 REMARK 3 BIN R VALUE (WORKING SET) : 0.2420 REMARK 3 BIN FREE R VALUE SET COUNT : 41 REMARK 3 BIN FREE R VALUE : 0.2700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1569 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.36000 REMARK 3 B22 (A**2) : 1.36000 REMARK 3 B33 (A**2) : -2.73000 REMARK 3 B12 (A**2) : 0.00000 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): 0.465 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.264 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.182 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 14.714 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.914 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1626 ; 0.007 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2208 ; 1.166 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 213 ; 5.517 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 62 ;22.171 ;22.581 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 230 ;15.183 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;22.093 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 252 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1243 ; 0.004 ; 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): 851 ; 1.919 ; 4.512 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1061 ; 3.076 ; 6.748 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 775 ; 2.048 ; 4.560 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): 1608 ; 1.604 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 4 ;21.187 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 1576 ;16.280 ; 5.000 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 : 13 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 73 A 90 REMARK 3 ORIGIN FOR THE GROUP (A): -2.3058 28.7688 3.8681 REMARK 3 T TENSOR REMARK 3 T11: 0.0565 T22: 0.0665 REMARK 3 T33: 0.1239 T12: -0.0038 REMARK 3 T13: 0.0004 T23: 0.0207 REMARK 3 L TENSOR REMARK 3 L11: 2.9920 L22: 1.3191 REMARK 3 L33: 8.0889 L12: 1.6566 REMARK 3 L13: 4.5420 L23: 1.8370 REMARK 3 S TENSOR REMARK 3 S11: -0.0081 S12: 0.0782 S13: 0.0468 REMARK 3 S21: -0.0198 S22: 0.1891 S23: 0.1334 REMARK 3 S31: 0.0166 S32: -0.1150 S33: -0.1810 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 : A 91 A 97 REMARK 3 ORIGIN FOR THE GROUP (A): 15.9592 39.0341 18.0722 REMARK 3 T TENSOR REMARK 3 T11: 0.1118 T22: 0.0066 REMARK 3 T33: 0.0890 T12: 0.0014 REMARK 3 T13: -0.0157 T23: 0.0072 REMARK 3 L TENSOR REMARK 3 L11: 5.6991 L22: 1.3820 REMARK 3 L33: 0.0579 L12: 1.3573 REMARK 3 L13: 0.0274 L23: 0.2317 REMARK 3 S TENSOR REMARK 3 S11: -0.1345 S12: 0.1014 S13: 0.2303 REMARK 3 S21: -0.0579 S22: 0.0918 S23: 0.1621 REMARK 3 S31: -0.0308 S32: 0.0128 S33: 0.0428 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 : A 98 A 121 REMARK 3 ORIGIN FOR THE GROUP (A): 27.4209 25.4720 25.7538 REMARK 3 T TENSOR REMARK 3 T11: 0.0332 T22: 0.0702 REMARK 3 T33: 0.1007 T12: -0.0156 REMARK 3 T13: -0.0170 T23: -0.0307 REMARK 3 L TENSOR REMARK 3 L11: 0.9737 L22: 3.7111 REMARK 3 L33: 1.4331 L12: -1.4238 REMARK 3 L13: 0.3410 L23: -0.7493 REMARK 3 S TENSOR REMARK 3 S11: -0.0597 S12: -0.1485 S13: 0.1140 REMARK 3 S21: 0.0373 S22: 0.1101 S23: -0.2460 REMARK 3 S31: -0.0930 S32: 0.1154 S33: -0.0504 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 122 A 130 REMARK 3 ORIGIN FOR THE GROUP (A): 22.0096 13.3041 20.6523 REMARK 3 T TENSOR REMARK 3 T11: 0.0317 T22: 0.1140 REMARK 3 T33: 0.0931 T12: 0.0046 REMARK 3 T13: -0.0143 T23: 0.0301 REMARK 3 L TENSOR REMARK 3 L11: 0.2552 L22: 4.9572 REMARK 3 L33: 0.6782 L12: -1.1187 REMARK 3 L13: -0.4151 L23: 1.8322 REMARK 3 S TENSOR REMARK 3 S11: 0.0584 S12: 0.0067 S13: -0.0283 REMARK 3 S21: -0.2487 S22: -0.0906 S23: 0.0674 REMARK 3 S31: -0.0935 S32: -0.0243 S33: 0.0322 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 131 A 141 REMARK 3 ORIGIN FOR THE GROUP (A): 16.4950 16.0812 25.1527 REMARK 3 T TENSOR REMARK 3 T11: 0.0133 T22: 0.1088 REMARK 3 T33: 0.1605 T12: 0.0070 REMARK 3 T13: 0.0109 T23: 0.0270 REMARK 3 L TENSOR REMARK 3 L11: 2.5486 L22: 1.2355 REMARK 3 L33: 1.6682 L12: 1.0012 REMARK 3 L13: -1.6305 L23: -1.3565 REMARK 3 S TENSOR REMARK 3 S11: -0.1515 S12: -0.0002 S13: -0.0590 REMARK 3 S21: 0.0059 S22: 0.1256 S23: -0.0809 REMARK 3 S31: 0.0346 S32: -0.1376 S33: 0.0259 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 142 A 160 REMARK 3 ORIGIN FOR THE GROUP (A): 9.8480 10.1106 28.1092 REMARK 3 T TENSOR REMARK 3 T11: 0.0729 T22: 0.0698 REMARK 3 T33: 0.1152 T12: -0.0064 REMARK 3 T13: 0.0037 T23: 0.0514 REMARK 3 L TENSOR REMARK 3 L11: 8.5902 L22: 1.0334 REMARK 3 L33: 5.9738 L12: 2.0501 REMARK 3 L13: 7.1349 L23: 1.8549 REMARK 3 S TENSOR REMARK 3 S11: 0.0734 S12: 0.1669 S13: -0.2067 REMARK 3 S21: 0.2041 S22: 0.0477 S23: 0.0405 REMARK 3 S31: 0.1048 S32: 0.1549 S33: -0.1211 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 161 A 200 REMARK 3 ORIGIN FOR THE GROUP (A): 15.4956 28.6615 26.0726 REMARK 3 T TENSOR REMARK 3 T11: 0.0770 T22: 0.0649 REMARK 3 T33: 0.0546 T12: -0.0003 REMARK 3 T13: -0.0090 T23: -0.0302 REMARK 3 L TENSOR REMARK 3 L11: 0.9795 L22: 1.0984 REMARK 3 L33: 0.0215 L12: -0.4158 REMARK 3 L13: 0.0256 L23: 0.1153 REMARK 3 S TENSOR REMARK 3 S11: -0.0513 S12: -0.1116 S13: 0.1108 REMARK 3 S21: 0.0311 S22: 0.0478 S23: -0.0611 REMARK 3 S31: -0.0161 S32: 0.0000 S33: 0.0035 REMARK 3 REMARK 3 TLS GROUP : 8 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 201 A 211 REMARK 3 ORIGIN FOR THE GROUP (A): 6.4475 16.8020 17.9882 REMARK 3 T TENSOR REMARK 3 T11: 0.1147 T22: 0.0516 REMARK 3 T33: 0.2071 T12: -0.0122 REMARK 3 T13: -0.0267 T23: -0.0393 REMARK 3 L TENSOR REMARK 3 L11: 1.1203 L22: 0.0105 REMARK 3 L33: 2.5649 L12: 0.0931 REMARK 3 L13: -1.6275 L23: -0.1245 REMARK 3 S TENSOR REMARK 3 S11: 0.0138 S12: -0.0411 S13: -0.1071 REMARK 3 S21: -0.0007 S22: 0.0112 S23: -0.0234 REMARK 3 S31: 0.0644 S32: 0.0860 S33: -0.0250 REMARK 3 REMARK 3 TLS GROUP : 9 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 212 A 225 REMARK 3 ORIGIN FOR THE GROUP (A): 13.5824 28.7507 17.4948 REMARK 3 T TENSOR REMARK 3 T11: 0.1151 T22: 0.0573 REMARK 3 T33: 0.0837 T12: -0.0125 REMARK 3 T13: 0.0035 T23: -0.0054 REMARK 3 L TENSOR REMARK 3 L11: 0.9164 L22: 0.3839 REMARK 3 L33: 0.2298 L12: -0.5928 REMARK 3 L13: -0.2535 L23: 0.1705 REMARK 3 S TENSOR REMARK 3 S11: -0.0021 S12: 0.0272 S13: 0.0351 REMARK 3 S21: -0.0037 S22: -0.0191 S23: -0.0180 REMARK 3 S31: -0.1283 S32: 0.0004 S33: 0.0211 REMARK 3 REMARK 3 TLS GROUP : 10 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 226 A 237 REMARK 3 ORIGIN FOR THE GROUP (A): 8.2677 18.1220 2.5021 REMARK 3 T TENSOR REMARK 3 T11: 0.1005 T22: 0.2070 REMARK 3 T33: 0.1496 T12: 0.0260 REMARK 3 T13: 0.0317 T23: -0.1360 REMARK 3 L TENSOR REMARK 3 L11: 0.8158 L22: 0.6875 REMARK 3 L33: 1.5749 L12: 0.7327 REMARK 3 L13: -1.1186 L23: -1.0391 REMARK 3 S TENSOR REMARK 3 S11: -0.0571 S12: 0.1726 S13: -0.0051 REMARK 3 S21: -0.0133 S22: 0.1228 S23: 0.0526 REMARK 3 S31: 0.0406 S32: -0.1878 S33: -0.0657 REMARK 3 REMARK 3 TLS GROUP : 11 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 238 A 248 REMARK 3 ORIGIN FOR THE GROUP (A): 7.9786 25.5151 1.8150 REMARK 3 T TENSOR REMARK 3 T11: 0.0979 T22: 0.0875 REMARK 3 T33: 0.0267 T12: -0.0082 REMARK 3 T13: 0.0056 T23: 0.0213 REMARK 3 L TENSOR REMARK 3 L11: 3.0094 L22: 6.8113 REMARK 3 L33: 6.7063 L12: 2.6869 REMARK 3 L13: 2.9828 L23: 6.7190 REMARK 3 S TENSOR REMARK 3 S11: -0.1672 S12: 0.3300 S13: 0.2410 REMARK 3 S21: -0.2152 S22: -0.0166 S23: 0.1683 REMARK 3 S31: -0.2414 S32: 0.0647 S33: 0.1837 REMARK 3 REMARK 3 TLS GROUP : 12 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 249 A 273 REMARK 3 ORIGIN FOR THE GROUP (A): 9.7510 25.9973 11.1974 REMARK 3 T TENSOR REMARK 3 T11: 0.0763 T22: 0.0581 REMARK 3 T33: 0.0948 T12: 0.0024 REMARK 3 T13: 0.0252 T23: -0.0304 REMARK 3 L TENSOR REMARK 3 L11: 0.6610 L22: 0.3431 REMARK 3 L33: 0.5528 L12: -0.2683 REMARK 3 L13: 0.4978 L23: -0.4045 REMARK 3 S TENSOR REMARK 3 S11: -0.0483 S12: 0.0753 S13: 0.0181 REMARK 3 S21: 0.0179 S22: 0.0528 S23: 0.0037 REMARK 3 S31: -0.0490 S32: -0.0163 S33: -0.0044 REMARK 3 REMARK 3 TLS GROUP : 13 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 274 A 292 REMARK 3 ORIGIN FOR THE GROUP (A): 11.9288 21.7753 22.9035 REMARK 3 T TENSOR REMARK 3 T11: 0.0978 T22: 0.0477 REMARK 3 T33: 0.0571 T12: 0.0001 REMARK 3 T13: 0.0345 T23: -0.0183 REMARK 3 L TENSOR REMARK 3 L11: 2.0792 L22: 0.2811 REMARK 3 L33: 0.3755 L12: 0.2580 REMARK 3 L13: 0.8308 L23: 0.2029 REMARK 3 S TENSOR REMARK 3 S11: 0.0631 S12: -0.1403 S13: -0.0362 REMARK 3 S21: 0.0158 S22: -0.0156 S23: -0.0737 REMARK 3 S31: 0.0093 S32: -0.0564 S33: -0.0476 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4NRO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-DEC-13. REMARK 100 THE DEPOSITION ID IS D_1000083571. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAR-12 REMARK 200 TEMPERATURE (KELVIN) : 130 REMARK 200 PH : 5 REMARK 200 NUMBER OF CRYSTALS USED : 3 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U 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 : 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 : 9906 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 90.0 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) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 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: BALBES REMARK 200 STARTING MODEL: 4NRM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 4K, 100MM CH3CO2NH4, 100MM NA REMARK 280 -CITRATE , PH 5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 72.47000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.08850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.08850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 108.70500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.08850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.08850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 36.23500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.08850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.08850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 108.70500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.08850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.08850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 36.23500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 72.47000 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 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 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 63 REMARK 465 HIS A 64 REMARK 465 MET A 65 REMARK 465 PRO A 66 REMARK 465 GLU A 67 REMARK 465 ARG A 68 REMARK 465 SER A 69 REMARK 465 ASP A 70 REMARK 465 TYR A 71 REMARK 465 GLU A 72 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 ARG A 148 REMARK 465 GLY A 149 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 73 CG CD OE1 OE2 REMARK 470 GLN A 74 CG CD OE1 NE2 REMARK 470 GLN A 75 CG CD OE1 NE2 REMARK 470 GLN A 77 CG CD OE1 NE2 REMARK 470 LYS A 78 CG CD CE NZ REMARK 470 GLU A 80 CG CD OE1 OE2 REMARK 470 GLU A 81 CG CD OE1 OE2 REMARK 470 ARG A 83 CZ NH1 NH2 REMARK 470 LYS A 86 CD CE NZ REMARK 470 ARG A 90 CD NE CZ NH1 NH2 REMARK 470 MET A 92 SD CE REMARK 470 ARG A 93 CG CD NE CZ NH1 NH2 REMARK 470 GLN A 97 OE1 NE2 REMARK 470 LYS A 102 CG CD CE NZ REMARK 470 ARG A 113 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 116 CG CD CE NZ REMARK 470 GLU A 121 CB CG CD OE1 OE2 REMARK 470 LEU A 129 CG CD1 CD2 REMARK 470 LYS A 132 NZ REMARK 470 GLN A 152 CG CD OE1 NE2 REMARK 470 GLU A 163 CG CD OE1 OE2 REMARK 470 GLU A 166 CG CD OE1 OE2 REMARK 470 GLN A 170 CG CD OE1 NE2 REMARK 470 GLN A 174 CD OE1 NE2 REMARK 470 GLU A 178 OE1 REMARK 470 ARG A 180 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 184 CD OE1 OE2 REMARK 470 GLN A 196 OE1 NE2 REMARK 470 LYS A 231 CG CD CE NZ REMARK 470 ILE A 237 CG1 CG2 CD1 REMARK 470 ARG A 238 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 249 CD NE CZ NH1 NH2 REMARK 470 GLU A 263 CG CD OE1 OE2 REMARK 470 LYS A 274 CG CD CE NZ REMARK 470 GLU A 275 CD OE1 OE2 REMARK 470 LYS A 284 NZ REMARK 470 LEU A 287 CD1 CD2 REMARK 470 ASP A 288 OD1 OD2 REMARK 470 ARG A 291 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 292 O CB CG CD1 CD2 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 THR A 140 -152.75 -79.48 REMARK 500 VAL A 172 -66.22 -107.44 REMARK 500 SER A 203 124.72 -33.64 REMARK 500 PHE A 220 -66.97 -120.08 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 301 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 204 NE2 REMARK 620 2 ASP A 206 OD1 87.0 REMARK 620 3 HIS A 266 NE2 84.4 102.1 REMARK 620 4 AKG A 302 O1 90.8 96.9 160.1 REMARK 620 5 AKG A 302 O5 89.2 173.3 83.0 77.6 REMARK 620 6 HOH A 401 O 173.5 86.5 96.9 90.0 97.3 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AKG A 302 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4NRM RELATED DB: PDB REMARK 900 RELATED ID: 4NRP RELATED DB: PDB REMARK 900 RELATED ID: 4NRQ RELATED DB: PDB DBREF 4NRO A 66 292 UNP Q6P6C2 ALKB5_HUMAN 66 292 SEQADV 4NRO GLY A 63 UNP Q6P6C2 EXPRESSION TAG SEQADV 4NRO HIS A 64 UNP Q6P6C2 EXPRESSION TAG SEQADV 4NRO MET A 65 UNP Q6P6C2 EXPRESSION TAG SEQRES 1 A 230 GLY HIS MET PRO GLU ARG SER ASP TYR GLU GLU GLN GLN SEQRES 2 A 230 LEU GLN LYS GLU GLU GLU ALA ARG LYS VAL LYS SER GLY SEQRES 3 A 230 ILE ARG GLN MET ARG LEU PHE SER GLN ASP GLU CYS ALA SEQRES 4 A 230 LYS ILE GLU ALA ARG ILE ASP GLU VAL VAL SER ARG ALA SEQRES 5 A 230 GLU LYS GLY LEU TYR ASN GLU HIS THR VAL ASP ARG ALA SEQRES 6 A 230 PRO LEU ARG ASN LYS TYR PHE PHE GLY GLU GLY TYR THR SEQRES 7 A 230 TYR GLY ALA GLN LEU GLN LYS ARG GLY PRO GLY GLN GLU SEQRES 8 A 230 ARG LEU TYR PRO PRO GLY ASP VAL ASP GLU ILE PRO GLU SEQRES 9 A 230 TRP VAL HIS GLN LEU VAL ILE GLN LYS LEU VAL GLU HIS SEQRES 10 A 230 ARG VAL ILE PRO GLU GLY PHE VAL ASN SER ALA VAL ILE SEQRES 11 A 230 ASN ASP TYR GLN PRO GLY GLY CYS ILE VAL SER HIS VAL SEQRES 12 A 230 ASP PRO ILE HIS ILE PHE GLU ARG PRO ILE VAL SER VAL SEQRES 13 A 230 SER PHE PHE SER ASP SER ALA LEU CYS PHE GLY CYS LYS SEQRES 14 A 230 PHE GLN PHE LYS PRO ILE ARG VAL SER GLU PRO VAL LEU SEQRES 15 A 230 SER LEU PRO VAL ARG ARG GLY SER VAL THR VAL LEU SER SEQRES 16 A 230 GLY TYR ALA ALA ASP GLU ILE THR HIS CYS ILE ARG PRO SEQRES 17 A 230 GLN ASP ILE LYS GLU ARG ARG ALA VAL ILE ILE LEU ARG SEQRES 18 A 230 LYS THR ARG LEU ASP ALA PRO ARG LEU HET MN A 301 1 HET AKG A 302 10 HETNAM MN MANGANESE (II) ION HETNAM AKG 2-OXOGLUTARIC ACID FORMUL 2 MN MN 2+ FORMUL 3 AKG C5 H6 O5 FORMUL 4 HOH *110(H2 O) HELIX 1 1 GLN A 75 SER A 87 1 13 HELIX 2 2 SER A 96 LYS A 116 1 21 HELIX 3 3 PRO A 165 VAL A 172 1 8 HELIX 4 4 VAL A 172 HIS A 179 1 8 HELIX 5 5 CYS A 230 PHE A 234 5 5 HELIX 6 6 SER A 257 GLU A 263 1 7 HELIX 7 7 ARG A 269 ILE A 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 253 N MET A 92 SHEET 3 A 7 ILE A 215 SER A 219 -1 N ILE A 215 O LEU A 256 SHEET 4 A 7 ARG A 277 ARG A 283 -1 O LEU A 282 N VAL A 216 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 ARG A 126 -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 246 N LEU A 226 SSBOND 1 CYS A 230 CYS A 267 1555 1555 2.07 LINK NE2 HIS A 204 MN MN A 301 1555 1555 2.25 LINK OD1 ASP A 206 MN MN A 301 1555 1555 2.22 LINK NE2 HIS A 266 MN MN A 301 1555 1555 2.25 LINK MN MN A 301 O1 AKG A 302 1555 1555 2.22 LINK MN MN A 301 O5 AKG A 302 1555 1555 2.28 LINK MN MN A 301 O HOH A 401 1555 1555 2.40 CISPEP 1 ARG A 213 PRO A 214 0 2.02 SITE 1 AC1 5 HIS A 204 ASP A 206 HIS A 266 AKG A 302 SITE 2 AC1 5 HOH A 401 SITE 1 AC2 12 ASN A 193 TYR A 195 ILE A 201 HIS A 204 SITE 2 AC2 12 ASP A 206 HIS A 266 ILE A 268 ARG A 277 SITE 3 AC2 12 VAL A 279 ILE A 281 MN A 301 HOH A 445 CRYST1 56.177 56.177 144.940 90.00 90.00 90.00 P 43 21 2 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 0.017801 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017801 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006899 0.00000