HEADER OXIDOREDUCTASE 29-AUG-12 4GUU TITLE CRYSTAL STRUCTURE OF LSD2-NPAC WITH TRANYLCYPROMINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC HISTONE DEMETHYLASE 1B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 51-822; COMPND 5 SYNONYM: LSD2, FLAVIN-CONTAINING AMINE OXIDASE DOMAIN-CONTAINING COMPND 6 PROTEIN 1, LYSINE-SPECIFIC HISTONE DEMETHYLASE 2; COMPND 7 EC: 1.-.-.-; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: PUTATIVE OXIDOREDUCTASE GLYR1; COMPND 11 CHAIN: B; COMPND 12 FRAGMENT: UNP RESIDUES 152-268; COMPND 13 SYNONYM: NPAC, 3-HYDROXYISOBUTYRATE DEHYDROGENASE-LIKE PROTEIN, COMPND 14 CYTOKINE-LIKE NUCLEAR FACTOR N-PAC, GLYOXYLATE REDUCTASE 1 HOMOLOG, COMPND 15 NUCLEAR PROTEIN NP60, NUCLEAR PROTEIN OF 60 KDA; COMPND 16 EC: 1.-.-.-; COMPND 17 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: LSD2; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PFASTBAC1; SOURCE 12 MOL_ID: 2; SOURCE 13 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 14 ORGANISM_COMMON: HUMAN; SOURCE 15 ORGANISM_TAXID: 9606; SOURCE 16 GENE: GLYR1; SOURCE 17 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 18 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HISTONE DEMETHYLASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR F.CHEN,Z.DONG,J.FANG,Y.YANG,Z.LI,Y.XU,H.YANG,P.WANG,Y.XU REVDAT 3 08-NOV-23 4GUU 1 REMARK SEQADV LINK REVDAT 2 10-JUL-13 4GUU 1 JRNL REVDAT 1 16-JAN-13 4GUU 0 JRNL AUTH R.FANG,F.CHEN,Z.DONG,D.HU,A.J.BARBERA,E.A.CLARK,J.FANG, JRNL AUTH 2 Y.YANG,P.MEI,M.RUTENBERG,Z.LI,Y.ZHANG,Y.XU,H.YANG,P.WANG, JRNL AUTH 3 M.D.SIMON,Q.ZHOU,J.LI,M.P.MARYNICK,X.LI,H.LU,U.B.KAISER, JRNL AUTH 4 R.E.KINGSTON,Y.XU,Y.G.SHI JRNL TITL LSD2/KDM1B AND ITS COFACTOR NPAC/GLYR1 ENDOW A STRUCTURAL JRNL TITL 2 AND MOLECULAR MODEL FOR REGULATION OF H3K4 DEMETHYLATION JRNL REF MOL.CELL V. 49 558 2013 JRNL REFN ISSN 1097-2765 JRNL PMID 23260659 JRNL DOI 10.1016/J.MOLCEL.2012.11.019 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.6.1_353) 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.23 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.110 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 3 NUMBER OF REFLECTIONS : 37948 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1922 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 36.2369 - 5.5415 0.95 2786 150 0.1806 0.2165 REMARK 3 2 5.5415 - 4.4009 0.96 2773 160 0.1672 0.1792 REMARK 3 3 4.4009 - 3.8453 0.89 2568 130 0.1651 0.1953 REMARK 3 4 3.8453 - 3.4941 0.41 1184 59 0.1934 0.2327 REMARK 3 5 3.4941 - 3.2438 0.96 2755 148 0.2098 0.2433 REMARK 3 6 3.2438 - 3.0526 0.97 2752 157 0.2139 0.2386 REMARK 3 7 3.0526 - 2.8998 0.96 2730 165 0.2164 0.2707 REMARK 3 8 2.8998 - 2.7737 0.97 2794 125 0.2189 0.2405 REMARK 3 9 2.7737 - 2.6669 0.96 2738 140 0.2207 0.2697 REMARK 3 10 2.6669 - 2.5749 0.96 2729 157 0.2252 0.2782 REMARK 3 11 2.5749 - 2.4944 0.95 2690 143 0.2199 0.2897 REMARK 3 12 2.4944 - 2.4231 0.93 2666 136 0.2178 0.2437 REMARK 3 13 2.4231 - 2.3593 0.93 2672 134 0.2263 0.2490 REMARK 3 14 2.3593 - 2.3018 0.78 2189 118 0.2405 0.2762 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 : 0.33 REMARK 3 B_SOL : 39.97 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.68 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.23 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.35880 REMARK 3 B22 (A**2) : 2.73740 REMARK 3 B33 (A**2) : 0.62130 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 9.74730 REMARK 3 B23 (A**2) : 0.00000 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 : 0.004 6181 REMARK 3 ANGLE : 0.772 8278 REMARK 3 CHIRALITY : 0.055 894 REMARK 3 PLANARITY : 0.003 1064 REMARK 3 DIHEDRAL : 14.871 2249 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 4GUU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000074660. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAY-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 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) : 0.97906 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37948 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 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 (%) : 90.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 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 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: 4GU1 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.69 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.02M CITRIC ACID, 0.03M BIS_TRIS REMARK 280 PROPANE, 10% PEG3350, PH 6.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 45.07850 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3460 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31920 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 THR A 175 REMARK 465 ALA A 176 REMARK 465 ILE A 177 REMARK 465 LYS A 178 REMARK 465 PRO A 179 REMARK 465 GLU A 180 REMARK 465 THR A 181 REMARK 465 SER A 236 REMARK 465 THR A 237 REMARK 465 ASN A 238 REMARK 465 ARG A 239 REMARK 465 ALA A 240 REMARK 465 ALA A 241 REMARK 465 ALA A 242 REMARK 465 THR A 243 REMARK 465 GLY A 244 REMARK 465 ASN A 245 REMARK 465 ALA A 246 REMARK 465 SER A 247 REMARK 465 PRO A 248 REMARK 465 GLY A 249 REMARK 465 LYS A 250 REMARK 465 LEU A 251 REMARK 465 GLU A 252 REMARK 465 HIS A 253 REMARK 465 SER A 254 REMARK 465 LYS A 255 REMARK 465 ALA A 256 REMARK 465 ALA A 257 REMARK 465 LEU A 258 REMARK 465 SER A 259 REMARK 465 VAL A 260 REMARK 465 HIS A 261 REMARK 465 VAL A 262 REMARK 465 PRO A 263 REMARK 465 PHE A 822 REMARK 465 PRO B 145 REMARK 465 LEU B 146 REMARK 465 GLY B 147 REMARK 465 SER B 148 REMARK 465 PRO B 149 REMARK 465 GLU B 150 REMARK 465 PHE B 151 REMARK 465 SER B 152 REMARK 465 GLU B 153 REMARK 465 ARG B 154 REMARK 465 GLY B 155 REMARK 465 SER B 156 REMARK 465 LYS B 157 REMARK 465 SER B 158 REMARK 465 PRO B 159 REMARK 465 LEU B 160 REMARK 465 LYS B 161 REMARK 465 ARG B 162 REMARK 465 ALA B 163 REMARK 465 GLN B 164 REMARK 465 GLU B 165 REMARK 465 GLN B 166 REMARK 465 SER B 167 REMARK 465 PRO B 168 REMARK 465 ARG B 169 REMARK 465 LYS B 170 REMARK 465 ARG B 171 REMARK 465 GLY B 172 REMARK 465 ARG B 173 REMARK 465 PRO B 174 REMARK 465 PRO B 175 REMARK 465 LYS B 176 REMARK 465 ASP B 177 REMARK 465 GLU B 178 REMARK 465 LYS B 179 REMARK 465 ASP B 180 REMARK 465 LEU B 181 REMARK 465 THR B 182 REMARK 465 ILE B 183 REMARK 465 PRO B 184 REMARK 465 GLU B 185 REMARK 465 SER B 186 REMARK 465 SER B 187 REMARK 465 THR B 188 REMARK 465 VAL B 189 REMARK 465 LYS B 190 REMARK 465 GLY B 191 REMARK 465 MET B 192 REMARK 465 MET B 193 REMARK 465 ALA B 194 REMARK 465 GLY B 195 REMARK 465 PRO B 196 REMARK 465 MET B 197 REMARK 465 ALA B 198 REMARK 465 ALA B 199 REMARK 465 PHE B 200 REMARK 465 LYS B 201 REMARK 465 TRP B 202 REMARK 465 GLN B 203 REMARK 465 PRO B 204 REMARK 465 THR B 205 REMARK 465 ALA B 206 REMARK 465 SER B 207 REMARK 465 GLU B 208 REMARK 465 PRO B 209 REMARK 465 VAL B 210 REMARK 465 LYS B 211 REMARK 465 ASP B 212 REMARK 465 ALA B 213 REMARK 465 GLU B 226 REMARK 465 LYS B 227 REMARK 465 PRO B 228 REMARK 465 ALA B 229 REMARK 465 VAL B 230 REMARK 465 CYS B 231 REMARK 465 TYR B 232 REMARK 465 GLN B 233 REMARK 465 ALA B 234 REMARK 465 ILE B 235 REMARK 465 THR B 236 REMARK 465 LYS B 237 REMARK 465 LYS B 238 REMARK 465 LEU B 239 REMARK 465 LYS B 240 REMARK 465 ILE B 241 REMARK 465 CYS B 242 REMARK 465 GLU B 243 REMARK 465 GLU B 244 REMARK 465 GLU B 245 REMARK 465 THR B 246 REMARK 465 GLY B 247 REMARK 465 SER B 248 REMARK 465 THR B 249 REMARK 465 SER B 250 REMARK 465 ILE B 251 REMARK 465 GLN B 252 REMARK 465 ALA B 253 REMARK 465 ALA B 254 REMARK 465 ASP B 255 REMARK 465 SER B 256 REMARK 465 THR B 257 REMARK 465 ALA B 258 REMARK 465 VAL B 259 REMARK 465 ASN B 260 REMARK 465 GLY B 261 REMARK 465 SER B 262 REMARK 465 ILE B 263 REMARK 465 THR B 264 REMARK 465 PRO B 265 REMARK 465 THR B 266 REMARK 465 ASP B 267 REMARK 465 LYS B 268 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 SER A 68 47.43 39.26 REMARK 500 LYS A 75 -122.78 50.87 REMARK 500 ASN A 120 47.91 -147.22 REMARK 500 PRO A 125 50.16 -94.84 REMARK 500 CYS A 147 -73.96 -102.57 REMARK 500 CYS A 169 132.79 -36.55 REMARK 500 ASP A 183 47.59 77.79 REMARK 500 ASN A 276 73.15 41.32 REMARK 500 LYS A 383 162.04 172.85 REMARK 500 GLN A 437 5.13 -157.93 REMARK 500 GLU A 523 -87.33 -60.15 REMARK 500 ILE A 526 133.79 -36.90 REMARK 500 PHE A 741 58.25 -115.77 REMARK 500 LYS A 751 136.12 178.30 REMARK 500 ILE A 763 -62.71 -132.21 REMARK 500 GLN A 803 -40.10 85.23 REMARK 500 PRO B 215 17.54 -63.69 REMARK 500 PHE B 217 -37.21 -132.35 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 ZN A 902 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 53 SG REMARK 620 2 CYS A 58 SG 120.6 REMARK 620 3 HIS A 84 ND1 108.3 105.8 REMARK 620 4 HIS A 90 NE2 101.1 112.3 108.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 903 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 65 SG REMARK 620 2 CYS A 73 SG 102.1 REMARK 620 3 CYS A 92 SG 115.7 110.2 REMARK 620 4 CYS A 95 SG 114.0 104.8 109.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 904 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 142 SG REMARK 620 2 CYS A 147 SG 113.7 REMARK 620 3 CYS A 169 SG 105.7 107.4 REMARK 620 4 CYS A 185 SG 109.0 115.1 105.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FA9 A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 904 DBREF 4GUU A 51 822 UNP Q8NB78 KDM1B_HUMAN 51 822 DBREF 4GUU B 152 268 UNP Q49A26 GLYR1_HUMAN 152 268 SEQADV 4GUU PRO A 47 UNP Q8NB78 EXPRESSION TAG SEQADV 4GUU LEU A 48 UNP Q8NB78 EXPRESSION TAG SEQADV 4GUU GLY A 49 UNP Q8NB78 EXPRESSION TAG SEQADV 4GUU SER A 50 UNP Q8NB78 EXPRESSION TAG SEQADV 4GUU PRO B 145 UNP Q49A26 EXPRESSION TAG SEQADV 4GUU LEU B 146 UNP Q49A26 EXPRESSION TAG SEQADV 4GUU GLY B 147 UNP Q49A26 EXPRESSION TAG SEQADV 4GUU SER B 148 UNP Q49A26 EXPRESSION TAG SEQADV 4GUU PRO B 149 UNP Q49A26 EXPRESSION TAG SEQADV 4GUU GLU B 150 UNP Q49A26 EXPRESSION TAG SEQADV 4GUU PHE B 151 UNP Q49A26 EXPRESSION TAG SEQRES 1 A 776 PRO LEU GLY SER ARG LYS CYS GLU LYS ALA GLY CYS THR SEQRES 2 A 776 ALA THR CYS PRO VAL CYS PHE ALA SER ALA SER GLU ARG SEQRES 3 A 776 CYS ALA LYS ASN GLY TYR THR SER ARG TRP TYR HIS LEU SEQRES 4 A 776 SER CYS GLY GLU HIS PHE CYS ASN GLU CYS PHE ASP HIS SEQRES 5 A 776 TYR TYR ARG SER HIS LYS ASP GLY TYR ASP LYS TYR THR SEQRES 6 A 776 THR TRP LYS LYS ILE TRP THR SER ASN GLY LYS THR GLU SEQRES 7 A 776 PRO SER PRO LYS ALA PHE MET ALA ASP GLN GLN LEU PRO SEQRES 8 A 776 TYR TRP VAL GLN CYS THR LYS PRO GLU CYS ARG LYS TRP SEQRES 9 A 776 ARG GLN LEU THR LYS GLU ILE GLN LEU THR PRO GLN ILE SEQRES 10 A 776 ALA LYS THR TYR ARG CYS GLY MET LYS PRO ASN THR ALA SEQRES 11 A 776 ILE LYS PRO GLU THR SER ASP HIS CYS SER LEU PRO GLU SEQRES 12 A 776 ASP LEU ARG VAL LEU GLU VAL SER ASN HIS TRP TRP TYR SEQRES 13 A 776 SER MET LEU ILE LEU PRO PRO LEU LEU LYS ASP SER VAL SEQRES 14 A 776 ALA ALA PRO LEU LEU SER ALA TYR TYR PRO ASP CYS VAL SEQRES 15 A 776 GLY MET SER PRO SER CYS THR SER THR ASN ARG ALA ALA SEQRES 16 A 776 ALA THR GLY ASN ALA SER PRO GLY LYS LEU GLU HIS SER SEQRES 17 A 776 LYS ALA ALA LEU SER VAL HIS VAL PRO GLY MET ASN ARG SEQRES 18 A 776 TYR PHE GLN PRO PHE TYR GLN PRO ASN GLU CYS GLY LYS SEQRES 19 A 776 ALA LEU CYS VAL ARG PRO ASP VAL MET GLU LEU ASP GLU SEQRES 20 A 776 LEU TYR GLU PHE PRO GLU TYR SER ARG ASP PRO THR MET SEQRES 21 A 776 TYR LEU ALA LEU ARG ASN LEU ILE LEU ALA LEU TRP TYR SEQRES 22 A 776 THR ASN CYS LYS GLU ALA LEU THR PRO GLN LYS CYS ILE SEQRES 23 A 776 PRO HIS ILE ILE VAL ARG GLY LEU VAL ARG ILE ARG CYS SEQRES 24 A 776 VAL GLN GLU VAL GLU ARG ILE LEU TYR PHE MET THR ARG SEQRES 25 A 776 LYS GLY LEU ILE ASN THR GLY VAL LEU SER VAL GLY ALA SEQRES 26 A 776 ASP GLN TYR LEU LEU PRO LYS ASP TYR HIS ASN LYS SER SEQRES 27 A 776 VAL ILE ILE ILE GLY ALA GLY PRO ALA GLY LEU ALA ALA SEQRES 28 A 776 ALA ARG GLN LEU HIS ASN PHE GLY ILE LYS VAL THR VAL SEQRES 29 A 776 LEU GLU ALA LYS ASP ARG ILE GLY GLY ARG VAL TRP ASP SEQRES 30 A 776 ASP LYS SER PHE LYS GLY VAL THR VAL GLY ARG GLY ALA SEQRES 31 A 776 GLN ILE VAL ASN GLY CYS ILE ASN ASN PRO VAL ALA LEU SEQRES 32 A 776 MET CYS GLU GLN LEU GLY ILE SER MET HIS LYS PHE GLY SEQRES 33 A 776 GLU ARG CYS ASP LEU ILE GLN GLU GLY GLY ARG ILE THR SEQRES 34 A 776 ASP PRO THR ILE ASP LYS ARG MET ASP PHE HIS PHE ASN SEQRES 35 A 776 ALA LEU LEU ASP VAL VAL SER GLU TRP ARG LYS ASP LYS SEQRES 36 A 776 THR GLN LEU GLN ASP VAL PRO LEU GLY GLU LYS ILE GLU SEQRES 37 A 776 GLU ILE TYR LYS ALA PHE ILE LYS GLU SER GLY ILE GLN SEQRES 38 A 776 PHE SER GLU LEU GLU GLY GLN VAL LEU GLN PHE HIS LEU SEQRES 39 A 776 SER ASN LEU GLU TYR ALA CYS GLY SER ASN LEU HIS GLN SEQRES 40 A 776 VAL SER ALA ARG SER TRP ASP HIS ASN GLU PHE PHE ALA SEQRES 41 A 776 GLN PHE ALA GLY ASP HIS THR LEU LEU THR PRO GLY TYR SEQRES 42 A 776 SER VAL ILE ILE GLU LYS LEU ALA GLU GLY LEU ASP ILE SEQRES 43 A 776 GLN LEU LYS SER PRO VAL GLN CYS ILE ASP TYR SER GLY SEQRES 44 A 776 ASP GLU VAL GLN VAL THR THR THR ASP GLY THR GLY TYR SEQRES 45 A 776 SER ALA GLN LYS VAL LEU VAL THR VAL PRO LEU ALA LEU SEQRES 46 A 776 LEU GLN LYS GLY ALA ILE GLN PHE ASN PRO PRO LEU SER SEQRES 47 A 776 GLU LYS LYS MET LYS ALA ILE ASN SER LEU GLY ALA GLY SEQRES 48 A 776 ILE ILE GLU LYS ILE ALA LEU GLN PHE PRO TYR ARG PHE SEQRES 49 A 776 TRP ASP SER LYS VAL GLN GLY ALA ASP PHE PHE GLY HIS SEQRES 50 A 776 VAL PRO PRO SER ALA SER LYS ARG GLY LEU PHE ALA VAL SEQRES 51 A 776 PHE TYR ASP MET ASP PRO GLN LYS LYS HIS SER VAL LEU SEQRES 52 A 776 MET SER VAL ILE ALA GLY GLU ALA VAL ALA SER VAL ARG SEQRES 53 A 776 THR LEU ASP ASP LYS GLN VAL LEU GLN GLN CYS MET ALA SEQRES 54 A 776 THR LEU ARG GLU LEU PHE LYS GLU GLN GLU VAL PRO ASP SEQRES 55 A 776 PRO THR LYS TYR PHE VAL THR ARG TRP SER THR ASP PRO SEQRES 56 A 776 TRP ILE GLN MET ALA TYR SER PHE VAL LYS THR GLY GLY SEQRES 57 A 776 SER GLY GLU ALA TYR ASP ILE ILE ALA GLU ASP ILE GLN SEQRES 58 A 776 GLY THR VAL PHE PHE ALA GLY GLU ALA THR ASN ARG HIS SEQRES 59 A 776 PHE PRO GLN THR VAL THR GLY ALA TYR LEU SER GLY VAL SEQRES 60 A 776 ARG GLU ALA SER LYS ILE ALA ALA PHE SEQRES 1 B 124 PRO LEU GLY SER PRO GLU PHE SER GLU ARG GLY SER LYS SEQRES 2 B 124 SER PRO LEU LYS ARG ALA GLN GLU GLN SER PRO ARG LYS SEQRES 3 B 124 ARG GLY ARG PRO PRO LYS ASP GLU LYS ASP LEU THR ILE SEQRES 4 B 124 PRO GLU SER SER THR VAL LYS GLY MET MET ALA GLY PRO SEQRES 5 B 124 MET ALA ALA PHE LYS TRP GLN PRO THR ALA SER GLU PRO SEQRES 6 B 124 VAL LYS ASP ALA ASP PRO HIS PHE HIS HIS PHE LEU LEU SEQRES 7 B 124 SER GLN THR GLU LYS PRO ALA VAL CYS TYR GLN ALA ILE SEQRES 8 B 124 THR LYS LYS LEU LYS ILE CYS GLU GLU GLU THR GLY SER SEQRES 9 B 124 THR SER ILE GLN ALA ALA ASP SER THR ALA VAL ASN GLY SEQRES 10 B 124 SER ILE THR PRO THR ASP LYS HET FA9 A 901 63 HET ZN A 902 1 HET ZN A 903 1 HET ZN A 904 1 HETNAM FA9 [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4- HETNAM 2 FA9 DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL (2R,3S,4S)-5- HETNAM 3 FA9 [(3R,3AS,7AR)-10,11-DIMETHYL-1,4,6-TRIOXO-3-PHENYL-2, HETNAM 4 FA9 3,5,6,7,7A-HEXAHYDRO-1H-BENZO[G]PYRROLO[2,1- HETNAM 5 FA9 E]PTERIDIN-8(4H)-YL]-2,3,4-TRIHYDROXYPENTYL DIHYDROGEN HETNAM 6 FA9 DIPHOSPHATE HETNAM ZN ZINC ION FORMUL 3 FA9 C36 H43 N9 O16 P2 FORMUL 4 ZN 3(ZN 2+) FORMUL 7 HOH *219(H2 O) HELIX 1 1 ASN A 93 ARG A 101 1 9 HELIX 2 2 GLY A 106 ASN A 120 1 15 HELIX 3 3 SER A 126 GLN A 135 1 10 HELIX 4 4 THR A 160 TYR A 167 1 8 HELIX 5 5 ASP A 183 LEU A 187 5 5 HELIX 6 6 LEU A 191 VAL A 196 1 6 HELIX 7 7 ALA A 216 SER A 221 5 6 HELIX 8 8 TYR A 224 GLY A 229 5 6 HELIX 9 9 GLU A 290 PHE A 297 1 8 HELIX 10 10 PRO A 298 SER A 301 5 4 HELIX 11 11 PRO A 304 ASN A 321 1 18 HELIX 12 12 THR A 327 ILE A 332 1 6 HELIX 13 13 PRO A 333 ILE A 335 5 3 HELIX 14 14 LEU A 340 LYS A 359 1 20 HELIX 15 15 GLY A 370 TYR A 374 5 5 HELIX 16 16 PRO A 377 ASN A 382 1 6 HELIX 17 17 GLY A 391 GLY A 405 1 15 HELIX 18 18 ASN A 445 GLY A 455 1 11 HELIX 19 19 ASP A 476 ARG A 498 1 23 HELIX 20 20 LYS A 499 LYS A 501 5 3 HELIX 21 21 THR A 502 ASP A 506 5 5 HELIX 22 22 PRO A 508 SER A 524 1 17 HELIX 23 23 SER A 529 GLY A 548 1 20 HELIX 24 24 ASP A 560 PHE A 565 5 6 HELIX 25 25 TYR A 579 GLU A 588 1 10 HELIX 26 26 PRO A 628 LYS A 634 1 7 HELIX 27 27 SER A 644 SER A 653 1 10 HELIX 28 28 TRP A 671 GLN A 676 1 6 HELIX 29 29 SER A 687 ARG A 691 5 5 HELIX 30 30 GLY A 715 THR A 723 1 9 HELIX 31 31 ASP A 725 PHE A 741 1 17 HELIX 32 32 ARG A 756 ASP A 760 5 5 HELIX 33 33 GLY A 776 GLU A 784 1 9 HELIX 34 34 GLY A 794 ASN A 798 5 5 HELIX 35 35 THR A 804 ALA A 821 1 18 HELIX 36 36 HIS B 219 SER B 223 5 5 SHEET 1 A 2 TRP A 82 HIS A 84 0 SHEET 2 A 2 HIS A 90 CYS A 92 -1 O PHE A 91 N TYR A 83 SHEET 1 B 2 TRP A 139 GLN A 141 0 SHEET 2 B 2 TRP A 150 GLN A 152 -1 O ARG A 151 N VAL A 140 SHEET 1 C 5 ILE A 592 GLN A 593 0 SHEET 2 C 5 LYS A 407 LEU A 411 1 N VAL A 410 O GLN A 593 SHEET 3 C 5 SER A 384 ILE A 388 1 N ILE A 387 O LEU A 411 SHEET 4 C 5 LYS A 622 VAL A 625 1 O LEU A 624 N ILE A 386 SHEET 5 C 5 VAL A 790 PHE A 792 1 O PHE A 791 N VAL A 625 SHEET 1 D 2 ASP A 423 ASP A 424 0 SHEET 2 D 2 VAL A 432 GLY A 433 -1 O VAL A 432 N ASP A 424 SHEET 1 E 3 ILE A 438 ASN A 440 0 SHEET 2 E 3 HIS A 572 LEU A 574 -1 O THR A 573 N VAL A 439 SHEET 3 E 3 HIS A 459 LYS A 460 -1 N HIS A 459 O LEU A 574 SHEET 1 F 6 LEU A 467 ILE A 468 0 SHEET 2 F 6 PHE A 680 HIS A 683 1 O GLY A 682 N ILE A 468 SHEET 3 F 6 LEU A 693 ASP A 699 -1 O ALA A 695 N HIS A 683 SHEET 4 F 6 VAL A 708 ILE A 713 -1 O MET A 710 N TYR A 698 SHEET 5 F 6 GLU A 660 GLN A 665 -1 N LEU A 664 O LEU A 709 SHEET 6 F 6 LYS A 751 VAL A 754 -1 O LYS A 751 N GLN A 665 SHEET 1 G 4 GLY A 617 ALA A 620 0 SHEET 2 G 4 VAL A 608 THR A 612 -1 N VAL A 610 O TYR A 618 SHEET 3 G 4 VAL A 598 ASP A 602 -1 N GLN A 599 O THR A 611 SHEET 4 G 4 GLN A 638 ASN A 640 1 O GLN A 638 N GLN A 599 SHEET 1 H 2 LEU A 654 GLY A 657 0 SHEET 2 H 2 TYR A 767 VAL A 770 -1 O PHE A 769 N GLY A 655 LINK SG CYS A 53 ZN ZN A 902 1555 1555 2.42 LINK SG CYS A 58 ZN ZN A 902 1555 1555 2.33 LINK SG CYS A 65 ZN ZN A 903 1555 1555 2.45 LINK SG CYS A 73 ZN ZN A 903 1555 1555 2.57 LINK ND1 HIS A 84 ZN ZN A 902 1555 1555 2.15 LINK NE2 HIS A 90 ZN ZN A 902 1555 1555 2.16 LINK SG CYS A 92 ZN ZN A 903 1555 1555 2.51 LINK SG CYS A 95 ZN ZN A 903 1555 1555 2.24 LINK SG CYS A 142 ZN ZN A 904 1555 1555 2.46 LINK SG CYS A 147 ZN ZN A 904 1555 1555 2.36 LINK SG CYS A 169 ZN ZN A 904 1555 1555 2.52 LINK SG CYS A 185 ZN ZN A 904 1555 1555 2.52 CISPEP 1 GLU A 470 GLY A 471 0 -0.69 CISPEP 2 ASN A 640 PRO A 641 0 2.65 SITE 1 AC1 34 ILE A 388 GLY A 389 GLY A 391 PRO A 392 SITE 2 AC1 34 ALA A 393 LEU A 411 GLU A 412 ALA A 413 SITE 3 AC1 34 LYS A 414 GLY A 418 GLY A 419 ARG A 420 SITE 4 AC1 34 ALA A 436 GLN A 437 ILE A 438 TYR A 545 SITE 5 AC1 34 VAL A 598 THR A 626 VAL A 627 PRO A 628 SITE 6 AC1 34 TRP A 757 TRP A 762 ALA A 766 TYR A 767 SITE 7 AC1 34 GLY A 794 GLU A 795 GLN A 803 THR A 804 SITE 8 AC1 34 VAL A 805 ALA A 808 HOH A1102 HOH A1121 SITE 9 AC1 34 HOH A1195 HOH A1246 SITE 1 AC2 4 CYS A 53 CYS A 58 HIS A 84 HIS A 90 SITE 1 AC3 4 CYS A 65 CYS A 73 CYS A 92 CYS A 95 SITE 1 AC4 4 CYS A 142 CYS A 147 CYS A 169 CYS A 185 CRYST1 62.820 90.157 87.824 90.00 104.20 90.00 P 1 21 1 2 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 0.015918 0.000000 0.004028 0.00000 SCALE2 0.000000 0.011092 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011745 0.00000