HEADER TRANSCRIPTION 15-DEC-09 2X0L TITLE CRYSTAL STRUCTURE OF A NEURO-SPECIFIC SPLICING VARIANT OF HUMAN TITLE 2 HISTONE LYSINE DEMETHYLASE LSD1. COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC HISTONE DEMETHYLASE 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FLAVIN-CONTAINING AMINE OXIDASE DOMAIN-CONTAINING PROTEIN 2, COMPND 5 BRAF35-HDAC COMPLEX PROTEIN BHC110; COMPND 6 EC: 1.-.-.-; COMPND 7 ENGINEERED: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: REST COREPRESSOR 1; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: PROTEIN COREST, COREPRESSOR COREST; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: HISTONE H3 PEPTIDE; COMPND 15 CHAIN: C; COMPND 16 FRAGMENT: RESIDUES 2-17; 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES; SOURCE 15 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 16 ORGANISM_COMMON: HUMAN; SOURCE 17 ORGANISM_TAXID: 9606 KEYWDS REPRESSOR COMPLEX, CHROMATIN REMODELLING, AMINE OXIDASE, KEYWDS 2 TRANSCRIPTION, HOST-VIRUS INTERACTION, TRANSCRIPTION REGULATION, KEYWDS 3 PHOSPHOPROTEIN, OXIDOREDUCTASE, NUCLEAR PROTEIN, CHROMATIN KEYWDS 4 REGULATOR, DEVELOPMENTAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.ZIBETTI,A.ADAMO,C.BINDA,F.FORNERIS,C.VERPELLI,E.GINELLI,A.MATTEVI, AUTHOR 2 C.SALA,E.BATTAGLIOLI REVDAT 3 20-DEC-23 2X0L 1 REMARK REVDAT 2 14-DEC-16 2X0L 1 COMPND SOURCE REMARK VERSN REVDAT 2 2 1 DBREF SEQADV REVDAT 1 02-MAR-10 2X0L 0 JRNL AUTH C.ZIBETTI,A.ADAMO,C.BINDA,F.FORNERIS,E.TOFFOLO,C.VERPELLI, JRNL AUTH 2 E.GINELLI,A.MATTEVI,C.SALA,E.BATTAGLIOLI JRNL TITL ALTERNATIVE SPLICING OF THE HISTONE DEMETHYLASE LSD1/KDM1 JRNL TITL 2 CONTRIBUTES TO THE MODULATION OF NEURITE MORPHOGENESIS IN JRNL TITL 3 THE MAMMALIAN NERVOUS SYSTEM. JRNL REF J.NEUROSCI. V. 30 2521 2010 JRNL REFN ISSN 0270-6474 JRNL PMID 20164337 JRNL DOI 10.1523/JNEUROSCI.5500-09.2010 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0078 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 71.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 49397 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) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.900 REMARK 3 FREE R VALUE TEST SET COUNT : 960 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3635 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.65 REMARK 3 BIN R VALUE (WORKING SET) : 0.3130 REMARK 3 BIN FREE R VALUE SET COUNT : 67 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6438 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 53 REMARK 3 SOLVENT ATOMS : 0 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 64.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 4.37000 REMARK 3 B22 (A**2) : -3.03000 REMARK 3 B33 (A**2) : -1.34000 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): 0.339 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.277 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.217 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.819 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.868 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6625 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8984 ; 1.571 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 816 ; 6.895 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 299 ;37.450 ;24.415 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1160 ;21.296 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 44 ;20.361 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1007 ; 0.103 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4973 ; 0.006 ; 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): 4082 ; 0.727 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 6593 ; 1.396 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2543 ; 1.716 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2391 ; 3.079 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2X0L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-DEC-09. REMARK 100 THE DEPOSITION ID IS D_1290042093. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49397 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 70.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.11300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.2000 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: NULL REMARK 200 STARTING MODEL: PDB ENTRY 2IW5 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 78.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 59.84500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 90.60500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 116.72500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 59.84500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 90.60500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 116.72500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 59.84500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 90.60500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 116.72500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 59.84500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 90.60500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 116.72500 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9020 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.7 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 123 REMARK 465 ASP A 124 REMARK 465 GLU A 125 REMARK 465 SER A 126 REMARK 465 LEU A 127 REMARK 465 ALA A 128 REMARK 465 ASN A 129 REMARK 465 LEU A 130 REMARK 465 SER A 131 REMARK 465 GLU A 132 REMARK 465 ASP A 133 REMARK 465 GLU A 134 REMARK 465 TYR A 135 REMARK 465 TYR A 136 REMARK 465 SER A 137 REMARK 465 GLU A 138 REMARK 465 GLU A 139 REMARK 465 GLU A 140 REMARK 465 ARG A 141 REMARK 465 ASN A 142 REMARK 465 ALA A 143 REMARK 465 LYS A 144 REMARK 465 ALA A 145 REMARK 465 GLU A 146 REMARK 465 LYS A 147 REMARK 465 GLU A 148 REMARK 465 LYS A 149 REMARK 465 LYS A 150 REMARK 465 LEU A 151 REMARK 465 PRO A 152 REMARK 465 PRO A 153 REMARK 465 PRO A 154 REMARK 465 PRO A 155 REMARK 465 PRO A 156 REMARK 465 GLN A 157 REMARK 465 ALA A 158 REMARK 465 PRO A 159 REMARK 465 PRO A 160 REMARK 465 GLU A 161 REMARK 465 GLU A 162 REMARK 465 GLU A 163 REMARK 465 ASN A 164 REMARK 465 GLU A 165 REMARK 465 SER A 166 REMARK 465 GLU A 167 REMARK 465 PRO A 168 REMARK 465 GLU A 169 REMARK 465 GLU A 170 REMARK 465 PRO A 837 REMARK 465 ARG A 838 REMARK 465 GLN A 839 REMARK 465 ALA A 840 REMARK 465 THR A 841 REMARK 465 PRO A 842 REMARK 465 GLY A 843 REMARK 465 VAL A 844 REMARK 465 PRO A 845 REMARK 465 ALA A 846 REMARK 465 GLN A 847 REMARK 465 GLN A 848 REMARK 465 SER A 849 REMARK 465 PRO A 850 REMARK 465 SER A 851 REMARK 465 MET A 852 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 OD1 ASN A 660 OG SER A 749 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 PRO A 635 C - N - CA ANGL. DEV. = 10.2 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 PHE A 196 50.67 -147.20 REMARK 500 ASN A 224 86.03 -164.51 REMARK 500 SER A 244 -71.28 -70.39 REMARK 500 PRO A 274 128.27 -28.91 REMARK 500 SER A 286 47.87 -108.18 REMARK 500 LYS A 322 111.11 168.74 REMARK 500 MET A 332 -29.11 -142.66 REMARK 500 THR A 335 56.15 -90.92 REMARK 500 ASN A 350 74.32 -52.52 REMARK 500 ASN A 366 65.57 -116.20 REMARK 500 ALA A 369 -161.28 -62.15 REMARK 500 LYS A 372 0.42 -51.73 REMARK 500 ASN A 402 36.69 77.67 REMARK 500 GLN A 438 -6.78 -55.58 REMARK 500 SER A 466 -38.31 -130.95 REMARK 500 GLU A 467 -79.30 61.87 REMARK 500 VAL A 468 96.23 -69.83 REMARK 500 TYR A 494 -8.06 -56.18 REMARK 500 LYS A 503 -76.89 -49.36 REMARK 500 GLU A 510 -81.58 -64.19 REMARK 500 ASN A 514 68.84 -107.91 REMARK 500 ALA A 541 58.01 35.37 REMARK 500 THR A 542 146.25 -174.83 REMARK 500 PRO A 543 121.58 -37.07 REMARK 500 ASN A 587 28.98 45.96 REMARK 500 THR A 610 21.64 -76.35 REMARK 500 ASN A 717 34.83 -89.63 REMARK 500 ALA A 729 -75.79 -43.75 REMARK 500 SER A 737 -33.46 -26.09 REMARK 500 ALA A 757 -59.82 -138.28 REMARK 500 SER A 768 -167.44 -105.97 REMARK 500 SER A 785 -74.27 -61.89 REMARK 500 GLN A 791 121.25 -35.37 REMARK 500 ILE A 793 147.27 -21.49 REMARK 500 TYR A 807 45.71 -145.30 REMARK 500 ALA A 809 14.65 49.84 REMARK 500 TYR A 834 -4.16 -51.46 REMARK 500 PRO B 310 173.57 -53.03 REMARK 500 ALA B 326 -19.77 -44.14 REMARK 500 MET B 340 -60.19 -90.80 REMARK 500 GLU B 341 -35.31 -31.99 REMARK 500 LEU B 363 7.01 -67.95 REMARK 500 PRO B 369 22.80 -73.35 REMARK 500 PRO B 373 147.05 -31.52 REMARK 500 ASP B 401 72.01 -67.69 REMARK 500 ASN B 429 61.44 13.00 REMARK 500 ALA B 439 12.47 -60.33 REMARK 500 THR C 11 -35.86 -137.65 REMARK 500 ALA C 15 66.10 -103.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO A 274 THR A 275 -147.23 REMARK 500 SER A 466 GLU A 467 51.74 REMARK 500 PRO A 792 ILE A 793 145.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FAD A 900 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2UXX RELATED DB: PDB REMARK 900 HUMAN LSD1 HISTONE DEMETHYLASE-COREST IN COMPLEX WITH AN FAD- REMARK 900 TRANYLCYPROMINE ADDUCT REMARK 900 RELATED ID: 2IW5 RELATED DB: PDB REMARK 900 STRUCTURAL BASIS FOR COREST-DEPENDENT DEMETHYLATION OF NUCLEOSOMES REMARK 900 BY THE HUMAN LSD1 HISTONE DEMETHYLASE REMARK 900 RELATED ID: 2V1D RELATED DB: PDB REMARK 900 STRUCTURAL BASIS OF LSD1-COREST SELECTIVITY IN HISTONE H3 REMARK 900 RECOGNITION REMARK 900 RELATED ID: 2UXN RELATED DB: PDB REMARK 900 STRUCTURAL BASIS OF HISTONE DEMETHYLATION BY LSD1 REVEALED BY REMARK 900 SUICIDE INACTIVATION REMARK 900 RELATED ID: 2COM RELATED DB: PDB REMARK 900 THE SOLUTION STRUCTURE OF THE 33RD FIBRONECTIN TYPE IIIDOMAIN OF REMARK 900 HUMAN TENASCIN- X REMARK 900 RELATED ID: 2H94 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE AND MECHANISM OF HUMAN LYSINE-SPECIFICDEMETHYLASE- REMARK 900 1 REMARK 999 REMARK 999 SEQUENCE REMARK 999 SPLICING VARIANT FORM OF THE PROTEIN LSD1: BETWEEN REMARK 999 RESIDUE 369 AND 370 OF CHAIN A THERE ARE 4 ADDITIONAL (DTVK) REMARK 999 RESIDUES THAT HAVE BEEN MARKED AS 369A, 369B, 369C, 369D. DBREF 2X0L A 123 852 UNP O60341 KDM1_HUMAN 123 852 DBREF 2X0L B 308 440 UNP Q9UKL0 RCOR1_HUMAN 308 440 DBREF 2X0L C 1 16 UNP Q5TEC6 Q5TEC6_HUMAN 2 17 SEQADV 2X0L ASP A 369A UNP O60341 INSERTION SEQADV 2X0L THR A 369B UNP O60341 INSERTION SEQADV 2X0L VAL A 369C UNP O60341 INSERTION SEQADV 2X0L LYS A 369D UNP O60341 INSERTION SEQADV 2X0L MET C 4 UNP Q5TEC6 LYS 5 ENGINEERED MUTATION SEQRES 1 A 734 MET ASP GLU SER LEU ALA ASN LEU SER GLU ASP GLU TYR SEQRES 2 A 734 TYR SER GLU GLU GLU ARG ASN ALA LYS ALA GLU LYS GLU SEQRES 3 A 734 LYS LYS LEU PRO PRO PRO PRO PRO GLN ALA PRO PRO GLU SEQRES 4 A 734 GLU GLU ASN GLU SER GLU PRO GLU GLU PRO SER GLY VAL SEQRES 5 A 734 GLU GLY ALA ALA PHE GLN SER ARG LEU PRO HIS ASP ARG SEQRES 6 A 734 MET THR SER GLN GLU ALA ALA CYS PHE PRO ASP ILE ILE SEQRES 7 A 734 SER GLY PRO GLN GLN THR GLN LYS VAL PHE LEU PHE ILE SEQRES 8 A 734 ARG ASN ARG THR LEU GLN LEU TRP LEU ASP ASN PRO LYS SEQRES 9 A 734 ILE GLN LEU THR PHE GLU ALA THR LEU GLN GLN LEU GLU SEQRES 10 A 734 ALA PRO TYR ASN SER ASP THR VAL LEU VAL HIS ARG VAL SEQRES 11 A 734 HIS SER TYR LEU GLU ARG HIS GLY LEU ILE ASN PHE GLY SEQRES 12 A 734 ILE TYR LYS ARG ILE LYS PRO LEU PRO THR LYS LYS THR SEQRES 13 A 734 GLY LYS VAL ILE ILE ILE GLY SER GLY VAL SER GLY LEU SEQRES 14 A 734 ALA ALA ALA ARG GLN LEU GLN SER PHE GLY MET ASP VAL SEQRES 15 A 734 THR LEU LEU GLU ALA ARG ASP ARG VAL GLY GLY ARG VAL SEQRES 16 A 734 ALA THR PHE ARG LYS GLY ASN TYR VAL ALA ASP LEU GLY SEQRES 17 A 734 ALA MET VAL VAL THR GLY LEU GLY GLY ASN PRO MET ALA SEQRES 18 A 734 VAL VAL SER LYS GLN VAL ASN MET GLU LEU ALA LYS ILE SEQRES 19 A 734 LYS GLN LYS CYS PRO LEU TYR GLU ALA ASN GLY GLN ALA SEQRES 20 A 734 ASP THR VAL LYS VAL PRO LYS GLU LYS ASP GLU MET VAL SEQRES 21 A 734 GLU GLN GLU PHE ASN ARG LEU LEU GLU ALA THR SER TYR SEQRES 22 A 734 LEU SER HIS GLN LEU ASP PHE ASN VAL LEU ASN ASN LYS SEQRES 23 A 734 PRO VAL SER LEU GLY GLN ALA LEU GLU VAL VAL ILE GLN SEQRES 24 A 734 LEU GLN GLU LYS HIS VAL LYS ASP GLU GLN ILE GLU HIS SEQRES 25 A 734 TRP LYS LYS ILE VAL LYS THR GLN GLU GLU LEU LYS GLU SEQRES 26 A 734 LEU LEU ASN LYS MET VAL ASN LEU LYS GLU LYS ILE LYS SEQRES 27 A 734 GLU LEU HIS GLN GLN TYR LYS GLU ALA SER GLU VAL LYS SEQRES 28 A 734 PRO PRO ARG ASP ILE THR ALA GLU PHE LEU VAL LYS SER SEQRES 29 A 734 LYS HIS ARG ASP LEU THR ALA LEU CYS LYS GLU TYR ASP SEQRES 30 A 734 GLU LEU ALA GLU THR GLN GLY LYS LEU GLU GLU LYS LEU SEQRES 31 A 734 GLN GLU LEU GLU ALA ASN PRO PRO SER ASP VAL TYR LEU SEQRES 32 A 734 SER SER ARG ASP ARG GLN ILE LEU ASP TRP HIS PHE ALA SEQRES 33 A 734 ASN LEU GLU PHE ALA ASN ALA THR PRO LEU SER THR LEU SEQRES 34 A 734 SER LEU LYS HIS TRP ASP GLN ASP ASP ASP PHE GLU PHE SEQRES 35 A 734 THR GLY SER HIS LEU THR VAL ARG ASN GLY TYR SER CYS SEQRES 36 A 734 VAL PRO VAL ALA LEU ALA GLU GLY LEU ASP ILE LYS LEU SEQRES 37 A 734 ASN THR ALA VAL ARG GLN VAL ARG TYR THR ALA SER GLY SEQRES 38 A 734 CYS GLU VAL ILE ALA VAL ASN THR ARG SER THR SER GLN SEQRES 39 A 734 THR PHE ILE TYR LYS CYS ASP ALA VAL LEU CYS THR LEU SEQRES 40 A 734 PRO LEU GLY VAL LEU LYS GLN GLN PRO PRO ALA VAL GLN SEQRES 41 A 734 PHE VAL PRO PRO LEU PRO GLU TRP LYS THR SER ALA VAL SEQRES 42 A 734 GLN ARG MET GLY PHE GLY ASN LEU ASN LYS VAL VAL LEU SEQRES 43 A 734 CYS PHE ASP ARG VAL PHE TRP ASP PRO SER VAL ASN LEU SEQRES 44 A 734 PHE GLY HIS VAL GLY SER THR THR ALA SER ARG GLY GLU SEQRES 45 A 734 LEU PHE LEU PHE TRP ASN LEU TYR LYS ALA PRO ILE LEU SEQRES 46 A 734 LEU ALA LEU VAL ALA GLY GLU ALA ALA GLY ILE MET GLU SEQRES 47 A 734 ASN ILE SER ASP ASP VAL ILE VAL GLY ARG CYS LEU ALA SEQRES 48 A 734 ILE LEU LYS GLY ILE PHE GLY SER SER ALA VAL PRO GLN SEQRES 49 A 734 PRO LYS GLU THR VAL VAL SER ARG TRP ARG ALA ASP PRO SEQRES 50 A 734 TRP ALA ARG GLY SER TYR SER TYR VAL ALA ALA GLY SER SEQRES 51 A 734 SER GLY ASN ASP TYR ASP LEU MET ALA GLN PRO ILE THR SEQRES 52 A 734 PRO GLY PRO SER ILE PRO GLY ALA PRO GLN PRO ILE PRO SEQRES 53 A 734 ARG LEU PHE PHE ALA GLY GLU HIS THR ILE ARG ASN TYR SEQRES 54 A 734 PRO ALA THR VAL HIS GLY ALA LEU LEU SER GLY LEU ARG SEQRES 55 A 734 GLU ALA GLY ARG ILE ALA ASP GLN PHE LEU GLY ALA MET SEQRES 56 A 734 TYR THR LEU PRO ARG GLN ALA THR PRO GLY VAL PRO ALA SEQRES 57 A 734 GLN GLN SER PRO SER MET SEQRES 1 B 133 ARG LYS PRO PRO LYS GLY MET PHE LEU SER GLN GLU ASP SEQRES 2 B 133 VAL GLU ALA VAL SER ALA ASN ALA THR ALA ALA THR THR SEQRES 3 B 133 VAL LEU ARG GLN LEU ASP MET GLU LEU VAL SER VAL LYS SEQRES 4 B 133 ARG GLN ILE GLN ASN ILE LYS GLN THR ASN SER ALA LEU SEQRES 5 B 133 LYS GLU LYS LEU ASP GLY GLY ILE GLU PRO TYR ARG LEU SEQRES 6 B 133 PRO GLU VAL ILE GLN LYS CYS ASN ALA ARG TRP THR THR SEQRES 7 B 133 GLU GLU GLN LEU LEU ALA VAL GLN ALA ILE ARG LYS TYR SEQRES 8 B 133 GLY ARG ASP PHE GLN ALA ILE SER ASP VAL ILE GLY ASN SEQRES 9 B 133 LYS SER VAL VAL GLN VAL LYS ASN PHE PHE VAL ASN TYR SEQRES 10 B 133 ARG ARG ARG PHE ASN ILE ASP GLU VAL LEU GLN GLU TRP SEQRES 11 B 133 GLU ALA GLU SEQRES 1 C 16 ALA ARG THR MET GLN THR ALA ARG LYS SER THR GLY GLY SEQRES 2 C 16 LYS ALA PRO HET FAD A 900 53 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE FORMUL 4 FAD C27 H33 N9 O15 P2 HELIX 1 1 GLY A 173 SER A 181 1 9 HELIX 2 2 THR A 189 PHE A 196 1 8 HELIX 3 3 PHE A 196 GLY A 202 1 7 HELIX 4 4 PRO A 203 ASP A 223 1 21 HELIX 5 5 THR A 230 GLN A 237 1 8 HELIX 6 6 ASP A 245 HIS A 259 1 15 HELIX 7 7 GLY A 287 PHE A 300 1 14 HELIX 8 8 ASN A 340 VAL A 349 1 10 HELIX 9 9 GLU A 373 GLN A 395 1 23 HELIX 10 10 SER A 407 ALA A 465 1 59 HELIX 11 11 ASP A 473 GLU A 512 1 40 HELIX 12 12 SER A 522 ASN A 540 1 19 HELIX 13 13 ASP A 555 GLU A 559 5 5 HELIX 14 14 SER A 572 GLU A 580 1 9 HELIX 15 15 PRO A 626 LYS A 631 1 6 HELIX 16 16 PRO A 644 MET A 654 1 11 HELIX 17 17 THR A 684 ARG A 688 5 5 HELIX 18 18 ALA A 708 MET A 715 1 8 HELIX 19 19 GLU A 716 ILE A 718 5 3 HELIX 20 20 SER A 719 GLY A 736 1 18 HELIX 21 21 ASN A 771 GLN A 778 1 8 HELIX 22 22 GLY A 800 ILE A 804 5 5 HELIX 23 23 THR A 810 GLY A 831 1 22 HELIX 24 24 ALA A 832 LEU A 836 5 5 HELIX 25 25 SER B 317 VAL B 324 1 8 HELIX 26 26 THR B 329 LEU B 363 1 35 HELIX 27 27 ILE B 367 ARG B 371 5 5 HELIX 28 28 THR B 384 GLY B 399 1 16 HELIX 29 29 ASP B 401 GLY B 410 1 10 HELIX 30 30 SER B 413 TYR B 424 1 12 HELIX 31 31 ASN B 429 ALA B 439 1 11 HELIX 32 32 ALA C 1 GLN C 5 5 5 SHEET 1 AA 5 ILE A 584 LYS A 585 0 SHEET 2 AA 5 ASP A 303 LEU A 307 1 O LEU A 306 N LYS A 585 SHEET 3 AA 5 LYS A 280 ILE A 284 1 O VAL A 281 N THR A 305 SHEET 4 AA 5 ALA A 620 CYS A 623 1 O ALA A 620 N ILE A 282 SHEET 5 AA 5 LEU A 796 PHE A 798 1 O PHE A 797 N CYS A 623 SHEET 1 AB 2 THR A 319 LYS A 322 0 SHEET 2 AB 2 TYR A 325 ASP A 328 -1 O TYR A 325 N LYS A 322 SHEET 1 AC 3 VAL A 333 VAL A 334 0 SHEET 2 AC 3 LEU A 565 VAL A 567 -1 O LEU A 565 N VAL A 334 SHEET 3 AC 3 LEU A 353 LYS A 355 -1 O ALA A 354 N THR A 566 SHEET 1 AD 2 TYR A 363 GLU A 364 0 SHEET 2 AD 2 VAL A 369C LYS A 369D-1 O VAL A 369C N GLU A 364 SHEET 1 AE 4 SER A 609 CYS A 618 0 SHEET 2 AE 4 GLY A 599 ASN A 606 -1 O CYS A 600 N CYS A 618 SHEET 3 AE 4 THR A 588 THR A 596 -1 O ALA A 589 N VAL A 605 SHEET 4 AE 4 GLN A 638 VAL A 640 1 O GLN A 638 N VAL A 593 SHEET 1 AF 2 GLY A 655 PHE A 656 0 SHEET 2 AF 2 SER A 762 TYR A 763 -1 O TYR A 763 N GLY A 655 SHEET 1 AG 5 LEU A 677 GLY A 679 0 SHEET 2 AG 5 LEU A 693 TRP A 695 -1 O PHE A 694 N PHE A 678 SHEET 3 AG 5 ILE A 702 VAL A 707 -1 O LEU A 704 N TRP A 695 SHEET 4 AG 5 ASN A 660 CYS A 665 -1 O ASN A 660 N VAL A 707 SHEET 5 AG 5 GLU A 745 VAL A 748 -1 O GLU A 745 N CYS A 665 CISPEP 1 ALA A 240 PRO A 241 0 -5.29 CISPEP 2 PRO A 470 PRO A 471 0 4.20 CISPEP 3 GLN A 633 PRO A 634 0 10.69 CISPEP 4 VAL A 640 PRO A 641 0 -1.39 SITE 1 AC1 30 GLY A 285 GLY A 287 VAL A 288 SER A 289 SITE 2 AC1 30 LEU A 307 GLU A 308 ALA A 309 ARG A 310 SITE 3 AC1 30 GLY A 314 GLY A 315 ARG A 316 LEU A 329 SITE 4 AC1 30 GLY A 330 ALA A 331 MET A 332 VAL A 333 SITE 5 AC1 30 THR A 588 VAL A 590 THR A 624 LEU A 625 SITE 6 AC1 30 PRO A 626 TRP A 756 SER A 760 TYR A 761 SITE 7 AC1 30 GLY A 800 GLU A 801 ALA A 809 THR A 810 SITE 8 AC1 30 VAL A 811 MET C 4 CRYST1 119.690 181.210 233.450 90.00 90.00 90.00 I 2 2 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 0.008355 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005518 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004284 0.00000