HEADER OXIDOREDUCTASE 01-JUL-12 4FWE TITLE NATIVE STRUCTURE OF LSD2 /AOF1/KDM1B IN SPACEGROUP OF C2221 AT 2.13A COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC HISTONE DEMETHYLASE 1B; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 30-822; COMPND 5 SYNONYM: FLAVIN-CONTAINING AMINE OXIDASE DOMAIN-CONTAINING PROTEIN 1, COMPND 6 LYSINE-SPECIFIC HISTONE DEMETHYLASE 2; COMPND 7 EC: 1.-.-.-; COMPND 8 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: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28A KEYWDS LSD2, FAD, HISTONE DEMETHYLASE, C4H2C2, CW, EPIGENETIC, KEYWDS 2 OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Q.ZHANG,Z.CHEN REVDAT 3 08-NOV-23 4FWE 1 REMARK SEQADV LINK REVDAT 2 03-JUL-13 4FWE 1 JRNL REVDAT 1 16-JAN-13 4FWE 0 JRNL AUTH Q.ZHANG,S.QI,M.XU,L.YU,Y.TAO,Z.DENG,W.WU,J.LI,Z.CHEN,J.WONG JRNL TITL STRUCTURE-FUNCTION ANALYSIS REVEALS A NOVEL MECHANISM FOR JRNL TITL 2 REGULATION OF HISTONE DEMETHYLASE LSD2/AOF1/KDM1B JRNL REF CELL RES. V. 23 225 2013 JRNL REFN ISSN 1001-0602 JRNL PMID 23266887 JRNL DOI 10.1038/CR.2012.177 REMARK 2 REMARK 2 RESOLUTION. 2.13 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) : 2.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 3.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.0 REMARK 3 NUMBER OF REFLECTIONS : 41665 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) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 2114 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) : 2.13 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.19 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2729 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.56 REMARK 3 BIN R VALUE (WORKING SET) : 0.3030 REMARK 3 BIN FREE R VALUE SET COUNT : 124 REMARK 3 BIN FREE R VALUE : 0.3550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5845 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 69 REMARK 3 SOLVENT ATOMS : 236 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.47000 REMARK 3 B22 (A**2) : 1.24000 REMARK 3 B33 (A**2) : -2.71000 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): 0.269 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.209 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.158 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.254 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6068 ; 0.008 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8250 ; 1.359 ; 1.965 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 749 ; 5.810 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 260 ;34.087 ;23.923 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 981 ;17.573 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 31 ;20.805 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 900 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4614 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4FWE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JUL-12. REMARK 100 THE DEPOSITION ID IS D_1000073439. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-APR-12 REMARK 200 TEMPERATURE (KELVIN) : 130 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NE3A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97943 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44518 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.130 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 (%) : 93.9 REMARK 200 DATA REDUNDANCY : 10.20 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) : 2.13 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.6 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.88900 REMARK 200 R SYM FOR SHELL (I) : 0.66300 REMARK 200 FOR SHELL : 2.200 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: 4FWJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% PEG3350, 200MM DIAMMONIUM CITRATE, REMARK 280 PH 7, EVAPORATION, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z 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 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 91.39850 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 91.39850 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 46.84550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.13650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 46.84550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.13650 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 91.39850 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 46.84550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.13650 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 91.39850 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 46.84550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 48.13650 REMARK 290 SMTRY3 8 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 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 61830 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -7.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -91.39850 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 27 REMARK 465 HIS A 28 REMARK 465 MET A 29 REMARK 465 ALA A 30 REMARK 465 LYS A 31 REMARK 465 LYS A 32 REMARK 465 LYS A 33 REMARK 465 ALA A 34 REMARK 465 THR A 35 REMARK 465 GLU A 36 REMARK 465 THR A 37 REMARK 465 THR A 38 REMARK 465 ASP A 39 REMARK 465 GLU A 40 REMARK 465 ASP A 41 REMARK 465 GLU A 42 REMARK 465 ASP A 43 REMARK 465 GLY A 44 REMARK 465 GLY A 45 REMARK 465 SER A 46 REMARK 465 GLU A 47 REMARK 465 LYS A 48 REMARK 465 ALA A 176 REMARK 465 ILE A 177 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 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 LYS A 52 CD CE NZ REMARK 470 ARG A 72 CZ NH1 NH2 REMARK 470 LYS A 104 CD CE NZ REMARK 470 LYS A 115 CG CD CE NZ REMARK 470 LYS A 122 CE NZ REMARK 470 GLU A 124 CG CD OE1 OE2 REMARK 470 GLU A 146 CG CD OE1 OE2 REMARK 470 LYS A 155 CG CD CE NZ REMARK 470 GLU A 156 CG CD OE1 OE2 REMARK 470 LYS A 172 CG CD CE NZ REMARK 470 THR A 175 OG1 CG2 REMARK 470 LYS A 178 CG CD CE NZ REMARK 470 GLU A 180 CG CD OE1 OE2 REMARK 470 THR A 181 OG1 CG2 REMARK 470 SER A 182 OG REMARK 470 HIS A 199 CG ND1 CD2 CE1 NE2 REMARK 470 MET A 265 CG SD CE REMARK 470 ARG A 267 CZ NH1 NH2 REMARK 470 ASP A 372 CG OD1 OD2 REMARK 470 LYS A 378 CG CD CE NZ REMARK 470 LYS A 481 CG CD CE NZ REMARK 470 GLU A 514 CG CD OE1 OE2 REMARK 470 LYS A 518 CD CE NZ REMARK 470 GLU A 523 CG CD OE1 OE2 REMARK 470 VAL A 581 CG2 REMARK 470 GLU A 607 CG CD OE1 OE2 REMARK 470 THR A 616 CG2 REMARK 470 GLU A 716 CG CD OE1 OE2 REMARK 470 VAL A 721 CG2 REMARK 470 GLU A 784 CD OE1 OE2 REMARK 470 PHE A 822 CG CD1 CD2 CE1 CE2 CZ 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 LEU A 631 CA - CB - CG ANGL. DEV. = -15.7 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 SER A 68 47.47 37.80 REMARK 500 LYS A 75 -112.99 53.40 REMARK 500 CYS A 147 -73.11 -111.14 REMARK 500 PRO A 173 -42.86 -29.42 REMARK 500 GLU A 180 -76.94 -61.18 REMARK 500 SER A 182 43.56 -100.51 REMARK 500 PRO A 263 124.19 -33.12 REMARK 500 ASN A 276 13.39 59.52 REMARK 500 ILE A 332 -59.39 -28.79 REMARK 500 ASN A 382 56.57 -98.90 REMARK 500 GLN A 437 -2.47 -152.48 REMARK 500 GLU A 523 31.78 -92.24 REMARK 500 ILE A 763 -64.02 -127.18 REMARK 500 GLN A 803 -33.87 82.12 REMARK 500 ALA A 821 -75.44 -65.51 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 901 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 53 SG REMARK 620 2 CYS A 58 SG 106.9 REMARK 620 3 HIS A 84 ND1 102.0 113.3 REMARK 620 4 HIS A 90 NE2 101.1 113.8 117.5 REMARK 620 N 1 2 3 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 65 SG REMARK 620 2 CYS A 73 SG 106.6 REMARK 620 3 CYS A 92 SG 113.4 114.1 REMARK 620 4 CYS A 95 SG 113.3 104.4 104.8 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 142 SG REMARK 620 2 CYS A 147 SG 106.3 REMARK 620 3 CYS A 169 SG 107.7 106.4 REMARK 620 4 CYS A 185 SG 110.5 107.8 117.5 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 ZN 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 FAD A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FLC A 905 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4FWF RELATED DB: PDB REMARK 900 RELATED ID: 4FWJ RELATED DB: PDB DBREF 4FWE A 30 822 UNP Q8NB78 KDM1B_HUMAN 30 822 SEQADV 4FWE GLY A 27 UNP Q8NB78 EXPRESSION TAG SEQADV 4FWE HIS A 28 UNP Q8NB78 EXPRESSION TAG SEQADV 4FWE MET A 29 UNP Q8NB78 EXPRESSION TAG SEQRES 1 A 796 GLY HIS MET ALA LYS LYS LYS ALA THR GLU THR THR ASP SEQRES 2 A 796 GLU ASP GLU ASP GLY GLY SER GLU LYS LYS TYR ARG LYS SEQRES 3 A 796 CYS GLU LYS ALA GLY CYS THR ALA THR CYS PRO VAL CYS SEQRES 4 A 796 PHE ALA SER ALA SER GLU ARG CYS ALA LYS ASN GLY TYR SEQRES 5 A 796 THR SER ARG TRP TYR HIS LEU SER CYS GLY GLU HIS PHE SEQRES 6 A 796 CYS ASN GLU CYS PHE ASP HIS TYR TYR ARG SER HIS LYS SEQRES 7 A 796 ASP GLY TYR ASP LYS TYR THR THR TRP LYS LYS ILE TRP SEQRES 8 A 796 THR SER ASN GLY LYS THR GLU PRO SER PRO LYS ALA PHE SEQRES 9 A 796 MET ALA ASP GLN GLN LEU PRO TYR TRP VAL GLN CYS THR SEQRES 10 A 796 LYS PRO GLU CYS ARG LYS TRP ARG GLN LEU THR LYS GLU SEQRES 11 A 796 ILE GLN LEU THR PRO GLN ILE ALA LYS THR TYR ARG CYS SEQRES 12 A 796 GLY MET LYS PRO ASN THR ALA ILE LYS PRO GLU THR SER SEQRES 13 A 796 ASP HIS CYS SER LEU PRO GLU ASP LEU ARG VAL LEU GLU SEQRES 14 A 796 VAL SER ASN HIS TRP TRP TYR SER MET LEU ILE LEU PRO SEQRES 15 A 796 PRO LEU LEU LYS ASP SER VAL ALA ALA PRO LEU LEU SER SEQRES 16 A 796 ALA TYR TYR PRO ASP CYS VAL GLY MET SER PRO SER CYS SEQRES 17 A 796 THR SER THR ASN ARG ALA ALA ALA THR GLY ASN ALA SER SEQRES 18 A 796 PRO GLY LYS LEU GLU HIS SER LYS ALA ALA LEU SER VAL SEQRES 19 A 796 HIS VAL PRO GLY MET ASN ARG TYR PHE GLN PRO PHE TYR SEQRES 20 A 796 GLN PRO ASN GLU CYS GLY LYS ALA LEU CYS VAL ARG PRO SEQRES 21 A 796 ASP VAL MET GLU LEU ASP GLU LEU TYR GLU PHE PRO GLU SEQRES 22 A 796 TYR SER ARG ASP PRO THR MET TYR LEU ALA LEU ARG ASN SEQRES 23 A 796 LEU ILE LEU ALA LEU TRP TYR THR ASN CYS LYS GLU ALA SEQRES 24 A 796 LEU THR PRO GLN LYS CYS ILE PRO HIS ILE ILE VAL ARG SEQRES 25 A 796 GLY LEU VAL ARG ILE ARG CYS VAL GLN GLU VAL GLU ARG SEQRES 26 A 796 ILE LEU TYR PHE MET THR ARG LYS GLY LEU ILE ASN THR SEQRES 27 A 796 GLY VAL LEU SER VAL GLY ALA ASP GLN TYR LEU LEU PRO SEQRES 28 A 796 LYS ASP TYR HIS ASN LYS SER VAL ILE ILE ILE GLY ALA SEQRES 29 A 796 GLY PRO ALA GLY LEU ALA ALA ALA ARG GLN LEU HIS ASN SEQRES 30 A 796 PHE GLY ILE LYS VAL THR VAL LEU GLU ALA LYS ASP ARG SEQRES 31 A 796 ILE GLY GLY ARG VAL TRP ASP ASP LYS SER PHE LYS GLY SEQRES 32 A 796 VAL THR VAL GLY ARG GLY ALA GLN ILE VAL ASN GLY CYS SEQRES 33 A 796 ILE ASN ASN PRO VAL ALA LEU MET CYS GLU GLN LEU GLY SEQRES 34 A 796 ILE SER MET HIS LYS PHE GLY GLU ARG CYS ASP LEU ILE SEQRES 35 A 796 GLN GLU GLY GLY ARG ILE THR ASP PRO THR ILE ASP LYS SEQRES 36 A 796 ARG MET ASP PHE HIS PHE ASN ALA LEU LEU ASP VAL VAL SEQRES 37 A 796 SER GLU TRP ARG LYS ASP LYS THR GLN LEU GLN ASP VAL SEQRES 38 A 796 PRO LEU GLY GLU LYS ILE GLU GLU ILE TYR LYS ALA PHE SEQRES 39 A 796 ILE LYS GLU SER GLY ILE GLN PHE SER GLU LEU GLU GLY SEQRES 40 A 796 GLN VAL LEU GLN PHE HIS LEU SER ASN LEU GLU TYR ALA SEQRES 41 A 796 CYS GLY SER ASN LEU HIS GLN VAL SER ALA ARG SER TRP SEQRES 42 A 796 ASP HIS ASN GLU PHE PHE ALA GLN PHE ALA GLY ASP HIS SEQRES 43 A 796 THR LEU LEU THR PRO GLY TYR SER VAL ILE ILE GLU LYS SEQRES 44 A 796 LEU ALA GLU GLY LEU ASP ILE GLN LEU LYS SER PRO VAL SEQRES 45 A 796 GLN CYS ILE ASP TYR SER GLY ASP GLU VAL GLN VAL THR SEQRES 46 A 796 THR THR ASP GLY THR GLY TYR SER ALA GLN LYS VAL LEU SEQRES 47 A 796 VAL THR VAL PRO LEU ALA LEU LEU GLN LYS GLY ALA ILE SEQRES 48 A 796 GLN PHE ASN PRO PRO LEU SER GLU LYS LYS MET LYS ALA SEQRES 49 A 796 ILE ASN SER LEU GLY ALA GLY ILE ILE GLU LYS ILE ALA SEQRES 50 A 796 LEU GLN PHE PRO TYR ARG PHE TRP ASP SER LYS VAL GLN SEQRES 51 A 796 GLY ALA ASP PHE PHE GLY HIS VAL PRO PRO SER ALA SER SEQRES 52 A 796 LYS ARG GLY LEU PHE ALA VAL PHE TYR ASP MET ASP PRO SEQRES 53 A 796 GLN LYS LYS HIS SER VAL LEU MET SER VAL ILE ALA GLY SEQRES 54 A 796 GLU ALA VAL ALA SER VAL ARG THR LEU ASP ASP LYS GLN SEQRES 55 A 796 VAL LEU GLN GLN CYS MET ALA THR LEU ARG GLU LEU PHE SEQRES 56 A 796 LYS GLU GLN GLU VAL PRO ASP PRO THR LYS TYR PHE VAL SEQRES 57 A 796 THR ARG TRP SER THR ASP PRO TRP ILE GLN MET ALA TYR SEQRES 58 A 796 SER PHE VAL LYS THR GLY GLY SER GLY GLU ALA TYR ASP SEQRES 59 A 796 ILE ILE ALA GLU ASP ILE GLN GLY THR VAL PHE PHE ALA SEQRES 60 A 796 GLY GLU ALA THR ASN ARG HIS PHE PRO GLN THR VAL THR SEQRES 61 A 796 GLY ALA TYR LEU SER GLY VAL ARG GLU ALA SER LYS ILE SEQRES 62 A 796 ALA ALA PHE HET ZN A 901 1 HET ZN A 902 1 HET ZN A 903 1 HET FAD A 904 53 HET FLC A 905 13 HETNAM ZN ZINC ION HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM FLC CITRATE ANION FORMUL 2 ZN 3(ZN 2+) FORMUL 5 FAD C27 H33 N9 O15 P2 FORMUL 6 FLC C6 H5 O7 3- FORMUL 7 HOH *236(H2 O) HELIX 1 1 ASN A 93 ARG A 101 1 9 HELIX 2 2 GLY A 106 GLY A 121 1 16 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 ASP A 190 SER A 197 1 8 HELIX 7 7 ASN A 198 MET A 204 1 7 HELIX 8 8 ALA A 216 LEU A 220 5 5 HELIX 9 9 TYR A 224 GLY A 229 5 6 HELIX 10 10 GLU A 290 PHE A 297 1 8 HELIX 11 11 PRO A 298 SER A 301 5 4 HELIX 12 12 PRO A 304 ASN A 321 1 18 HELIX 13 13 THR A 327 ILE A 332 1 6 HELIX 14 14 PRO A 333 ILE A 335 5 3 HELIX 15 15 LEU A 340 LYS A 359 1 20 HELIX 16 16 PRO A 377 HIS A 381 5 5 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 LYS A 499 1 24 HELIX 20 20 THR A 502 ASP A 506 5 5 HELIX 21 21 PRO A 508 GLU A 523 1 16 HELIX 22 22 SER A 529 GLY A 548 1 20 HELIX 23 23 ASP A 560 PHE A 565 5 6 HELIX 24 24 GLY A 578 GLU A 588 1 11 HELIX 25 25 PRO A 628 LYS A 634 1 7 HELIX 26 26 SER A 644 SER A 653 1 10 HELIX 27 27 TRP A 671 GLN A 676 1 6 HELIX 28 28 SER A 687 ARG A 691 5 5 HELIX 29 29 GLY A 715 ARG A 722 1 8 HELIX 30 30 ASP A 725 PHE A 741 1 17 HELIX 31 31 ARG A 756 ASP A 760 5 5 HELIX 32 32 GLY A 776 GLU A 784 1 9 HELIX 33 33 GLY A 794 ASN A 798 5 5 HELIX 34 34 THR A 804 PHE A 822 1 19 SHEET 1 A 2 TRP A 82 SER A 86 0 SHEET 2 A 2 GLU A 89 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 THR A 409 SHEET 4 C 5 LYS A 622 VAL A 625 1 O LEU A 624 N ILE A 388 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 PHE A 697 N PHE A 681 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 GLU A 660 O ILE A 713 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 ASP A 602 O GLN A 609 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 901 1555 1555 2.25 LINK SG CYS A 58 ZN ZN A 901 1555 1555 2.17 LINK SG CYS A 65 ZN ZN A 902 1555 1555 2.33 LINK SG CYS A 73 ZN ZN A 902 1555 1555 2.37 LINK ND1 HIS A 84 ZN ZN A 901 1555 1555 2.06 LINK NE2 HIS A 90 ZN ZN A 901 1555 1555 1.96 LINK SG CYS A 92 ZN ZN A 902 1555 1555 2.22 LINK SG CYS A 95 ZN ZN A 902 1555 1555 2.26 LINK SG CYS A 142 ZN ZN A 903 1555 1555 2.38 LINK SG CYS A 147 ZN ZN A 903 1555 1555 2.13 LINK SG CYS A 169 ZN ZN A 903 1555 1555 2.26 LINK SG CYS A 185 ZN ZN A 903 1555 1555 2.38 CISPEP 1 ASN A 640 PRO A 641 0 -4.18 SITE 1 AC1 4 CYS A 53 CYS A 58 HIS A 84 HIS A 90 SITE 1 AC2 4 CYS A 65 CYS A 73 CYS A 92 CYS A 95 SITE 1 AC3 4 CYS A 142 CYS A 147 CYS A 169 CYS A 185 SITE 1 AC4 39 ILE A 388 GLY A 389 GLY A 391 PRO A 392 SITE 2 AC4 39 ALA A 393 LEU A 411 GLU A 412 ALA A 413 SITE 3 AC4 39 LYS A 414 GLY A 418 GLY A 419 ARG A 420 SITE 4 AC4 39 ARG A 434 GLY A 435 ALA A 436 GLN A 437 SITE 5 AC4 39 ILE A 438 TYR A 579 PRO A 597 VAL A 598 SITE 6 AC4 39 THR A 626 VAL A 627 PRO A 628 ILE A 637 SITE 7 AC4 39 TRP A 757 TRP A 762 ILE A 763 ALA A 766 SITE 8 AC4 39 GLY A 794 GLU A 795 GLN A 803 THR A 804 SITE 9 AC4 39 VAL A 805 ALA A 808 HOH A1011 HOH A1022 SITE 10 AC4 39 HOH A1024 HOH A1059 HOH A1060 SITE 1 AC5 9 TYR A 273 CYS A 278 GLY A 279 PHE A 565 SITE 2 AC5 9 ALA A 566 HIS A 800 HOH A1030 HOH A1126 SITE 3 AC5 9 HOH A1130 CRYST1 93.691 96.273 182.797 90.00 90.00 90.00 C 2 2 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 0.010673 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010387 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005471 0.00000