HEADER OXIDOREDUCTASE 29-MAR-20 6WC6 TITLE CRYSTAL STRUCTURE OF A TRUNCATED LSD1:COREST IN THE PRESENCE OF AN TITLE 2 LSD1-NT PEPTIDE CAVEAT 6WC6 FAD A 901 HAS 0 OCCUPANCY COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: BRAF35-HDAC COMPLEX PROTEIN BHC110,FLAVIN-CONTAINING AMINE COMPND 5 OXIDASE DOMAIN-CONTAINING PROTEIN 2; 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; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: LSD1-NT PEPTIDE; COMPND 15 CHAIN: C; COMPND 16 SYNONYM: LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A; 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: KDM1A, AOF2, KDM1, KIAA0601, LSD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: RCOR1, KIAA0071, RCOR; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 15 MOL_ID: 3; SOURCE 16 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 17 ORGANISM_COMMON: HUMAN; SOURCE 18 ORGANISM_TAXID: 9606; SOURCE 19 GENE: KDM1A, AOF2, KDM1, KIAA0601, LSD1; SOURCE 20 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 21 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS LSD1/COREST, N TERMINAL PEPTIDE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR N.J.REITER,D.ZENG,D.SENANAYAKA REVDAT 2 18-OCT-23 6WC6 1 REMARK REVDAT 1 30-JUN-21 6WC6 0 JRNL AUTH D.ZENG,D.SENANAYAKA,B.P.BROWN,Z.LUKA,W.J.MARTIN,K.I.MOORE, JRNL AUTH 2 R.PATEL,S.PAKHOMOVA,J.MEILER,N.J.REITER JRNL TITL IDENTIFICATION OF STRUCTURE AND NUCLEOSOME BINDING WITHIN JRNL TITL 2 THE N-TERMINUS OF LYSINE SPECIFIC DEMETHYLASE 1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5-3.1 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 100.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 46920 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.880 REMARK 3 FREE R VALUE TEST SET COUNT : 2290 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.14 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2935 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.87 REMARK 3 BIN R VALUE (WORKING SET) : 0.4567 REMARK 3 BIN FREE R VALUE SET COUNT : 143 REMARK 3 BIN FREE R VALUE : 0.4535 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6417 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) : 83.45 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 101.8 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.449 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : NULL REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): NULL ; NULL ; NULL REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): NULL ; NULL ; NULL 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 : 3 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 : NULL NULL NULL NULL REMARK 3 ORIGIN FOR THE GROUP (A): 182.5434 50.3494 33.8385 REMARK 3 T TENSOR REMARK 3 T11: 0.8232 T22: 0.6270 REMARK 3 T33: 0.6351 T12: 0.0773 REMARK 3 T13: 0.1002 T23: 0.1144 REMARK 3 L TENSOR REMARK 3 L11: 0.2893 L22: 1.3994 REMARK 3 L33: 0.4776 L12: 0.6032 REMARK 3 L13: -0.2322 L23: -0.7177 REMARK 3 S TENSOR REMARK 3 S11: 0.0016 S12: -0.1601 S13: -0.2294 REMARK 3 S21: 0.1858 S22: -0.1793 S23: -0.1416 REMARK 3 S31: 0.1078 S32: 0.1186 S33: 0.2003 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 : NULL NULL NULL NULL REMARK 3 ORIGIN FOR THE GROUP (A): 146.2738 -0.9885 58.1584 REMARK 3 T TENSOR REMARK 3 T11: 1.0866 T22: 1.0154 REMARK 3 T33: 0.8756 T12: 0.0829 REMARK 3 T13: 0.2527 T23: 0.1304 REMARK 3 L TENSOR REMARK 3 L11: 0.6099 L22: 1.2564 REMARK 3 L33: 0.2373 L12: 0.9688 REMARK 3 L13: -0.4422 L23: -0.5333 REMARK 3 S TENSOR REMARK 3 S11: 0.0458 S12: 0.2048 S13: 0.1312 REMARK 3 S21: -0.4014 S22: -0.1503 S23: -0.1550 REMARK 3 S31: 0.2446 S32: -0.0551 S33: 0.1115 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 : NULL NULL NULL NULL REMARK 3 ORIGIN FOR THE GROUP (A): 187.1348 80.9728 44.5338 REMARK 3 T TENSOR REMARK 3 T11: 2.2050 T22: 1.4213 REMARK 3 T33: 1.5479 T12: 0.1205 REMARK 3 T13: -0.1349 T23: 0.1637 REMARK 3 L TENSOR REMARK 3 L11: 0.0031 L22: 0.0059 REMARK 3 L33: 0.0086 L12: 0.0037 REMARK 3 L13: -0.0022 L23: 0.0032 REMARK 3 S TENSOR REMARK 3 S11: -0.2100 S12: 0.0554 S13: 0.2397 REMARK 3 S21: -0.0100 S22: -0.0358 S23: -0.1606 REMARK 3 S31: -0.2320 S32: 0.2481 S33: 0.1884 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.11 REMARK 3 ION PROBE RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6WC6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-APR-20. REMARK 100 THE DEPOSITION ID IS D_1000247706. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-AUG-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-F REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46959 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 142.460 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 15.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.21 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 : 1.600 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: 4XBF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE LSD1-COREST COMPLEX 10MG/ML REMARK 280 CONCENTRATION (IN 25 MM HEPES-NA, PH 7.4, 100 MM NACL, 1 MM TCEP) REMARK 280 WAS MIXED (1:1) WITH THE RESERVOIR SOLUTION [0.60 M LI2SO4, REMARK 280 0.63 M (NH4)2SO4, 0.25 M NACL, 100 MM NA-CITRATE, PH 5.6, 5 MM REMARK 280 TCEP]. WHEN GET CRYSTALS, SOAK THE CRYSTALS WITHIN 5MM LSD1-NT REMARK 280 PEPTIDE., VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 60.89150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 89.58200 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 117.45350 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 60.89150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 89.58200 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 117.45350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 60.89150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 89.58200 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 117.45350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 60.89150 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 89.58200 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 117.45350 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 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 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 CB ALA A 331 C4X FAD A 901 1.50 REMARK 500 CB ALA A 331 N5 FAD A 901 1.88 REMARK 500 NE1 TRP A 671 OD1 ASN A 696 2.09 REMARK 500 CB ALA A 331 C4 FAD A 901 2.09 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 ILE A 270 -61.26 -98.13 REMARK 500 GLN A 358 2.46 -67.23 REMARK 500 PRO A 516 -169.26 -71.89 REMARK 500 ASN A 696 63.15 -119.61 REMARK 500 PRO A 701 68.54 -69.43 REMARK 500 ALA A 757 -53.17 -155.61 REMARK 500 SER A 760 -69.79 -96.37 REMARK 500 ASN B 327 -165.00 -161.13 REMARK 500 PRO B 369 12.78 -69.88 REMARK 500 TYR B 424 50.00 -89.01 REMARK 500 ARG B 426 -12.92 -140.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 FAD A 901 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4XBF RELATED DB: PDB REMARK 900 TEMPLATE OF MOLECULAR REPLACEMENT DBREF 6WC6 A 171 836 UNP O60341 KDM1A_HUMAN 171 836 DBREF 6WC6 B 308 440 UNP Q9UKL0 RCOR1_HUMAN 308 440 DBREF 6WC6 C 4 18 UNP O60341 KDM1A_HUMAN 137 151 SEQRES 1 A 666 PRO SER GLY VAL GLU GLY ALA ALA PHE GLN SER ARG LEU SEQRES 2 A 666 PRO HIS ASP ARG MET THR SER GLN GLU ALA ALA CYS PHE SEQRES 3 A 666 PRO ASP ILE ILE SER GLY PRO GLN GLN THR GLN LYS VAL SEQRES 4 A 666 PHE LEU PHE ILE ARG ASN ARG THR LEU GLN LEU TRP LEU SEQRES 5 A 666 ASP ASN PRO LYS ILE GLN LEU THR PHE GLU ALA THR LEU SEQRES 6 A 666 GLN GLN LEU GLU ALA PRO TYR ASN SER ASP THR VAL LEU SEQRES 7 A 666 VAL HIS ARG VAL HIS SER TYR LEU GLU ARG HIS GLY LEU SEQRES 8 A 666 ILE ASN PHE GLY ILE TYR LYS ARG ILE LYS PRO LEU PRO SEQRES 9 A 666 THR LYS LYS THR GLY LYS VAL ILE ILE ILE GLY SER GLY SEQRES 10 A 666 VAL SER GLY LEU ALA ALA ALA ARG GLN LEU GLN SER PHE SEQRES 11 A 666 GLY MET ASP VAL THR LEU LEU GLU ALA ARG ASP ARG VAL SEQRES 12 A 666 GLY GLY ARG VAL ALA THR PHE ARG LYS GLY ASN TYR VAL SEQRES 13 A 666 ALA ASP LEU GLY ALA MET VAL VAL THR GLY LEU GLY GLY SEQRES 14 A 666 ASN PRO MET ALA VAL VAL SER LYS GLN VAL ASN MET GLU SEQRES 15 A 666 LEU ALA LYS ILE LYS GLN LYS CYS PRO LEU TYR GLU ALA SEQRES 16 A 666 ASN GLY GLN ALA VAL PRO LYS GLU LYS ASP GLU MET VAL SEQRES 17 A 666 GLU GLN GLU PHE ASN ARG LEU LEU GLU ALA THR SER TYR SEQRES 18 A 666 LEU SER HIS GLN LEU ASP PHE ASN VAL LEU ASN ASN LYS SEQRES 19 A 666 PRO VAL SER LEU GLY GLN ALA LEU GLU VAL VAL ILE GLN SEQRES 20 A 666 LEU GLN GLU LYS HIS VAL LYS ASP GLU GLN ILE GLU HIS SEQRES 21 A 666 TRP LYS LYS ILE VAL LYS THR GLN GLU GLU LEU LYS GLU SEQRES 22 A 666 LEU LEU ASN LYS MET VAL ASN LEU LYS GLU LYS ILE LYS SEQRES 23 A 666 GLU LEU HIS GLN GLN TYR LYS GLU ALA SER GLU VAL LYS SEQRES 24 A 666 PRO PRO ARG ASP ILE THR ALA GLU PHE LEU VAL LYS SER SEQRES 25 A 666 LYS HIS ARG ASP LEU THR ALA LEU CYS LYS GLU TYR ASP SEQRES 26 A 666 GLU LEU ALA GLU THR GLN GLY LYS LEU GLU GLU LYS LEU SEQRES 27 A 666 GLN GLU LEU GLU ALA ASN PRO PRO SER ASP VAL TYR LEU SEQRES 28 A 666 SER SER ARG ASP ARG GLN ILE LEU ASP TRP HIS PHE ALA SEQRES 29 A 666 ASN LEU GLU PHE ALA ASN ALA THR PRO LEU SER THR LEU SEQRES 30 A 666 SER LEU LYS HIS TRP ASP GLN ASP ASP ASP PHE GLU PHE SEQRES 31 A 666 THR GLY SER HIS LEU THR VAL ARG ASN GLY TYR SER CYS SEQRES 32 A 666 VAL PRO VAL ALA LEU ALA GLU GLY LEU ASP ILE LYS LEU SEQRES 33 A 666 ASN THR ALA VAL ARG GLN VAL ARG TYR THR ALA SER GLY SEQRES 34 A 666 CYS GLU VAL ILE ALA VAL ASN THR ARG SER THR SER GLN SEQRES 35 A 666 THR PHE ILE TYR LYS CYS ASP ALA VAL LEU CYS THR LEU SEQRES 36 A 666 PRO LEU GLY VAL LEU LYS GLN GLN PRO PRO ALA VAL GLN SEQRES 37 A 666 PHE VAL PRO PRO LEU PRO GLU TRP LYS THR SER ALA VAL SEQRES 38 A 666 GLN ARG MET GLY PHE GLY ASN LEU ASN LYS VAL VAL LEU SEQRES 39 A 666 CYS PHE ASP ARG VAL PHE TRP ASP PRO SER VAL ASN LEU SEQRES 40 A 666 PHE GLY HIS VAL GLY SER THR THR ALA SER ARG GLY GLU SEQRES 41 A 666 LEU PHE LEU PHE TRP ASN LEU TYR LYS ALA PRO ILE LEU SEQRES 42 A 666 LEU ALA LEU VAL ALA GLY GLU ALA ALA GLY ILE MET GLU SEQRES 43 A 666 ASN ILE SER ASP ASP VAL ILE VAL GLY ARG CYS LEU ALA SEQRES 44 A 666 ILE LEU LYS GLY ILE PHE GLY SER SER ALA VAL PRO GLN SEQRES 45 A 666 PRO LYS GLU THR VAL VAL SER ARG TRP ARG ALA ASP PRO SEQRES 46 A 666 TRP ALA ARG GLY SER TYR SER TYR VAL ALA ALA GLY SER SEQRES 47 A 666 SER GLY ASN ASP TYR ASP LEU MET ALA GLN PRO ILE THR SEQRES 48 A 666 PRO GLY PRO SER ILE PRO GLY ALA PRO GLN PRO ILE PRO SEQRES 49 A 666 ARG LEU PHE PHE ALA GLY GLU HIS THR ILE ARG ASN TYR SEQRES 50 A 666 PRO ALA THR VAL HIS GLY ALA LEU LEU SER GLY LEU ARG SEQRES 51 A 666 GLU ALA GLY ARG ILE ALA ASP GLN PHE LEU GLY ALA MET SEQRES 52 A 666 TYR THR LEU 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 15 SER GLU GLU GLU ARG ASN ALA LYS ALA GLU LYS GLU LYS SEQRES 2 C 15 LYS LEU HET FAD A 901 53 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE FORMUL 4 FAD C27 H33 N9 O15 P2 HELIX 1 AA1 GLY A 173 SER A 181 1 9 HELIX 2 AA2 THR A 189 PHE A 196 1 8 HELIX 3 AA3 PHE A 196 SER A 201 1 6 HELIX 4 AA4 PRO A 203 ASN A 224 1 22 HELIX 5 AA5 THR A 230 GLN A 237 1 8 HELIX 6 AA6 PRO A 241 SER A 244 5 4 HELIX 7 AA7 ASP A 245 HIS A 259 1 15 HELIX 8 AA8 GLY A 287 PHE A 300 1 14 HELIX 9 AA9 ASN A 340 VAL A 349 1 10 HELIX 10 AB1 PRO A 371 GLN A 395 1 25 HELIX 11 AB2 SER A 407 GLU A 467 1 61 HELIX 12 AB3 ASP A 473 ASN A 514 1 42 HELIX 13 AB4 SER A 522 ALA A 541 1 20 HELIX 14 AB5 ASP A 553 GLU A 559 5 7 HELIX 15 AB6 SER A 572 GLU A 580 1 9 HELIX 16 AB7 PRO A 626 GLN A 632 1 7 HELIX 17 AB8 PRO A 644 MET A 654 1 11 HELIX 18 AB9 THR A 685 GLU A 690 5 6 HELIX 19 AC1 GLY A 709 MET A 715 1 7 HELIX 20 AC2 GLU A 716 ILE A 718 5 3 HELIX 21 AC3 SER A 719 GLY A 736 1 18 HELIX 22 AC4 SER A 769 GLN A 778 1 10 HELIX 23 AC5 GLY A 800 ILE A 804 5 5 HELIX 24 AC6 THR A 810 GLY A 831 1 22 HELIX 25 AC7 ALA A 832 LEU A 836 5 5 HELIX 26 AC8 SER B 317 SER B 325 1 9 HELIX 27 AC9 THR B 329 LEU B 363 1 35 HELIX 28 AD1 ILE B 367 ARG B 371 5 5 HELIX 29 AD2 THR B 384 GLY B 399 1 16 HELIX 30 AD3 ASP B 401 GLY B 410 1 10 HELIX 31 AD4 SER B 413 TYR B 424 1 12 HELIX 32 AD5 ASN B 429 ALA B 439 1 11 HELIX 33 AD6 GLU C 5 LEU C 18 1 14 SHEET 1 AA1 5 ASP A 583 LYS A 585 0 SHEET 2 AA1 5 ASP A 303 LEU A 307 1 N LEU A 306 O LYS A 585 SHEET 3 AA1 5 LYS A 280 ILE A 284 1 N ILE A 283 O LEU A 307 SHEET 4 AA1 5 ALA A 620 CYS A 623 1 O LEU A 622 N ILE A 284 SHEET 5 AA1 5 LEU A 796 PHE A 798 1 O PHE A 797 N CYS A 623 SHEET 1 AA2 2 THR A 319 LYS A 322 0 SHEET 2 AA2 2 TYR A 325 ASP A 328 -1 O ALA A 327 N PHE A 320 SHEET 1 AA3 3 VAL A 333 VAL A 334 0 SHEET 2 AA3 3 LEU A 565 VAL A 567 -1 N LEU A 565 O VAL A 334 SHEET 3 AA3 3 LEU A 353 LYS A 355 -1 N ALA A 354 O THR A 566 SHEET 1 AA4 2 VAL A 400 LEU A 401 0 SHEET 2 AA4 2 LYS A 404 PRO A 405 -1 O LYS A 404 N LEU A 401 SHEET 1 AA5 4 THR A 613 CYS A 618 0 SHEET 2 AA5 4 GLY A 599 ASN A 606 -1 N ALA A 604 O PHE A 614 SHEET 3 AA5 4 THR A 588 THR A 596 -1 N THR A 596 O GLY A 599 SHEET 4 AA5 4 GLN A 638 VAL A 640 1 O VAL A 640 N VAL A 593 SHEET 1 AA6 2 GLY A 655 PHE A 656 0 SHEET 2 AA6 2 SER A 762 TYR A 763 -1 O TYR A 763 N GLY A 655 SHEET 1 AA7 5 LEU A 677 GLY A 679 0 SHEET 2 AA7 5 LEU A 693 TRP A 695 -1 O PHE A 694 N PHE A 678 SHEET 3 AA7 5 ILE A 702 VAL A 707 -1 O LEU A 706 N LEU A 693 SHEET 4 AA7 5 ASN A 660 CYS A 665 -1 N ASN A 660 O VAL A 707 SHEET 5 AA7 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 7.04 CISPEP 2 PRO A 470 PRO A 471 0 7.28 CISPEP 3 GLN A 633 PRO A 634 0 0.69 CISPEP 4 VAL A 640 PRO A 641 0 -0.30 CRYST1 121.783 179.164 234.907 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 0.008211 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005581 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004257 0.00000