HEADER OXIDOREDUCTASE 09-JUL-18 6E1F TITLE CRYSTAL STRUCTURE OF THE SWIRM DOMAIN OF HUMAN HISTONE LYSINE-SPECIFIC TITLE 2 DEMETHYLASE LSD1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC HISTONE DEMETHYLASE 1A; COMPND 3 CHAIN: A, B, C, D; COMPND 4 FRAGMENT: SWIRM DOMAIN (UNP RESIDUES 183-267); COMPND 5 SYNONYM: BRAF35-HDAC COMPLEX PROTEIN BHC110, FLAVIN-CONTAINING AMINE COMPND 6 OXIDASE DOMAIN-CONTAINING PROTEIN 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: KDM1A, AOF2, KDM1, KIAA0601, LSD1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HISTONE LYSINE SPECIFIC DEMETHYLASE, SWIRM DOMAIN, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.LUKA,S.PAKHOMOVA,N.J.REITER REVDAT 3 11-OCT-23 6E1F 1 REMARK REVDAT 2 18-DEC-19 6E1F 1 REMARK REVDAT 1 10-JUL-19 6E1F 0 JRNL AUTH D.ZENG,B.P.BROWN,Z.LUKA,S.PAKHOMOVA,B.MARTIN,K.MOORE, JRNL AUTH 2 J.MEILER,N.J.REITER JRNL TITL TRANSIENT AND HIGHLY ORDERED STRUCTURAL DOMAINS EXIST WITHIN JRNL TITL 2 THE N-TERMINUS OF LSD1 AND DIFFERENTIALLY INTERACT WITH JRNL TITL 3 MONONUCLEOSOMES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.16 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0230 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) : 1.16 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.18 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 92362 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) : 0.133 REMARK 3 R VALUE (WORKING SET) : 0.133 REMARK 3 FREE R VALUE : 0.169 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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) : 1.16 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.19 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6010 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 86.13 REMARK 3 BIN R VALUE (WORKING SET) : 0.2110 REMARK 3 BIN FREE R VALUE SET COUNT : 130 REMARK 3 BIN FREE R VALUE : 0.2520 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2885 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 383 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.21 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.01000 REMARK 3 B22 (A**2) : -0.14000 REMARK 3 B33 (A**2) : 0.15000 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): 0.037 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.038 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.024 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.150 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.980 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.970 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3151 ; 0.015 ; 0.014 REMARK 3 BOND LENGTHS OTHERS (A): 2747 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4319 ; 1.907 ; 1.661 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6483 ; 1.192 ; 1.622 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 397 ; 5.803 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 178 ;31.086 ;22.528 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 518 ;12.753 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;19.467 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 417 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3573 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 591 ; 0.001 ; 0.020 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): 1503 ; 2.215 ; 1.234 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1502 ; 2.215 ; 1.233 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1888 ; 2.756 ; 1.855 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1889 ; 2.755 ; 1.855 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1648 ; 3.335 ; 1.505 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1640 ; 3.233 ; 1.497 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2406 ; 3.988 ; 2.160 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3739 ; 4.036 ;16.094 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3666 ; 3.873 ;15.571 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 5898 ; 3.469 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 201 ;22.147 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 5983 ;12.715 ; 5.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 6 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 179 267 B 179 267 2709 0.18 0.05 REMARK 3 2 A 179 267 C 179 267 2958 0.11 0.05 REMARK 3 3 A 179 267 D 179 267 2675 0.18 0.05 REMARK 3 4 B 179 267 C 179 267 2634 0.17 0.05 REMARK 3 5 B 179 267 D 179 267 2746 0.15 0.05 REMARK 3 6 C 179 267 D 179 267 2580 0.18 0.05 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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 6E1F COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUL-18. REMARK 100 THE DEPOSITION ID IS D_1000235476. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 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-G REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97857 REMARK 200 MONOCHROMATOR : DIAMOND(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 94426 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.160 REMARK 200 RESOLUTION RANGE LOW (A) : 35.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 11.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07200 REMARK 200 FOR THE DATA SET : 50.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.16 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.4 REMARK 200 DATA REDUNDANCY IN SHELL : 8.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.50700 REMARK 200 FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: PDB ENTRY 5IT3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 27.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS, PH 6.5, 0.1 M REMARK 280 POTASSIUM CHLORIDE, 1.5 M AMMONIUM SULFATE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 24.97850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.50950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.75700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.50950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.97850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.75700 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3, 4 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 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 4 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: D 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 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 TYR C 267 CG CD1 CD2 CE1 CE2 CZ OH 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 HE ARG A 187 O HOH A 403 1.53 REMARK 500 O GLN B 205 O HOH B 301 1.87 REMARK 500 NH1 ARG A 258 O HOH A 401 2.03 REMARK 500 OH TYR C 255 O HOH C 401 2.04 REMARK 500 O HOH C 401 O HOH C 438 2.09 REMARK 500 O HOH D 366 O HOH D 386 2.16 REMARK 500 OG1 THR B 206 O HOH B 302 2.17 REMARK 500 O TYR B 242 O HOH B 303 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 483 O HOH D 399 1455 2.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 232 CD GLU A 232 OE1 0.112 REMARK 500 GLU C 239 CD GLU C 239 OE1 0.070 REMARK 500 ASP C 245 CG ASP C 245 OD1 0.139 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 ARG A 187 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 216 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 THR B 206 OG1 - CB - CG2 ANGL. DEV. = -22.5 DEGREES REMARK 500 ARG B 258 NE - CZ - NH1 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG B 258 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG D 187 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 TYR D 255 CB - CG - CD2 ANGL. DEV. = -4.9 DEGREES REMARK 500 TYR D 255 CB - CG - CD1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG D 258 NE - CZ - NH1 ANGL. DEV. = 3.3 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 ASN A 224 68.26 -152.39 REMARK 500 ASN A 224 52.67 -145.22 REMARK 500 ASN B 224 58.41 -142.27 REMARK 500 ASN C 224 64.50 -151.83 REMARK 500 ASN D 224 56.81 -142.62 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 ILE C 266 TYR C 267 -144.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 187 0.11 SIDE CHAIN REMARK 500 ARG A 214 0.10 SIDE CHAIN REMARK 500 ARG A 258 0.08 SIDE CHAIN REMARK 500 ARG B 214 0.11 SIDE CHAIN REMARK 500 ARG C 214 0.10 SIDE CHAIN REMARK 500 ARG D 214 0.10 SIDE CHAIN 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 SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 C 301 DBREF 6E1F A 183 267 UNP O60341 KDM1A_HUMAN 183 267 DBREF 6E1F B 183 267 UNP O60341 KDM1A_HUMAN 183 267 DBREF 6E1F C 183 267 UNP O60341 KDM1A_HUMAN 183 267 DBREF 6E1F D 183 267 UNP O60341 KDM1A_HUMAN 183 267 SEQADV 6E1F GLY A 179 UNP O60341 EXPRESSION TAG SEQADV 6E1F PRO A 180 UNP O60341 EXPRESSION TAG SEQADV 6E1F GLY A 181 UNP O60341 EXPRESSION TAG SEQADV 6E1F SER A 182 UNP O60341 EXPRESSION TAG SEQADV 6E1F GLY B 179 UNP O60341 EXPRESSION TAG SEQADV 6E1F PRO B 180 UNP O60341 EXPRESSION TAG SEQADV 6E1F GLY B 181 UNP O60341 EXPRESSION TAG SEQADV 6E1F SER B 182 UNP O60341 EXPRESSION TAG SEQADV 6E1F GLY C 179 UNP O60341 EXPRESSION TAG SEQADV 6E1F PRO C 180 UNP O60341 EXPRESSION TAG SEQADV 6E1F GLY C 181 UNP O60341 EXPRESSION TAG SEQADV 6E1F SER C 182 UNP O60341 EXPRESSION TAG SEQADV 6E1F GLY D 179 UNP O60341 EXPRESSION TAG SEQADV 6E1F PRO D 180 UNP O60341 EXPRESSION TAG SEQADV 6E1F GLY D 181 UNP O60341 EXPRESSION TAG SEQADV 6E1F SER D 182 UNP O60341 EXPRESSION TAG SEQRES 1 A 89 GLY PRO GLY SER LEU PRO HIS ASP ARG MET THR SER GLN SEQRES 2 A 89 GLU ALA ALA CYS PHE PRO ASP ILE ILE SER GLY PRO GLN SEQRES 3 A 89 GLN THR GLN LYS VAL PHE LEU PHE ILE ARG ASN ARG THR SEQRES 4 A 89 LEU GLN LEU TRP LEU ASP ASN PRO LYS ILE GLN LEU THR SEQRES 5 A 89 PHE GLU ALA THR LEU GLN GLN LEU GLU ALA PRO TYR ASN SEQRES 6 A 89 SER ASP THR VAL LEU VAL HIS ARG VAL HIS SER TYR LEU SEQRES 7 A 89 GLU ARG HIS GLY LEU ILE ASN PHE GLY ILE TYR SEQRES 1 B 89 GLY PRO GLY SER LEU PRO HIS ASP ARG MET THR SER GLN SEQRES 2 B 89 GLU ALA ALA CYS PHE PRO ASP ILE ILE SER GLY PRO GLN SEQRES 3 B 89 GLN THR GLN LYS VAL PHE LEU PHE ILE ARG ASN ARG THR SEQRES 4 B 89 LEU GLN LEU TRP LEU ASP ASN PRO LYS ILE GLN LEU THR SEQRES 5 B 89 PHE GLU ALA THR LEU GLN GLN LEU GLU ALA PRO TYR ASN SEQRES 6 B 89 SER ASP THR VAL LEU VAL HIS ARG VAL HIS SER TYR LEU SEQRES 7 B 89 GLU ARG HIS GLY LEU ILE ASN PHE GLY ILE TYR SEQRES 1 C 89 GLY PRO GLY SER LEU PRO HIS ASP ARG MET THR SER GLN SEQRES 2 C 89 GLU ALA ALA CYS PHE PRO ASP ILE ILE SER GLY PRO GLN SEQRES 3 C 89 GLN THR GLN LYS VAL PHE LEU PHE ILE ARG ASN ARG THR SEQRES 4 C 89 LEU GLN LEU TRP LEU ASP ASN PRO LYS ILE GLN LEU THR SEQRES 5 C 89 PHE GLU ALA THR LEU GLN GLN LEU GLU ALA PRO TYR ASN SEQRES 6 C 89 SER ASP THR VAL LEU VAL HIS ARG VAL HIS SER TYR LEU SEQRES 7 C 89 GLU ARG HIS GLY LEU ILE ASN PHE GLY ILE TYR SEQRES 1 D 89 GLY PRO GLY SER LEU PRO HIS ASP ARG MET THR SER GLN SEQRES 2 D 89 GLU ALA ALA CYS PHE PRO ASP ILE ILE SER GLY PRO GLN SEQRES 3 D 89 GLN THR GLN LYS VAL PHE LEU PHE ILE ARG ASN ARG THR SEQRES 4 D 89 LEU GLN LEU TRP LEU ASP ASN PRO LYS ILE GLN LEU THR SEQRES 5 D 89 PHE GLU ALA THR LEU GLN GLN LEU GLU ALA PRO TYR ASN SEQRES 6 D 89 SER ASP THR VAL LEU VAL HIS ARG VAL HIS SER TYR LEU SEQRES 7 D 89 GLU ARG HIS GLY LEU ILE ASN PHE GLY ILE TYR HET SO4 A 301 5 HET SO4 C 301 5 HETNAM SO4 SULFATE ION FORMUL 5 SO4 2(O4 S 2-) FORMUL 7 HOH *383(H2 O) HELIX 1 AA1 THR A 189 PHE A 196 1 8 HELIX 2 AA2 PHE A 196 SER A 201 1 6 HELIX 3 AA3 PRO A 203 ASN A 224 1 22 HELIX 4 AA4 THR A 230 GLN A 237 1 8 HELIX 5 AA5 PRO A 241 SER A 244 5 4 HELIX 6 AA6 ASP A 245 HIS A 259 1 15 HELIX 7 AA7 GLY B 179 LEU B 183 5 5 HELIX 8 AA8 THR B 189 PHE B 196 1 8 HELIX 9 AA9 PHE B 196 SER B 201 1 6 HELIX 10 AB1 PRO B 203 THR B 206 5 4 HELIX 11 AB2 GLN B 207 ASN B 224 1 18 HELIX 12 AB3 THR B 230 LEU B 238 1 9 HELIX 13 AB4 PRO B 241 SER B 244 5 4 HELIX 14 AB5 ASP B 245 HIS B 259 1 15 HELIX 15 AB6 ILE B 262 ILE B 266 5 5 HELIX 16 AB7 THR C 189 PHE C 196 1 8 HELIX 17 AB8 PHE C 196 SER C 201 1 6 HELIX 18 AB9 PRO C 203 ASN C 224 1 22 HELIX 19 AC1 THR C 230 GLN C 237 1 8 HELIX 20 AC2 PRO C 241 SER C 244 5 4 HELIX 21 AC3 ASP C 245 HIS C 259 1 15 HELIX 22 AC4 THR D 189 PHE D 196 1 8 HELIX 23 AC5 PHE D 196 SER D 201 1 6 HELIX 24 AC6 PRO D 203 THR D 206 5 4 HELIX 25 AC7 GLN D 207 ASN D 224 1 18 HELIX 26 AC8 THR D 230 LEU D 238 1 9 HELIX 27 AC9 ASP D 245 HIS D 259 1 15 HELIX 28 AD1 ILE D 262 ILE D 266 5 5 CISPEP 1 ALA A 240 PRO A 241 0 5.75 CISPEP 2 ALA B 240 PRO B 241 0 4.03 CISPEP 3 ALA C 240 PRO C 241 0 3.29 CISPEP 4 ALA D 240 PRO D 241 0 4.53 SITE 1 AC1 9 THR A 189 SER A 190 HOH A 430 HOH A 442 SITE 2 AC1 9 HOH A 453 HOH A 464 PRO D 203 THR D 206 SITE 3 AC1 9 LYS D 226 SITE 1 AC2 7 PRO B 203 GLN B 204 LYS B 226 THR C 189 SITE 2 AC2 7 SER C 190 GLN C 191 HOH C 447 CRYST1 49.957 57.514 97.019 90.00 90.00 90.00 P 21 21 21 16 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 0.020017 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017387 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010307 0.00000