HEADER GENE REGULATION 29-APR-22 7UVA TITLE CRYSTAL STRUCTURE OF KDM2A HISTONE DEMETHYLASE CATALYTIC DOMAIN IN TITLE 2 COMPLEX WITH AN H3C36 PEPTIDE MODIFIED BY UNC8015 COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 2A; COMPND 3 CHAIN: A, D; COMPND 4 FRAGMENT: UNP RESIDUES 36-364; COMPND 5 SYNONYM: F-BOX AND LEUCINE-RICH REPEAT PROTEIN 11,F-BOX/LRR-REPEAT COMPND 6 PROTEIN 11,JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 1A, COMPND 7 [HISTONE-H3]-LYSINE-36 DEMETHYLASE 1A; COMPND 8 EC: 1.14.11.27; COMPND 9 ENGINEERED: YES; COMPND 10 MOL_ID: 2; COMPND 11 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 2A; COMPND 12 CHAIN: B, E; COMPND 13 FRAGMENT: UNP RESIDUES 450-517; COMPND 14 SYNONYM: F-BOX AND LEUCINE-RICH REPEAT PROTEIN 11,F-BOX/LRR-REPEAT COMPND 15 PROTEIN 11,JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 1A, COMPND 16 [HISTONE-H3]-LYSINE-36 DEMETHYLASE 1A; COMPND 17 EC: 1.14.11.27; COMPND 18 ENGINEERED: YES; COMPND 19 MOL_ID: 3; COMPND 20 MOLECULE: HISTONE H3.2; COMPND 21 CHAIN: C, F; COMPND 22 FRAGMENT: UNP RESIDUES 30-42; COMPND 23 SYNONYM: H3-CLUSTERED HISTONE 13,H3-CLUSTERED HISTONE 14,H3-CLUSTERED COMPND 24 HISTONE 15,HISTONE H3/M,HISTONE H3/O; COMPND 25 ENGINEERED: YES; COMPND 26 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: KDM2A, FBL11, FBXL11, JHDM1A, KIAA1004; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 12 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 13 ORGANISM_TAXID: 10090; SOURCE 14 GENE: KDM2A, FBL11, FBXL11, JHDM1A, KIAA1004; SOURCE 15 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 16 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 18 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 19 MOL_ID: 3; SOURCE 20 SYNTHETIC: YES; SOURCE 21 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 22 ORGANISM_COMMON: HUMAN; SOURCE 23 ORGANISM_TAXID: 9606 KEYWDS DEMETHYLASE, HISTONE, INHIBITOR, GENE REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR G.R.BUDZISZEWSKI,D.N.AZZAM,C.J.SPANGLER,A.SKRAJNA,C.A.FOLEY, AUTHOR 2 L.I.JAMES,S.V.FRYE,R.K.MCGINTY REVDAT 4 25-OCT-23 7UVA 1 REMARK REVDAT 3 17-MAY-23 7UVA 1 JRNL REVDAT 2 01-MAR-23 7UVA 1 JRNL REVDAT 1 22-FEB-23 7UVA 0 JRNL AUTH C.J.SPANGLER,A.SKRAJNA,C.A.FOLEY,A.NGUYEN,G.R.BUDZISZEWSKI, JRNL AUTH 2 D.N.AZZAM,E.C.ARTEAGA,H.C.SIMMONS,C.B.SMITH,N.A.WESLEY, JRNL AUTH 3 E.M.WILKERSON,J.E.MCPHERSON,D.KIREEV,L.I.JAMES,S.V.FRYE, JRNL AUTH 4 D.GOLDFARB,R.K.MCGINTY JRNL TITL STRUCTURAL BASIS OF PARALOG-SPECIFIC KDM2A/B NUCLEOSOME JRNL TITL 2 RECOGNITION. JRNL REF NAT.CHEM.BIOL. V. 19 624 2023 JRNL REFN ESSN 1552-4469 JRNL PMID 36797403 JRNL DOI 10.1038/S41589-023-01256-Y REMARK 2 REMARK 2 RESOLUTION. 1.98 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 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) : 1.98 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 88.09 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 55260 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2914 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) : 1.98 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.03 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4078 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE SET COUNT : 203 REMARK 3 BIN FREE R VALUE : 0.3230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6645 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 429 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.82 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.47 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.64000 REMARK 3 B22 (A**2) : 1.56000 REMARK 3 B33 (A**2) : -2.21000 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): 0.191 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.173 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.128 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.623 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.966 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): 6859 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6414 ; 0.006 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9290 ; 1.764 ; 1.954 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14795 ; 1.034 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 807 ; 6.297 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 337 ;35.424 ;24.125 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1193 ;14.700 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 39 ;21.838 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 994 ; 0.105 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7660 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1611 ; 0.002 ; 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): 3245 ; 2.329 ; 2.737 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3246 ; 2.329 ; 2.738 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4045 ; 3.252 ; 4.084 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4046 ; 3.255 ; 4.085 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3614 ; 3.622 ; 3.162 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3615 ; 3.622 ; 3.162 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 5246 ; 5.550 ; 4.566 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 8028 ; 7.166 ;22.508 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7877 ; 7.077 ;22.237 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 7UVA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAY-22. REMARK 100 THE DEPOSITION ID IS D_1000264550. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAR-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58130 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 REMARK 200 RESOLUTION RANGE LOW (A) : 88.090 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.19000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.4800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 4QX7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS-CL, PH 8.5, 150 MM LITHIUM REMARK 280 SULFATE, 20% PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 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 27.45150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 88.08850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.52700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 88.08850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.45150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 43.52700 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 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: 5590 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 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 350 REMARK 350 BIOMOLECULE: 2 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: 5260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -59.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, F 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 35 REMARK 465 MET B 449 REMARK 465 ARG C 40 REMARK 465 TYR C 41 REMARK 465 MET D 35 REMARK 465 MET E 449 REMARK 465 ALA F 29 REMARK 465 PRO F 30 REMARK 465 ALA F 31 REMARK 465 PRO F 38 REMARK 465 HIS F 39 REMARK 465 ARG F 40 REMARK 465 TYR F 41 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 HIS C 39 CG ND1 CD2 CE1 NE2 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 ASP D 210 CB - CG - OD1 ANGL. DEV. = 5.6 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 TYR A 49 67.88 -106.87 REMARK 500 ASP A 90 137.88 -39.92 REMARK 500 SER A 145 30.26 -140.72 REMARK 500 LYS A 252 40.46 -108.53 REMARK 500 ASN A 304 48.78 -144.27 REMARK 500 GLU B 483 -86.34 -83.20 REMARK 500 GLU D 138 -70.58 -71.42 REMARK 500 SER D 145 20.87 -143.72 REMARK 500 ASN D 186 30.66 -94.14 REMARK 500 ASN D 304 38.50 -142.40 REMARK 500 GLU E 483 -77.74 -84.32 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 FE A 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 212 NE2 REMARK 620 2 ASP A 214 OD1 95.6 REMARK 620 3 HIS A 284 NE2 92.1 97.9 REMARK 620 4 OH0 A 402 O 95.1 164.8 92.4 REMARK 620 5 OH0 A 402 O3 92.7 89.0 171.2 79.8 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE D 401 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS D 212 NE2 REMARK 620 2 ASP D 214 OD1 90.8 REMARK 620 3 HIS D 284 NE2 90.2 99.1 REMARK 620 4 OH0 D 402 O3 89.1 90.5 170.3 REMARK 620 5 OH0 D 402 O 96.5 167.6 91.0 79.5 REMARK 620 N 1 2 3 4 DBREF 7UVA A 36 364 UNP P59997 KDM2A_MOUSE 36 364 DBREF 7UVA B 450 517 UNP P59997 KDM2A_MOUSE 450 517 DBREF 7UVA C 29 41 UNP Q71DI3 H32_HUMAN 30 42 DBREF 7UVA D 36 364 UNP P59997 KDM2A_MOUSE 36 364 DBREF 7UVA E 450 517 UNP P59997 KDM2A_MOUSE 450 517 DBREF 7UVA F 29 41 UNP Q71DI3 H32_HUMAN 30 42 SEQADV 7UVA MET A 35 UNP P59997 INITIATING METHIONINE SEQADV 7UVA ARG A 159 UNP P59997 TRP 159 CONFLICT SEQADV 7UVA MET A 202 UNP P59997 ILE 202 CONFLICT SEQADV 7UVA MET B 449 UNP P59997 INITIATING METHIONINE SEQADV 7UVA CYS C 36 UNP Q71DI3 LYS 37 CONFLICT SEQADV 7UVA MET D 35 UNP P59997 INITIATING METHIONINE SEQADV 7UVA ARG D 159 UNP P59997 TRP 159 CONFLICT SEQADV 7UVA MET D 202 UNP P59997 ILE 202 CONFLICT SEQADV 7UVA MET E 449 UNP P59997 INITIATING METHIONINE SEQADV 7UVA CYS F 36 UNP Q71DI3 LYS 37 CONFLICT SEQRES 1 A 330 MET ARG THR PHE ASP LEU GLU GLU LYS LEU GLN THR ASN SEQRES 2 A 330 LYS TYR ASN ALA ASN PHE VAL THR PHE MET GLU GLY LYS SEQRES 3 A 330 ASP PHE ASN VAL GLU TYR ILE GLN ARG GLY GLY LEU ARG SEQRES 4 A 330 ASP PRO LEU ILE PHE LYS ASN SER ASP GLY LEU GLY ILE SEQRES 5 A 330 LYS MET PRO ASP PRO ASP PHE THR VAL ASN ASP VAL LYS SEQRES 6 A 330 MET CYS VAL GLY SER ARG ARG MET VAL ASP VAL MET ASP SEQRES 7 A 330 VAL ASN THR GLN LYS GLY ILE GLU MET THR MET ALA GLN SEQRES 8 A 330 TRP THR ARG TYR TYR GLU THR PRO GLU GLU GLU ARG GLU SEQRES 9 A 330 LYS LEU TYR ASN VAL ILE SER LEU GLU PHE SER HIS THR SEQRES 10 A 330 ARG LEU GLU ASN MET VAL GLN ARG PRO SER THR VAL ASP SEQRES 11 A 330 PHE ILE ASP TRP VAL ASP ASN MET TRP PRO ARG HIS LEU SEQRES 12 A 330 LYS GLU SER GLN THR GLU SER THR ASN ALA ILE LEU GLU SEQRES 13 A 330 MET GLN TYR PRO LYS VAL GLN LYS TYR CYS LEU MET SER SEQRES 14 A 330 VAL ARG GLY CYS TYR THR ASP PHE HIS VAL ASP PHE GLY SEQRES 15 A 330 GLY THR SER VAL TRP TYR HIS ILE HIS GLN GLY GLY LYS SEQRES 16 A 330 VAL PHE TRP LEU ILE PRO PRO THR ALA HIS ASN LEU GLU SEQRES 17 A 330 LEU TYR GLU ASN TRP LEU LEU SER GLY LYS GLN GLY ASP SEQRES 18 A 330 ILE PHE LEU GLY ASP ARG VAL SER ASP CYS GLN ARG ILE SEQRES 19 A 330 GLU LEU LYS GLN GLY TYR THR PHE VAL ILE PRO SER GLY SEQRES 20 A 330 TRP ILE HIS ALA VAL TYR THR PRO THR ASP THR LEU VAL SEQRES 21 A 330 PHE GLY GLY ASN PHE LEU HIS SER PHE ASN ILE PRO MET SEQRES 22 A 330 GLN LEU LYS ILE TYR SER ILE GLU ASP ARG THR ARG VAL SEQRES 23 A 330 PRO ASN LYS PHE ARG TYR PRO PHE TYR TYR GLU MET CYS SEQRES 24 A 330 TRP TYR VAL LEU GLU ARG TYR VAL TYR CYS ILE THR ASN SEQRES 25 A 330 ARG SER HIS LEU THR LYS ASP PHE GLN LYS GLU SER LEU SEQRES 26 A 330 SER MET ASP MET GLU SEQRES 1 B 69 MET GLN VAL HIS LEU THR HIS PHE GLU LEU GLU GLY LEU SEQRES 2 B 69 ARG CYS LEU VAL ASP LYS LEU GLU SER LEU PRO LEU HIS SEQRES 3 B 69 LYS LYS CYS VAL PRO THR GLY ILE GLU ASP GLU ASP ALA SEQRES 4 B 69 LEU ILE ALA ASP VAL LYS ILE LEU LEU GLU GLU LEU ALA SEQRES 5 B 69 SER SER ASP PRO LYS LEU ALA LEU THR GLY VAL PRO ILE SEQRES 6 B 69 VAL GLN TRP PRO SEQRES 1 C 13 ALA PRO ALA THR GLY GLY VAL CYS LYS PRO HIS ARG TYR SEQRES 1 D 330 MET ARG THR PHE ASP LEU GLU GLU LYS LEU GLN THR ASN SEQRES 2 D 330 LYS TYR ASN ALA ASN PHE VAL THR PHE MET GLU GLY LYS SEQRES 3 D 330 ASP PHE ASN VAL GLU TYR ILE GLN ARG GLY GLY LEU ARG SEQRES 4 D 330 ASP PRO LEU ILE PHE LYS ASN SER ASP GLY LEU GLY ILE SEQRES 5 D 330 LYS MET PRO ASP PRO ASP PHE THR VAL ASN ASP VAL LYS SEQRES 6 D 330 MET CYS VAL GLY SER ARG ARG MET VAL ASP VAL MET ASP SEQRES 7 D 330 VAL ASN THR GLN LYS GLY ILE GLU MET THR MET ALA GLN SEQRES 8 D 330 TRP THR ARG TYR TYR GLU THR PRO GLU GLU GLU ARG GLU SEQRES 9 D 330 LYS LEU TYR ASN VAL ILE SER LEU GLU PHE SER HIS THR SEQRES 10 D 330 ARG LEU GLU ASN MET VAL GLN ARG PRO SER THR VAL ASP SEQRES 11 D 330 PHE ILE ASP TRP VAL ASP ASN MET TRP PRO ARG HIS LEU SEQRES 12 D 330 LYS GLU SER GLN THR GLU SER THR ASN ALA ILE LEU GLU SEQRES 13 D 330 MET GLN TYR PRO LYS VAL GLN LYS TYR CYS LEU MET SER SEQRES 14 D 330 VAL ARG GLY CYS TYR THR ASP PHE HIS VAL ASP PHE GLY SEQRES 15 D 330 GLY THR SER VAL TRP TYR HIS ILE HIS GLN GLY GLY LYS SEQRES 16 D 330 VAL PHE TRP LEU ILE PRO PRO THR ALA HIS ASN LEU GLU SEQRES 17 D 330 LEU TYR GLU ASN TRP LEU LEU SER GLY LYS GLN GLY ASP SEQRES 18 D 330 ILE PHE LEU GLY ASP ARG VAL SER ASP CYS GLN ARG ILE SEQRES 19 D 330 GLU LEU LYS GLN GLY TYR THR PHE VAL ILE PRO SER GLY SEQRES 20 D 330 TRP ILE HIS ALA VAL TYR THR PRO THR ASP THR LEU VAL SEQRES 21 D 330 PHE GLY GLY ASN PHE LEU HIS SER PHE ASN ILE PRO MET SEQRES 22 D 330 GLN LEU LYS ILE TYR SER ILE GLU ASP ARG THR ARG VAL SEQRES 23 D 330 PRO ASN LYS PHE ARG TYR PRO PHE TYR TYR GLU MET CYS SEQRES 24 D 330 TRP TYR VAL LEU GLU ARG TYR VAL TYR CYS ILE THR ASN SEQRES 25 D 330 ARG SER HIS LEU THR LYS ASP PHE GLN LYS GLU SER LEU SEQRES 26 D 330 SER MET ASP MET GLU SEQRES 1 E 69 MET GLN VAL HIS LEU THR HIS PHE GLU LEU GLU GLY LEU SEQRES 2 E 69 ARG CYS LEU VAL ASP LYS LEU GLU SER LEU PRO LEU HIS SEQRES 3 E 69 LYS LYS CYS VAL PRO THR GLY ILE GLU ASP GLU ASP ALA SEQRES 4 E 69 LEU ILE ALA ASP VAL LYS ILE LEU LEU GLU GLU LEU ALA SEQRES 5 E 69 SER SER ASP PRO LYS LEU ALA LEU THR GLY VAL PRO ILE SEQRES 6 E 69 VAL GLN TRP PRO SEQRES 1 F 13 ALA PRO ALA THR GLY GLY VAL CYS LYS PRO HIS ARG TYR HET FE A 401 1 HET OH0 A 402 15 HET FE D 401 1 HET OH0 D 402 15 HETNAM FE FE (III) ION HETNAM OH0 N-HEPTANOYL-N-HYDROXY-BETA-ALANINE FORMUL 7 FE 2(FE 3+) FORMUL 8 OH0 2(C10 H19 N O4) FORMUL 11 HOH *429(H2 O) HELIX 1 AA1 ASP A 39 THR A 46 1 8 HELIX 2 AA2 GLU A 58 PHE A 62 5 5 HELIX 3 AA3 ASN A 63 GLY A 71 1 9 HELIX 4 AA4 THR A 94 GLY A 103 1 10 HELIX 5 AA5 MET A 123 THR A 132 1 10 HELIX 6 AA6 PRO A 133 ARG A 137 5 5 HELIX 7 AA7 LEU A 153 VAL A 157 5 5 HELIX 8 AA8 PRO A 160 ASP A 167 1 8 HELIX 9 AA9 ASP A 167 TRP A 173 1 7 HELIX 10 AB1 PRO A 174 GLU A 179 1 6 HELIX 11 AB2 ALA A 187 MET A 191 5 5 HELIX 12 AB3 ASP A 214 THR A 218 5 5 HELIX 13 AB4 THR A 237 GLY A 251 1 15 HELIX 14 AB5 PHE A 257 VAL A 262 1 6 HELIX 15 AB6 ASN A 304 THR A 318 1 15 HELIX 16 AB7 PRO A 321 ARG A 325 5 5 HELIX 17 AB8 PHE A 328 ASN A 346 1 19 HELIX 18 AB9 THR A 351 MET A 363 1 13 HELIX 19 AC1 THR B 454 SER B 470 1 17 HELIX 20 AC2 PRO B 472 CYS B 477 1 6 HELIX 21 AC3 ASP B 484 ALA B 500 1 17 HELIX 22 AC4 ASP B 503 LEU B 508 1 6 HELIX 23 AC5 ASP D 39 THR D 46 1 8 HELIX 24 AC6 GLU D 58 PHE D 62 5 5 HELIX 25 AC7 ASN D 63 GLY D 71 1 9 HELIX 26 AC8 THR D 94 GLY D 103 1 10 HELIX 27 AC9 MET D 123 THR D 132 1 10 HELIX 28 AD1 PRO D 133 ARG D 137 5 5 HELIX 29 AD2 THR D 151 VAL D 157 5 7 HELIX 30 AD3 PRO D 160 ASP D 167 1 8 HELIX 31 AD4 ASP D 167 TRP D 173 1 7 HELIX 32 AD5 PRO D 174 GLN D 181 1 8 HELIX 33 AD6 ALA D 187 MET D 191 5 5 HELIX 34 AD7 PHE D 215 THR D 218 5 4 HELIX 35 AD8 THR D 237 GLY D 251 1 15 HELIX 36 AD9 PHE D 257 VAL D 262 1 6 HELIX 37 AE1 ASN D 304 THR D 318 1 15 HELIX 38 AE2 PRO D 321 ARG D 325 5 5 HELIX 39 AE3 PHE D 328 ASN D 346 1 19 HELIX 40 AE4 THR D 351 GLU D 364 1 14 HELIX 41 AE5 THR E 454 LEU E 471 1 18 HELIX 42 AE6 PRO E 472 LYS E 476 5 5 HELIX 43 AE7 ASP E 484 ALA E 500 1 17 HELIX 44 AE8 ASP E 503 LEU E 508 1 6 SHEET 1 AA1 9 THR A 55 PHE A 56 0 SHEET 2 AA1 9 LEU A 76 PHE A 78 1 O ILE A 77 N THR A 55 SHEET 3 AA1 9 THR A 275 ILE A 278 -1 O THR A 275 N PHE A 78 SHEET 4 AA1 9 SER A 219 GLN A 226 -1 N VAL A 220 O ILE A 278 SHEET 5 AA1 9 THR A 292 PHE A 299 -1 O PHE A 295 N HIS A 223 SHEET 6 AA1 9 TYR A 199 SER A 203 -1 N SER A 203 O THR A 292 SHEET 7 AA1 9 TYR A 141 GLU A 147 -1 N VAL A 143 O MET A 202 SHEET 8 AA1 9 MET A 107 ASP A 112 -1 N MET A 111 O ASN A 142 SHEET 9 AA1 9 LYS A 117 THR A 122 -1 O LYS A 117 N ASP A 112 SHEET 1 AA2 4 TYR A 208 HIS A 212 0 SHEET 2 AA2 4 ILE A 283 TYR A 287 -1 O VAL A 286 N THR A 209 SHEET 3 AA2 4 GLY A 228 ILE A 234 -1 N VAL A 230 O TYR A 287 SHEET 4 AA2 4 GLN A 266 LYS A 271 -1 O LEU A 270 N LYS A 229 SHEET 1 AA3 9 THR D 55 PHE D 56 0 SHEET 2 AA3 9 LEU D 76 PHE D 78 1 O ILE D 77 N THR D 55 SHEET 3 AA3 9 THR D 275 ILE D 278 -1 O VAL D 277 N LEU D 76 SHEET 4 AA3 9 SER D 219 GLN D 226 -1 N TYR D 222 O PHE D 276 SHEET 5 AA3 9 THR D 292 PHE D 299 -1 O PHE D 295 N HIS D 223 SHEET 6 AA3 9 TYR D 199 SER D 203 -1 N TYR D 199 O GLY D 296 SHEET 7 AA3 9 TYR D 141 GLU D 147 -1 N VAL D 143 O MET D 202 SHEET 8 AA3 9 MET D 107 ASP D 112 -1 N MET D 111 O ASN D 142 SHEET 9 AA3 9 LYS D 117 THR D 122 -1 O LYS D 117 N ASP D 112 SHEET 1 AA4 4 TYR D 208 VAL D 213 0 SHEET 2 AA4 4 ILE D 283 TYR D 287 -1 O VAL D 286 N THR D 209 SHEET 3 AA4 4 GLY D 228 ILE D 234 -1 N VAL D 230 O TYR D 287 SHEET 4 AA4 4 GLN D 266 LYS D 271 -1 O LEU D 270 N LYS D 229 LINK C OH0 A 402 SG CYS C 36 1555 1555 1.78 LINK C OH0 D 402 SG CYS F 36 1555 1555 1.76 LINK NE2 HIS A 212 FE FE A 401 1555 1555 2.21 LINK OD1 ASP A 214 FE FE A 401 1555 1555 2.16 LINK NE2 HIS A 284 FE FE A 401 1555 1555 2.23 LINK FE FE A 401 O OH0 A 402 1555 1555 2.04 LINK FE FE A 401 O3 OH0 A 402 1555 1555 2.20 LINK NE2 HIS D 212 FE FE D 401 1555 1555 2.29 LINK OD1 ASP D 214 FE FE D 401 1555 1555 2.14 LINK NE2 HIS D 284 FE FE D 401 1555 1555 2.24 LINK FE FE D 401 O3 OH0 D 402 1555 1555 2.22 LINK FE FE D 401 O OH0 D 402 1555 1555 2.07 CRYST1 54.903 87.054 176.177 90.00 90.00 90.00 P 21 21 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 0.018214 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011487 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005676 0.00000