HEADER OXIDOREDUCTASE 27-MAR-17 5VAR TITLE CRYSTAL STRUCTURE OF KDM4A TANDEM TUDOR DOMAIN IN COMPLEX WITH A TRI- TITLE 2 METHYL LYSINE COMPETITIVE INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 4A; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3A, COMPND 5 JUMONJI DOMAIN-CONTAINING PROTEIN 2A; COMPND 6 EC: 1.14.11.-; COMPND 7 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: KDM4A, JHDM3A, JMJD2, JMJD2A, KIAA0677; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS KDM4A TANDEM TUDOR DOMAIN, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR R.A.JUDGE,A.K.UPADHYAY REVDAT 5 04-OCT-23 5VAR 1 REMARK REVDAT 4 05-SEP-18 5VAR 1 REMARK REVDAT 3 16-MAY-18 5VAR 1 JRNL REVDAT 2 09-MAY-18 5VAR 1 JRNL REVDAT 1 28-MAR-18 5VAR 0 JRNL AUTH A.K.UPADHYAY,R.A.JUDGE,L.LI,R.PITHAWALLA,J.SIMANIS, JRNL AUTH 2 P.M.BODELLE,V.L.MARIN,R.F.HENRY,A.M.PETROS,C.SUN JRNL TITL TARGETING LYSINE SPECIFIC DEMETHYLASE 4A (KDM4A) TANDEM JRNL TITL 2 TUDOR DOMAIN - A FRAGMENT BASED APPROACH. JRNL REF BIOORG. MED. CHEM. LETT. V. 28 1708 2018 JRNL REFN ESSN 1464-3405 JRNL PMID 29691138 JRNL DOI 10.1016/J.BMCL.2018.04.050 REMARK 2 REMARK 2 RESOLUTION. 1.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.7 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.59 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 9841 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) : 0.196 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 494 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.000 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.83 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.05 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.84 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2702 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2140 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2565 REMARK 3 BIN R VALUE (WORKING SET) : 0.2110 REMARK 3 BIN FREE R VALUE : 0.2740 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.07 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 137 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 869 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 74 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.67 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.55 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.65850 REMARK 3 B22 (A**2) : 2.06380 REMARK 3 B33 (A**2) : -5.72230 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.19710 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.260 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.148 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.142 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.145 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.140 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 932 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 1287 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 318 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 30 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 139 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 932 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 113 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1054 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.03 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 3.67 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 16.11 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5VAR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1000227137. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-OCT-15 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 : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.12 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9890 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.830 REMARK 200 RESOLUTION RANGE LOW (A) : 39.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.08600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.65400 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: MOLREP REMARK 200 STARTING MODEL: 2GFA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18%(W/V) PEG 8000, 0.2M CALCIUM REMARK 280 ACETATE, 0.1M SODIUM CACODYLATE PH 6.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 19.92000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 893 REMARK 465 SER A 894 REMARK 465 HIS A 895 REMARK 465 MET A 896 REMARK 465 THR A 1005 REMARK 465 LEU A 1006 REMARK 465 ASP A 1007 REMARK 465 GLU A 1008 REMARK 465 GLU A 1009 REMARK 465 LEU A 1010 REMARK 465 PRO A 1011 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1274 DISTANCE = 5.91 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 92Y A 1101 DBREF 5VAR A 897 1011 UNP O75164 KDM4A_HUMAN 897 1011 SEQADV 5VAR GLY A 893 UNP O75164 EXPRESSION TAG SEQADV 5VAR SER A 894 UNP O75164 EXPRESSION TAG SEQADV 5VAR HIS A 895 UNP O75164 EXPRESSION TAG SEQADV 5VAR MET A 896 UNP O75164 EXPRESSION TAG SEQRES 1 A 119 GLY SER HIS MET GLN SER ILE THR ALA GLY GLN LYS VAL SEQRES 2 A 119 ILE SER LYS HIS LYS ASN GLY ARG PHE TYR GLN CYS GLU SEQRES 3 A 119 VAL VAL ARG LEU THR THR GLU THR PHE TYR GLU VAL ASN SEQRES 4 A 119 PHE ASP ASP GLY SER PHE SER ASP ASN LEU TYR PRO GLU SEQRES 5 A 119 ASP ILE VAL SER GLN ASP CYS LEU GLN PHE GLY PRO PRO SEQRES 6 A 119 ALA GLU GLY GLU VAL VAL GLN VAL ARG TRP THR ASP GLY SEQRES 7 A 119 GLN VAL TYR GLY ALA LYS PHE VAL ALA SER HIS PRO ILE SEQRES 8 A 119 GLN MET TYR GLN VAL GLU PHE GLU ASP GLY SER GLN LEU SEQRES 9 A 119 VAL VAL LYS ARG ASP ASP VAL TYR THR LEU ASP GLU GLU SEQRES 10 A 119 LEU PRO HET 92Y A1101 18 HETNAM 92Y (1R,2S,3R,4S)-3-[(DIMETHYLAMINO)METHYL]-1- HETNAM 2 92Y PHENYLBICYCLO[2.2.1]HEPTAN-2-OL FORMUL 2 92Y C16 H23 N O FORMUL 3 HOH *74(H2 O) HELIX 1 AA1 TYR A 942 ILE A 946 5 5 HELIX 2 AA2 ASP A 950 GLY A 955 1 6 HELIX 3 AA3 LYS A 999 ASP A 1001 5 3 SHEET 1 AA1 4 PHE A 937 LEU A 941 0 SHEET 2 AA1 4 PHE A 914 PHE A 932 -1 N TYR A 928 O LEU A 941 SHEET 3 AA1 4 VAL A 972 GLU A 989 -1 O ILE A 983 N GLU A 925 SHEET 4 AA1 4 GLN A 995 VAL A 998 -1 O VAL A 998 N TYR A 986 SHEET 1 AA2 5 VAL A 962 ARG A 966 0 SHEET 2 AA2 5 VAL A 972 GLU A 989 -1 O ALA A 975 N VAL A 963 SHEET 3 AA2 5 PHE A 914 PHE A 932 -1 N GLU A 925 O ILE A 983 SHEET 4 AA2 5 LYS A 904 LYS A 908 -1 N VAL A 905 O CYS A 917 SHEET 5 AA2 5 VAL A1003 TYR A1004 -1 O TYR A1004 N ILE A 906 SITE 1 AC1 6 ASP A 934 SER A 936 PHE A 937 TRP A 967 SITE 2 AC1 6 TYR A 973 GLY A 993 CRYST1 33.270 39.840 44.300 90.00 101.61 90.00 P 1 21 1 2 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 0.030057 0.000000 0.006175 0.00000 SCALE2 0.000000 0.025100 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023045 0.00000