HEADER OXIDOREDUCTASE 07-FEB-17 5PH8 TITLE PANDDA ANALYSIS GROUP DEPOSITION -- CRYSTAL STRUCTURE OF JMJD2D IN TITLE 2 COMPLEX WITH N09552A COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE-SPECIFIC DEMETHYLASE 4D; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3D, COMPND 5 JUMONJI DOMAIN-CONTAINING PROTEIN 2D; COMPND 6 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: KDM4D, JHDM3D, JMJD2D; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PANDDA, SGC - DIAMOND I04-1 FRAGMENT SCREENING, JMJ DOMAIN, KEYWDS 2 EPIGENETICS, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR N.M.PEARCE,T.KROJER,R.TALON,A.R.BRADLEY,M.FAIRHEAD,R.SETHI,N.WRIGHT, AUTHOR 2 E.MACLEAN,P.COLLINS,J.BRANDAO-NETO,A.DOUANGAMATH,Z.RENJIE,A.DIAS, AUTHOR 3 M.VOLLMAR,J.NG,A.SZYKOWSKA,N.BURGESS-BROWN,P.E.BRENNAN,O.COX, AUTHOR 4 U.OPPERMANN,C.BOUNTRA,C.H.ARROWSMITH,A.EDWARDS,F.VON DELFT REVDAT 4 06-MAR-24 5PH8 1 LINK REVDAT 3 04-OCT-17 5PH8 1 REMARK REVDAT 2 27-SEP-17 5PH8 1 JRNL REMARK REVDAT 1 15-MAR-17 5PH8 0 JRNL AUTH N.M.PEARCE,T.KROJER,A.R.BRADLEY,P.COLLINS,R.P.NOWAK,R.TALON, JRNL AUTH 2 B.D.MARSDEN,S.KELM,J.SHI,C.M.DEANE,F.VON DELFT JRNL TITL A MULTI-CRYSTAL METHOD FOR EXTRACTING OBSCURED JRNL TITL 2 CRYSTALLOGRAPHIC STATES FROM CONVENTIONALLY UNINTERPRETABLE JRNL TITL 3 ELECTRON DENSITY. JRNL REF NAT COMMUN V. 8 15123 2017 JRNL REFN ESSN 2041-1723 JRNL PMID 28436492 JRNL DOI 10.1038/NCOMMS15123 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1682 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 77222 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.130 REMARK 3 R VALUE (WORKING SET) : 0.128 REMARK 3 FREE R VALUE : 0.167 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 3802 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 29.3381 - 4.1845 1.00 3010 138 0.1509 0.1734 REMARK 3 2 4.1845 - 3.3229 1.00 2852 140 0.1301 0.1615 REMARK 3 3 3.3229 - 2.9033 1.00 2790 151 0.1360 0.1746 REMARK 3 4 2.9033 - 2.6380 1.00 2753 149 0.1403 0.1736 REMARK 3 5 2.6380 - 2.4490 1.00 2759 145 0.1341 0.1876 REMARK 3 6 2.4490 - 2.3047 1.00 2726 142 0.1280 0.1617 REMARK 3 7 2.3047 - 2.1893 1.00 2761 131 0.1214 0.1734 REMARK 3 8 2.1893 - 2.0940 1.00 2741 122 0.1156 0.1668 REMARK 3 9 2.0940 - 2.0134 1.00 2754 118 0.1116 0.1409 REMARK 3 10 2.0134 - 1.9440 1.00 2704 151 0.1106 0.1546 REMARK 3 11 1.9440 - 1.8832 1.00 2684 160 0.1033 0.1348 REMARK 3 12 1.8832 - 1.8294 1.00 2698 141 0.1069 0.1443 REMARK 3 13 1.8294 - 1.7812 1.00 2714 140 0.1053 0.1396 REMARK 3 14 1.7812 - 1.7378 1.00 2679 146 0.1044 0.1334 REMARK 3 15 1.7378 - 1.6983 1.00 2728 124 0.1066 0.1495 REMARK 3 16 1.6983 - 1.6621 1.00 2683 154 0.1033 0.1578 REMARK 3 17 1.6621 - 1.6289 1.00 2689 137 0.1090 0.1548 REMARK 3 18 1.6289 - 1.5982 1.00 2695 142 0.1027 0.1467 REMARK 3 19 1.5982 - 1.5696 1.00 2709 132 0.1064 0.1529 REMARK 3 20 1.5696 - 1.5430 1.00 2680 127 0.1109 0.1702 REMARK 3 21 1.5430 - 1.5181 1.00 2677 142 0.1198 0.2001 REMARK 3 22 1.5181 - 1.4948 1.00 2691 148 0.1212 0.1707 REMARK 3 23 1.4948 - 1.4728 1.00 2689 145 0.1324 0.1881 REMARK 3 24 1.4728 - 1.4520 1.00 2652 144 0.1423 0.1893 REMARK 3 25 1.4520 - 1.4324 1.00 2690 144 0.1558 0.2084 REMARK 3 26 1.4324 - 1.4138 1.00 2677 145 0.1790 0.2469 REMARK 3 27 1.4138 - 1.3961 0.96 2535 144 0.2085 0.2698 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.37 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.29 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 3181 REMARK 3 ANGLE : 1.065 4357 REMARK 3 CHIRALITY : 0.077 427 REMARK 3 PLANARITY : 0.005 582 REMARK 3 DIHEDRAL : 12.688 1241 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5PH8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1001400656. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.97630 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.1.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 77324 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 29.330 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 12.40 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.50 REMARK 200 R MERGE FOR SHELL (I) : 0.72200 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: FOURIER SYNTHESIS REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: 4D6R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 28% PEG3350 -- 0.1M HEPES PH 7.0 -- REMARK 280 0.25M AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 74.90300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 35.64000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 35.64000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 112.35450 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 35.64000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 35.64000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.45150 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 35.64000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 35.64000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 112.35450 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 35.64000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 35.64000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 37.45150 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 74.90300 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 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 800 LIES ON A SPECIAL POSITION. 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 -21 REMARK 465 HIS A -20 REMARK 465 HIS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 SER A -14 REMARK 465 SER A -13 REMARK 465 GLY A -12 REMARK 465 VAL A -11 REMARK 465 ASP A -10 REMARK 465 LEU A -9 REMARK 465 GLY A -8 REMARK 465 THR A -7 REMARK 465 GLU A -6 REMARK 465 ASN A -5 REMARK 465 LEU A -4 REMARK 465 TYR A -3 REMARK 465 PHE A -2 REMARK 465 GLN A -1 REMARK 465 SER A 0 REMARK 465 MET A 1 REMARK 465 GLU A 2 REMARK 465 THR A 3 REMARK 465 MET A 4 REMARK 465 LYS A 5 REMARK 465 SER A 6 REMARK 465 LYS A 7 REMARK 465 ALA A 8 REMARK 465 ASN A 9 REMARK 465 CYS A 10 REMARK 465 ARG A 342 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 58 CG CD CE NZ REMARK 470 LYS A 92 NZ REMARK 470 ARG A 316 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 338 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 341 CG OD1 OD2 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 O ASN A 65 O HOH A 501 2.05 REMARK 500 O HOH A 507 O HOH A 742 2.18 REMARK 500 OD1 ASP A 334 O HOH A 502 2.19 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 ASP A 64 -74.22 -40.61 REMARK 500 ASN A 65 39.25 -99.33 REMARK 500 ASN A 176 89.53 -152.43 REMARK 500 LYS A 186 -9.04 77.86 REMARK 500 MET A 196 18.72 57.72 REMARK 500 ARG A 316 95.34 46.36 REMARK 500 REMARK 500 REMARK: NULL 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 A 906 DISTANCE = 6.89 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 YES C1CCC2C(=N)NC(C2C1)=N 2.29 -19.68 REMARK 600 -19.68 C1CCC2C(=N)NC(C2C1)=N < REMARK 600 CONFIDENCE>4 - HIGH CONFIDENCE NONE REMARK 600 0.41 31.44 REMARK 600 1.698219678098279 0.91100000000000003 REMARK 600 0.11899999999999999 0.69999999999999996 REMARK 600 0.8903729555641277 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 NI A 402 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 192 NE2 REMARK 620 2 GLU A 194 OE1 98.3 REMARK 620 3 HIS A 280 NE2 85.3 87.4 REMARK 620 4 OGA A 403 O1 168.6 92.9 96.9 REMARK 620 5 OGA A 403 O2' 90.9 169.2 99.0 77.8 REMARK 620 6 HOH A 614 O 89.3 88.7 172.8 89.3 85.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 401 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 238 SG REMARK 620 2 HIS A 244 NE2 109.3 REMARK 620 3 CYS A 310 SG 116.7 110.3 REMARK 620 4 CYS A 312 SG 113.6 99.0 106.5 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue OGA A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 409 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 410 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 411 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 412 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 413 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PHT A 414 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 1XN A 415 DBREF 5PH8 A 1 342 UNP Q6B0I6 KDM4D_HUMAN 1 342 SEQADV 5PH8 MET A -21 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PH8 HIS A -20 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PH8 HIS A -19 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PH8 HIS A -18 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PH8 HIS A -17 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PH8 HIS A -16 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PH8 HIS A -15 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PH8 SER A -14 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PH8 SER A -13 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PH8 GLY A -12 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PH8 VAL A -11 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PH8 ASP A -10 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PH8 LEU A -9 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PH8 GLY A -8 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PH8 THR A -7 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PH8 GLU A -6 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PH8 ASN A -5 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PH8 LEU A -4 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PH8 TYR A -3 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PH8 PHE A -2 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PH8 GLN A -1 UNP Q6B0I6 EXPRESSION TAG SEQADV 5PH8 SER A 0 UNP Q6B0I6 EXPRESSION TAG SEQRES 1 A 364 MET HIS HIS HIS HIS HIS HIS SER SER GLY VAL ASP LEU SEQRES 2 A 364 GLY THR GLU ASN LEU TYR PHE GLN SER MET GLU THR MET SEQRES 3 A 364 LYS SER LYS ALA ASN CYS ALA GLN ASN PRO ASN CYS ASN SEQRES 4 A 364 ILE MET ILE PHE HIS PRO THR LYS GLU GLU PHE ASN ASP SEQRES 5 A 364 PHE ASP LYS TYR ILE ALA TYR MET GLU SER GLN GLY ALA SEQRES 6 A 364 HIS ARG ALA GLY LEU ALA LYS ILE ILE PRO PRO LYS GLU SEQRES 7 A 364 TRP LYS ALA ARG GLU THR TYR ASP ASN ILE SER GLU ILE SEQRES 8 A 364 LEU ILE ALA THR PRO LEU GLN GLN VAL ALA SER GLY ARG SEQRES 9 A 364 ALA GLY VAL PHE THR GLN TYR HIS LYS LYS LYS LYS ALA SEQRES 10 A 364 MET THR VAL GLY GLU TYR ARG HIS LEU ALA ASN SER LYS SEQRES 11 A 364 LYS TYR GLN THR PRO PRO HIS GLN ASN PHE GLU ASP LEU SEQRES 12 A 364 GLU ARG LYS TYR TRP LYS ASN ARG ILE TYR ASN SER PRO SEQRES 13 A 364 ILE TYR GLY ALA ASP ILE SER GLY SER LEU PHE ASP GLU SEQRES 14 A 364 ASN THR LYS GLN TRP ASN LEU GLY HIS LEU GLY THR ILE SEQRES 15 A 364 GLN ASP LEU LEU GLU LYS GLU CYS GLY VAL VAL ILE GLU SEQRES 16 A 364 GLY VAL ASN THR PRO TYR LEU TYR PHE GLY MET TRP LYS SEQRES 17 A 364 THR THR PHE ALA TRP HIS THR GLU ASP MET ASP LEU TYR SEQRES 18 A 364 SER ILE ASN TYR LEU HIS LEU GLY GLU PRO LYS THR TRP SEQRES 19 A 364 TYR VAL VAL PRO PRO GLU HIS GLY GLN ARG LEU GLU ARG SEQRES 20 A 364 LEU ALA ARG GLU LEU PHE PRO GLY SER SER ARG GLY CYS SEQRES 21 A 364 GLY ALA PHE LEU ARG HIS LYS VAL ALA LEU ILE SER PRO SEQRES 22 A 364 THR VAL LEU LYS GLU ASN GLY ILE PRO PHE ASN ARG ILE SEQRES 23 A 364 THR GLN GLU ALA GLY GLU PHE MET VAL THR PHE PRO TYR SEQRES 24 A 364 GLY TYR HIS ALA GLY PHE ASN HIS GLY PHE ASN CYS ALA SEQRES 25 A 364 GLU ALA ILE ASN PHE ALA THR PRO ARG TRP ILE ASP TYR SEQRES 26 A 364 GLY LYS MET ALA SER GLN CYS SER CYS GLY GLU ALA ARG SEQRES 27 A 364 VAL THR PHE SER MET ASP ALA PHE VAL ARG ILE LEU GLN SEQRES 28 A 364 PRO GLU ARG TYR ASP LEU TRP LYS ARG GLY GLN ASP ARG HET ZN A 401 1 HET NI A 402 1 HET OGA A 403 10 HET EDO A 404 4 HET EDO A 405 4 HET EDO A 406 4 HET EDO A 407 4 HET EDO A 408 4 HET EDO A 409 4 HET SO4 A 410 5 HET SO4 A 411 5 HET SO4 A 412 5 HET SO4 A 413 5 HET PHT A 414 12 HET 1XN A 415 18 HETNAM ZN ZINC ION HETNAM NI NICKEL (II) ION HETNAM OGA N-OXALYLGLYCINE HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETNAM PHT PHTHALIC ACID HETNAM 1XN 2H-ISOINDOLE-1,3-DIAMINE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 ZN ZN 2+ FORMUL 3 NI NI 2+ FORMUL 4 OGA C4 H5 N O5 FORMUL 5 EDO 6(C2 H6 O2) FORMUL 11 SO4 4(O4 S 2-) FORMUL 15 PHT C8 H6 O4 FORMUL 16 1XN C8 H9 N3 FORMUL 17 HOH *406(H2 O) HELIX 1 AA1 ASP A 30 GLN A 41 1 12 HELIX 2 AA2 GLY A 42 ALA A 46 5 5 HELIX 3 AA3 VAL A 98 ASN A 106 1 9 HELIX 4 AA4 ASN A 117 ARG A 129 1 13 HELIX 5 AA5 ILE A 130 ASN A 132 5 3 HELIX 6 AA6 THR A 159 GLY A 169 1 11 HELIX 7 AA7 GLU A 194 LEU A 198 5 5 HELIX 8 AA8 PRO A 216 GLU A 218 5 3 HELIX 9 AA9 HIS A 219 PHE A 231 1 13 HELIX 10 AB1 PHE A 231 CYS A 238 1 8 HELIX 11 AB2 ALA A 240 LYS A 245 5 6 HELIX 12 AB3 SER A 250 ASN A 257 1 8 HELIX 13 AB4 ARG A 299 ALA A 307 1 9 HELIX 14 AB5 THR A 318 GLN A 329 1 12 HELIX 15 AB6 GLN A 329 ASP A 341 1 13 SHEET 1 AA110 MET A 19 PHE A 21 0 SHEET 2 AA110 LEU A 48 ILE A 51 1 O LYS A 50 N PHE A 21 SHEET 3 AA110 PHE A 271 THR A 274 -1 O PHE A 271 N ILE A 51 SHEET 4 AA110 TYR A 199 GLY A 207 -1 N ASN A 202 O MET A 272 SHEET 5 AA110 ASN A 288 PHE A 295 -1 O GLU A 291 N TYR A 203 SHEET 6 AA110 TYR A 179 GLY A 183 -1 N TYR A 181 O ALA A 290 SHEET 7 AA110 ILE A 135 SER A 141 -1 N GLY A 137 O PHE A 182 SHEET 8 AA110 LEU A 75 ARG A 82 -1 N LEU A 75 O TYR A 136 SHEET 9 AA110 VAL A 85 LYS A 92 -1 O LYS A 91 N GLN A 76 SHEET 10 AA110 ALA A 247 ILE A 249 -1 O LEU A 248 N PHE A 86 SHEET 1 AA2 2 LEU A 70 ILE A 71 0 SHEET 2 AA2 2 MET A 96 THR A 97 -1 O MET A 96 N ILE A 71 SHEET 1 AA3 4 THR A 188 HIS A 192 0 SHEET 2 AA3 4 HIS A 280 ASN A 284 -1 O GLY A 282 N PHE A 189 SHEET 3 AA3 4 LYS A 210 VAL A 214 -1 N TYR A 213 O ALA A 281 SHEET 4 AA3 4 ASN A 262 GLN A 266 -1 O GLN A 266 N LYS A 210 LINK NE2 HIS A 192 NI NI A 402 1555 1555 2.21 LINK OE1 GLU A 194 NI NI A 402 1555 1555 2.03 LINK SG CYS A 238 ZN ZN A 401 1555 1555 2.29 LINK NE2 HIS A 244 ZN ZN A 401 1555 1555 2.06 LINK NE2 HIS A 280 NI NI A 402 1555 1555 2.15 LINK SG CYS A 310 ZN ZN A 401 1555 1555 2.27 LINK SG CYS A 312 ZN ZN A 401 1555 1555 2.31 LINK NI NI A 402 O1 OGA A 403 1555 1555 2.07 LINK NI NI A 402 O2' OGA A 403 1555 1555 2.07 LINK NI NI A 402 O HOH A 614 1555 1555 2.13 SITE 1 AC1 4 CYS A 238 HIS A 244 CYS A 310 CYS A 312 SITE 1 AC2 5 HIS A 192 GLU A 194 HIS A 280 OGA A 403 SITE 2 AC2 5 HOH A 614 SITE 1 AC3 13 TYR A 136 PHE A 189 HIS A 192 GLU A 194 SITE 2 AC3 13 SER A 200 ASN A 202 LYS A 210 TRP A 212 SITE 3 AC3 13 HIS A 280 NI A 402 EDO A 409 HOH A 614 SITE 4 AC3 13 HOH A 634 SITE 1 AC4 7 LYS A 150 GLN A 151 TRP A 152 ASN A 153 SITE 2 AC4 7 HIS A 156 HOH A 590 HOH A 636 SITE 1 AC5 4 THR A 252 LYS A 255 ARG A 263 HOH A 694 SITE 1 AC6 4 PHE A 118 ILE A 264 THR A 265 HOH A 521 SITE 1 AC7 10 TRP A 57 LYS A 58 ALA A 59 ARG A 60 SITE 2 AC7 10 TYR A 63 TYR A 203 HOH A 510 HOH A 566 SITE 3 AC7 10 HOH A 599 HOH A 631 SITE 1 AC8 7 SER A 80 THR A 87 CYS A 168 LYS A 305 SITE 2 AC8 7 1XN A 415 HOH A 534 HOH A 730 SITE 1 AC9 7 TYR A 179 TYR A 181 SER A 200 ALA A 292 SITE 2 AC9 7 ASN A 294 OGA A 403 HOH A 614 SITE 1 AD1 6 ARG A 102 HIS A 103 ASN A 106 HOH A 506 SITE 2 AD1 6 HOH A 518 HOH A 642 SITE 1 AD2 7 ARG A 60 GLU A 61 THR A 62 HOH A 509 SITE 2 AD2 7 HOH A 522 HOH A 638 HOH A 639 SITE 1 AD3 4 ARG A 123 LYS A 124 LYS A 127 ASN A 128 SITE 1 AD4 5 PRO A 113 LYS A 124 ASN A 128 TRP A 185 SITE 2 AD4 5 LYS A 186 SITE 1 AD5 16 GLU A 224 ARG A 228 GLY A 239 ALA A 240 SITE 2 AD5 16 PHE A 241 LEU A 242 ARG A 243 SER A 308 SITE 3 AD5 16 HOH A 515 HOH A 569 HOH A 577 HOH A 653 SITE 4 AD5 16 HOH A 704 HOH A 790 HOH A 798 HOH A 813 SITE 1 AD6 15 SER A 80 THR A 87 GLU A 167 CYS A 168 SITE 2 AD6 15 PHE A 231 PRO A 232 GLY A 233 SER A 234 SITE 3 AD6 15 ILE A 301 LYS A 305 EDO A 408 HOH A 534 SITE 4 AD6 15 HOH A 693 HOH A 730 HOH A 886 CRYST1 71.280 71.280 149.806 90.00 90.00 90.00 P 43 21 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 0.014029 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014029 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006675 0.00000