HEADER TRANSCRIPTION/DNA 17-MAY-14 4QEP TITLE CRYSTAL STRUCTURE OF KRYPTONITE IN COMPLEX WITH MCHG DNA AND SAH COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-9 SPECIFIC COMPND 3 SUVH4; COMPND 4 CHAIN: A; COMPND 5 FRAGMENT: FUNCTIONAL FRAGMENT; COMPND 6 SYNONYM: HISTONE H3-K9 METHYLTRANSFERASE 4, H3-K9-HMTASE 4, PROTEIN COMPND 7 KRYPTONITE, PROTEIN SET DOMAIN GROUP 33, SUPPRESSOR OF VARIEGATION 3- COMPND 8 9 HOMOLOG PROTEIN 4, SU(VAR)3-9 HOMOLOG PROTEIN 4; COMPND 9 EC: 2.1.1.43; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: DNA (5'-D(*GP*GP*TP*AP*CP*TP*(5CM) COMPND 13 P*AP*GP*CP*AP*GP*TP*AP*T)-3'); COMPND 14 CHAIN: C; COMPND 15 ENGINEERED: YES; COMPND 16 MOL_ID: 3; COMPND 17 MOLECULE: DNA (5'-D(*AP*CP*TP*GP*CP*TP*GP*AP*GP*TP*AP*CP*CP*AP*T)- COMPND 18 3'); COMPND 19 CHAIN: D; COMPND 20 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS,THALE-CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: SUVH4, KYP, SDG33, SET33, AT5G13960, MAC12.7; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-SUMO; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS SRA, SET, HISTONE METHYLATION, METHYLATED DNA, METHYLATION, KEYWDS 2 TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR J.DU,S.LI,D.J.PATEL REVDAT 3 20-SEP-23 4QEP 1 REMARK SEQADV LINK REVDAT 2 20-AUG-14 4QEP 1 JRNL REVDAT 1 30-JUL-14 4QEP 0 JRNL AUTH J.DU,L.M.JOHNSON,M.GROTH,S.FENG,C.J.HALE,S.LI,A.A.VASHISHT, JRNL AUTH 2 J.GALLEGO-BARTOLOME,J.A.WOHLSCHLEGEL,D.J.PATEL,S.E.JACOBSEN JRNL TITL MECHANISM OF DNA METHYLATION-DIRECTED HISTONE METHYLATION BY JRNL TITL 2 KRYPTONITE. JRNL REF MOL.CELL V. 55 495 2014 JRNL REFN ISSN 1097-2765 JRNL PMID 25018018 JRNL DOI 10.1016/J.MOLCEL.2014.06.009 REMARK 2 REMARK 2 RESOLUTION. 3.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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) : 3.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.63 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.8 REMARK 3 NUMBER OF REFLECTIONS : 10811 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.210 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.770 REMARK 3 FREE R VALUE TEST SET COUNT : 516 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 49.6330 - 4.9198 0.85 2558 120 0.2192 0.2599 REMARK 3 2 4.9198 - 3.9055 0.90 2564 118 0.1801 0.1964 REMARK 3 3 3.9055 - 3.4119 0.92 2585 143 0.2047 0.2441 REMARK 3 4 3.4119 - 3.1000 0.92 2588 135 0.2556 0.3464 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) : 0.440 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.016 4344 REMARK 3 ANGLE : 1.601 5964 REMARK 3 CHIRALITY : 0.091 650 REMARK 3 PLANARITY : 0.007 681 REMARK 3 DIHEDRAL : 22.092 1653 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 99 THROUGH 302 ) REMARK 3 ORIGIN FOR THE GROUP (A): -9.2863 19.1529 -14.4850 REMARK 3 T TENSOR REMARK 3 T11: 0.2097 T22: 0.2108 REMARK 3 T33: 0.2033 T12: -0.0264 REMARK 3 T13: 0.0009 T23: -0.0225 REMARK 3 L TENSOR REMARK 3 L11: 1.8672 L22: 0.9419 REMARK 3 L33: 3.4195 L12: 0.5361 REMARK 3 L13: 0.6981 L23: 0.6392 REMARK 3 S TENSOR REMARK 3 S11: -0.0449 S12: 0.1410 S13: -0.0752 REMARK 3 S21: -0.1425 S22: 0.0426 S23: -0.0105 REMARK 3 S31: -0.0783 S32: -0.0570 S33: 0.0022 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 303 THROUGH 564 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.5479 4.0560 -43.6655 REMARK 3 T TENSOR REMARK 3 T11: 0.2198 T22: 0.2263 REMARK 3 T33: 0.3250 T12: 0.0209 REMARK 3 T13: 0.0207 T23: 0.0030 REMARK 3 L TENSOR REMARK 3 L11: 1.2833 L22: 1.7182 REMARK 3 L33: 2.8504 L12: 0.2024 REMARK 3 L13: 0.9034 L23: 1.6066 REMARK 3 S TENSOR REMARK 3 S11: -0.0309 S12: -0.0068 S13: -0.0331 REMARK 3 S21: -0.0770 S22: -0.1663 S23: 0.2170 REMARK 3 S31: 0.1199 S32: -0.2627 S33: 0.1256 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 565 THROUGH 624 ) REMARK 3 ORIGIN FOR THE GROUP (A): -32.4605 14.9148 -42.3902 REMARK 3 T TENSOR REMARK 3 T11: 0.3255 T22: 0.4439 REMARK 3 T33: 0.5255 T12: 0.1288 REMARK 3 T13: -0.0200 T23: -0.1726 REMARK 3 L TENSOR REMARK 3 L11: 1.5390 L22: 2.0497 REMARK 3 L33: 1.8662 L12: 0.0516 REMARK 3 L13: 0.2054 L23: -0.1728 REMARK 3 S TENSOR REMARK 3 S11: -0.1382 S12: -0.1779 S13: 0.6132 REMARK 3 S21: 0.0203 S22: -0.1024 S23: 0.6473 REMARK 3 S31: -0.3073 S32: -0.7849 S33: 0.1245 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'C' AND (RESID 1 THROUGH 11 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.5498 18.3570 -18.4039 REMARK 3 T TENSOR REMARK 3 T11: 0.3773 T22: 0.4380 REMARK 3 T33: 0.3069 T12: 0.0709 REMARK 3 T13: 0.1431 T23: -0.1800 REMARK 3 L TENSOR REMARK 3 L11: 6.4053 L22: 5.9688 REMARK 3 L33: 5.0301 L12: 1.8279 REMARK 3 L13: 1.2428 L23: -0.6426 REMARK 3 S TENSOR REMARK 3 S11: -0.0755 S12: 1.0331 S13: -0.3338 REMARK 3 S21: -0.4452 S22: 0.4045 S23: -1.1458 REMARK 3 S31: -0.0463 S32: -0.0504 S33: -0.2569 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 3 THROUGH 7 ) REMARK 3 ORIGIN FOR THE GROUP (A): 7.7064 7.4389 -20.8996 REMARK 3 T TENSOR REMARK 3 T11: 0.4959 T22: 0.6358 REMARK 3 T33: 0.4261 T12: 0.3158 REMARK 3 T13: 0.0313 T23: 0.0530 REMARK 3 L TENSOR REMARK 3 L11: 4.2947 L22: 3.5766 REMARK 3 L33: 4.9483 L12: -0.5283 REMARK 3 L13: 0.4649 L23: -4.2020 REMARK 3 S TENSOR REMARK 3 S11: -0.1271 S12: 0.0896 S13: -0.2150 REMARK 3 S21: -0.2895 S22: -0.3269 S23: -0.5347 REMARK 3 S31: 0.7010 S32: 0.7020 S33: 0.2982 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'D' AND (RESID 8 THROUGH 15 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.3460 30.1320 -15.5234 REMARK 3 T TENSOR REMARK 3 T11: 0.6164 T22: 0.3539 REMARK 3 T33: 0.3731 T12: -0.1512 REMARK 3 T13: -0.1276 T23: 0.0751 REMARK 3 L TENSOR REMARK 3 L11: 4.4582 L22: 3.3312 REMARK 3 L33: 2.0085 L12: -1.6502 REMARK 3 L13: -0.1230 L23: -0.1022 REMARK 3 S TENSOR REMARK 3 S11: -0.7376 S12: -0.2374 S13: 0.3302 REMARK 3 S21: -0.1373 S22: -0.0657 S23: -0.8008 REMARK 3 S31: -0.6480 S32: 0.1672 S33: 0.3810 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 4QEP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1000085960. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-MAR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMETER REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10851 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.6 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.15500 REMARK 200 R SYM (I) : 0.15500 REMARK 200 FOR THE DATA SET : 9.5000 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 (%) : 92.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.61500 REMARK 200 R SYM FOR SHELL (I) : 0.61500 REMARK 200 FOR SHELL : 2.000 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 4QEN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG200, 5% PEG3000, AND 0.1 M MES, REMARK 280 PH 6.0, VAPOR DIFFUSION, HANGING 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 27.17300 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.87700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.78450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.87700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.17300 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.78450 REMARK 290 SMTRY3 4 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS THE ASYMMETRIC UNIT. 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: 4280 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, C, 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 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 SER A 92 REMARK 465 ASN A 93 REMARK 465 GLY A 94 REMARK 465 LYS A 95 REMARK 465 ASP A 96 REMARK 465 VAL A 97 REMARK 465 ASN A 98 REMARK 465 GLN A 313 REMARK 465 VAL A 314 REMARK 465 ASN A 315 REMARK 465 PHE A 316 REMARK 465 VAL A 317 REMARK 465 ALA A 318 REMARK 465 GLY A 319 REMARK 465 ARG A 320 REMARK 465 ILE A 321 REMARK 465 PRO A 322 REMARK 465 THR A 323 REMARK 465 SER A 324 REMARK 465 THR A 325 REMARK 465 SER A 326 REMARK 465 GLU A 327 REMARK 465 ILE A 328 REMARK 465 ASP A 486 REMARK 465 THR A 487 REMARK 465 ILE A 488 REMARK 465 SER A 489 REMARK 465 ASP A 490 REMARK 465 GLN A 500 REMARK 465 GLN A 501 REMARK 465 THR A 502 REMARK 465 MET A 503 REMARK 465 GLN A 504 REMARK 465 GLY A 505 REMARK 465 LEU A 506 REMARK 465 GLY A 507 REMARK 465 GLY A 508 REMARK 465 ARG A 509 REMARK 465 GLN A 510 REMARK 465 ARG A 511 REMARK 465 ARG A 512 REMARK 465 LEU A 513 REMARK 465 ARG A 514 REMARK 465 ASP A 515 REMARK 465 VAL A 516 REMARK 465 ALA A 517 REMARK 465 VAL A 518 REMARK 465 PRO A 519 REMARK 465 MET A 520 REMARK 465 ASN A 521 REMARK 465 ASN A 522 REMARK 465 GLY A 523 REMARK 465 VAL A 524 REMARK 465 SER A 525 REMARK 465 GLN A 526 REMARK 465 SER A 527 REMARK 465 SER A 528 REMARK 465 GLU A 529 REMARK 465 ASP A 530 REMARK 465 GLU A 531 REMARK 465 ASN A 532 REMARK 465 ALA A 533 REMARK 465 GLY A 602 REMARK 465 PRO A 603 REMARK 465 ASP A 604 REMARK 465 GLY A 605 REMARK 465 DG C 12 REMARK 465 DT C 13 REMARK 465 DA C 14 REMARK 465 DT C 15 REMARK 465 DA D 1 REMARK 465 DC D 2 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 CYS A 397 CB CYS A 397 SG 0.107 REMARK 500 DA C 4 O3' DC C 5 P -0.096 REMARK 500 DC C 5 O3' DT C 6 P -0.092 REMARK 500 DT C 6 O3' 5CM C 7 P -0.086 REMARK 500 DC D 5 O3' DT D 6 P -0.131 REMARK 500 DT D 6 O3' DG D 7 P -0.081 REMARK 500 DG D 7 O3' DA D 8 P -0.087 REMARK 500 DA D 8 O3' DG D 9 P -0.080 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 ASP A 312 CB - CG - OD1 ANGL. DEV. = 5.5 DEGREES REMARK 500 CYS A 397 CA - CB - SG ANGL. DEV. = 13.6 DEGREES REMARK 500 CYS A 612 CA - CB - SG ANGL. DEV. = 9.2 DEGREES REMARK 500 DT C 3 O3' - P - O5' ANGL. DEV. = -12.3 DEGREES REMARK 500 DT C 6 O3' - P - O5' ANGL. DEV. = -13.2 DEGREES REMARK 500 DA C 8 O4' - C4' - C3' ANGL. DEV. = -2.9 DEGREES REMARK 500 DC C 10 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT D 6 C3' - C2' - C1' ANGL. DEV. = -4.9 DEGREES REMARK 500 DG D 7 O5' - P - OP1 ANGL. DEV. = -5.6 DEGREES REMARK 500 DC D 12 O4' - C1' - N1 ANGL. DEV. = 2.2 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 ALA A 214 -71.30 78.35 REMARK 500 THR A 228 -155.24 -104.76 REMARK 500 ARG A 241 -93.58 -148.82 REMARK 500 SER A 266 103.24 -55.21 REMARK 500 SER A 267 -54.72 -22.46 REMARK 500 PRO A 355 42.06 -76.96 REMARK 500 CYS A 435 124.62 -36.47 REMARK 500 LYS A 455 16.92 -144.52 REMARK 500 ASN A 545 -156.03 -104.29 REMARK 500 SER A 565 -49.66 -141.18 REMARK 500 VAL A 607 -163.27 56.09 REMARK 500 LYS A 608 150.56 177.80 REMARK 500 CYS A 614 -68.66 -29.84 REMARK 500 LYS A 621 -0.82 70.03 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 ZN A 802 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 383 SG REMARK 620 2 CYS A 397 SG 143.5 REMARK 620 3 CYS A 425 SG 118.7 81.6 REMARK 620 4 CYS A 429 SG 102.8 93.1 115.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 804 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 383 SG REMARK 620 2 CYS A 385 SG 101.2 REMARK 620 3 CYS A 389 SG 118.5 116.7 REMARK 620 4 CYS A 395 SG 114.5 94.5 108.9 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 803 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 389 SG REMARK 620 2 CYS A 425 SG 99.5 REMARK 620 3 CYS A 431 SG 110.4 128.5 REMARK 620 4 CYS A 435 SG 88.2 116.8 105.4 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 805 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 554 SG REMARK 620 2 CYS A 612 SG 110.9 REMARK 620 3 CYS A 614 SG 84.9 96.8 REMARK 620 4 CYS A 619 SG 117.2 109.7 134.1 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 SAH A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 805 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4QEN RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX MCHH DNA AND SAH. REMARK 900 RELATED ID: 4QEO RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN COMPLEX MCHH DNA, H3(1-15) PEPTIDE AND SAH. DBREF 4QEP A 93 624 UNP Q8GZB6 SUVH4_ARATH 93 624 DBREF 4QEP C 1 15 PDB 4QEP 4QEP 1 15 DBREF 4QEP D 1 15 PDB 4QEP 4QEP 1 15 SEQADV 4QEP SER A 92 UNP Q8GZB6 EXPRESSION TAG SEQRES 1 A 533 SER ASN GLY LYS ASP VAL ASN LEU GLU PRO HIS LEU LYS SEQRES 2 A 533 VAL THR LYS CYS LEU ARG LEU PHE ASN LYS GLN TYR LEU SEQRES 3 A 533 LEU CYS VAL GLN ALA LYS LEU SER ARG PRO ASP LEU LYS SEQRES 4 A 533 GLY VAL THR GLU MET ILE LYS ALA LYS ALA ILE LEU TYR SEQRES 5 A 533 PRO ARG LYS ILE ILE GLY ASP LEU PRO GLY ILE ASP VAL SEQRES 6 A 533 GLY HIS ARG PHE PHE SER ARG ALA GLU MET CYS ALA VAL SEQRES 7 A 533 GLY PHE HIS ASN HIS TRP LEU ASN GLY ILE ASP TYR MET SEQRES 8 A 533 SER MET GLU TYR GLU LYS GLU TYR SER ASN TYR LYS LEU SEQRES 9 A 533 PRO LEU ALA VAL SER ILE VAL MET SER GLY GLN TYR GLU SEQRES 10 A 533 ASP ASP LEU ASP ASN ALA ASP THR VAL THR TYR THR GLY SEQRES 11 A 533 GLN GLY GLY HIS ASN LEU THR GLY ASN LYS ARG GLN ILE SEQRES 12 A 533 LYS ASP GLN LEU LEU GLU ARG GLY ASN LEU ALA LEU LYS SEQRES 13 A 533 HIS CYS CYS GLU TYR ASN VAL PRO VAL ARG VAL THR ARG SEQRES 14 A 533 GLY HIS ASN CYS LYS SER SER TYR THR LYS ARG VAL TYR SEQRES 15 A 533 THR TYR ASP GLY LEU TYR LYS VAL GLU LYS PHE TRP ALA SEQRES 16 A 533 GLN LYS GLY VAL SER GLY PHE THR VAL TYR LYS TYR ARG SEQRES 17 A 533 LEU LYS ARG LEU GLU GLY GLN PRO GLU LEU THR THR ASP SEQRES 18 A 533 GLN VAL ASN PHE VAL ALA GLY ARG ILE PRO THR SER THR SEQRES 19 A 533 SER GLU ILE GLU GLY LEU VAL CYS GLU ASP ILE SER GLY SEQRES 20 A 533 GLY LEU GLU PHE LYS GLY ILE PRO ALA THR ASN ARG VAL SEQRES 21 A 533 ASP ASP SER PRO VAL SER PRO THR SER GLY PHE THR TYR SEQRES 22 A 533 ILE LYS SER LEU ILE ILE GLU PRO ASN VAL ILE ILE PRO SEQRES 23 A 533 LYS SER SER THR GLY CYS ASN CYS ARG GLY SER CYS THR SEQRES 24 A 533 ASP SER LYS LYS CYS ALA CYS ALA LYS LEU ASN GLY GLY SEQRES 25 A 533 ASN PHE PRO TYR VAL ASP LEU ASN ASP GLY ARG LEU ILE SEQRES 26 A 533 GLU SER ARG ASP VAL VAL PHE GLU CYS GLY PRO HIS CYS SEQRES 27 A 533 GLY CYS GLY PRO LYS CYS VAL ASN ARG THR SER GLN LYS SEQRES 28 A 533 ARG LEU ARG PHE ASN LEU GLU VAL PHE ARG SER ALA LYS SEQRES 29 A 533 LYS GLY TRP ALA VAL ARG SER TRP GLU TYR ILE PRO ALA SEQRES 30 A 533 GLY SER PRO VAL CYS GLU TYR ILE GLY VAL VAL ARG ARG SEQRES 31 A 533 THR ALA ASP VAL ASP THR ILE SER ASP ASN GLU TYR ILE SEQRES 32 A 533 PHE GLU ILE ASP CYS GLN GLN THR MET GLN GLY LEU GLY SEQRES 33 A 533 GLY ARG GLN ARG ARG LEU ARG ASP VAL ALA VAL PRO MET SEQRES 34 A 533 ASN ASN GLY VAL SER GLN SER SER GLU ASP GLU ASN ALA SEQRES 35 A 533 PRO GLU PHE CYS ILE ASP ALA GLY SER THR GLY ASN PHE SEQRES 36 A 533 ALA ARG PHE ILE ASN HIS SER CYS GLU PRO ASN LEU PHE SEQRES 37 A 533 VAL GLN CYS VAL LEU SER SER HIS GLN ASP ILE ARG LEU SEQRES 38 A 533 ALA ARG VAL VAL LEU PHE ALA ALA ASP ASN ILE SER PRO SEQRES 39 A 533 MET GLN GLU LEU THR TYR ASP TYR GLY TYR ALA LEU ASP SEQRES 40 A 533 SER VAL HIS GLY PRO ASP GLY LYS VAL LYS GLN LEU ALA SEQRES 41 A 533 CYS TYR CYS GLY ALA LEU ASN CYS ARG LYS ARG LEU TYR SEQRES 1 C 15 DG DG DT DA DC DT 5CM DA DG DC DA DG DT SEQRES 2 C 15 DA DT SEQRES 1 D 15 DA DC DT DG DC DT DG DA DG DT DA DC DC SEQRES 2 D 15 DA DT MODRES 4QEP 5CM C 7 DC HET 5CM C 7 20 HET SAH A 801 26 HET ZN A 802 1 HET ZN A 803 1 HET ZN A 804 1 HET ZN A 805 1 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM ZN ZINC ION FORMUL 2 5CM C10 H16 N3 O7 P FORMUL 4 SAH C14 H20 N6 O5 S FORMUL 5 ZN 4(ZN 2+) HELIX 1 1 GLU A 100 ALA A 122 1 23 HELIX 2 2 ARG A 126 ALA A 138 1 13 HELIX 3 3 SER A 162 VAL A 169 1 8 HELIX 4 4 SER A 183 GLU A 187 5 5 HELIX 5 5 ARG A 241 ASN A 253 1 13 HELIX 6 6 CYS A 395 ASN A 401 1 7 HELIX 7 7 CYS A 435 LYS A 442 5 8 HELIX 8 8 ALA A 483 VAL A 485 5 3 HELIX 9 9 ASN A 545 ILE A 550 5 6 HELIX 10 10 ASP A 569 ALA A 573 5 5 SHEET 1 A 5 ARG A 159 PHE A 160 0 SHEET 2 A 5 ARG A 271 LYS A 288 -1 O TYR A 273 N PHE A 160 SHEET 3 A 5 VAL A 256 ASN A 263 -1 N VAL A 256 O TYR A 279 SHEET 4 A 5 LEU A 197 MET A 203 1 N VAL A 199 O ARG A 257 SHEET 5 A 5 ILE A 179 MET A 182 -1 N ASP A 180 O SER A 200 SHEET 1 B 5 ARG A 159 PHE A 160 0 SHEET 2 B 5 ARG A 271 LYS A 288 -1 O TYR A 273 N PHE A 160 SHEET 3 B 5 THR A 294 ARG A 302 -1 O VAL A 295 N GLN A 287 SHEET 4 B 5 THR A 216 THR A 220 -1 N TYR A 219 O TYR A 298 SHEET 5 B 5 LEU A 211 ASP A 212 -1 N LEU A 211 O THR A 218 SHEET 1 C 4 LEU A 331 CYS A 333 0 SHEET 2 C 4 ALA A 347 THR A 348 -1 O ALA A 347 N VAL A 332 SHEET 3 C 4 LEU A 448 ARG A 452 1 O ARG A 452 N THR A 348 SHEET 4 C 4 TRP A 458 SER A 462 -1 O ARG A 461 N GLU A 449 SHEET 1 D 2 THR A 363 TYR A 364 0 SHEET 2 D 2 THR A 543 GLY A 544 1 O GLY A 544 N THR A 363 SHEET 1 E 4 ILE A 369 ILE A 370 0 SHEET 2 E 4 VAL A 478 ARG A 481 1 O VAL A 479 N ILE A 369 SHEET 3 E 4 PHE A 536 ASP A 539 -1 O ASP A 539 N VAL A 478 SHEET 4 E 4 ILE A 494 GLU A 496 -1 N PHE A 495 O ILE A 538 SHEET 1 F 2 TYR A 407 VAL A 408 0 SHEET 2 F 2 ARG A 414 LEU A 415 -1 O ARG A 414 N VAL A 408 SHEET 1 G 4 VAL A 421 PHE A 423 0 SHEET 2 G 4 LEU A 558 LEU A 564 1 O LEU A 564 N VAL A 422 SHEET 3 G 4 ARG A 574 ALA A 579 -1 O VAL A 576 N GLN A 561 SHEET 4 G 4 PRO A 471 GLU A 474 -1 N CYS A 473 O LEU A 577 SHEET 1 H 2 ASN A 551 HIS A 552 0 SHEET 2 H 2 THR A 590 TYR A 591 1 O TYR A 591 N ASN A 551 LINK O3' DT C 6 P 5CM C 7 1555 1555 1.52 LINK O3' 5CM C 7 P DA C 8 1555 1555 1.61 LINK SG CYS A 383 ZN ZN A 802 1555 1555 2.40 LINK SG CYS A 383 ZN ZN A 804 1555 1555 2.36 LINK SG CYS A 385 ZN ZN A 804 1555 1555 2.46 LINK SG CYS A 389 ZN ZN A 803 1555 1555 2.38 LINK SG CYS A 389 ZN ZN A 804 1555 1555 2.37 LINK SG CYS A 395 ZN ZN A 804 1555 1555 2.11 LINK SG CYS A 397 ZN ZN A 802 1555 1555 2.60 LINK SG CYS A 425 ZN ZN A 802 1555 1555 2.57 LINK SG CYS A 425 ZN ZN A 803 1555 1555 2.17 LINK SG CYS A 429 ZN ZN A 802 1555 1555 2.32 LINK SG CYS A 431 ZN ZN A 803 1555 1555 2.22 LINK SG CYS A 435 ZN ZN A 803 1555 1555 2.28 LINK SG CYS A 554 ZN ZN A 805 1555 1555 2.75 LINK SG CYS A 612 ZN ZN A 805 1555 1555 2.37 LINK SG CYS A 614 ZN ZN A 805 1555 1555 2.73 LINK SG CYS A 619 ZN ZN A 805 1555 1555 2.41 CISPEP 1 LEU A 195 PRO A 196 0 3.20 SITE 1 AC1 10 LYS A 456 GLY A 457 TRP A 458 TYR A 493 SITE 2 AC1 10 ARG A 548 ASN A 551 HIS A 552 TYR A 593 SITE 3 AC1 10 CYS A 612 TYR A 613 SITE 1 AC2 5 CYS A 383 CYS A 397 CYS A 425 CYS A 429 SITE 2 AC2 5 ZN A 804 SITE 1 AC3 4 CYS A 389 CYS A 425 CYS A 431 CYS A 435 SITE 1 AC4 5 CYS A 383 CYS A 385 CYS A 389 CYS A 395 SITE 2 AC4 5 ZN A 802 SITE 1 AC5 4 CYS A 554 CYS A 612 CYS A 614 CYS A 619 CRYST1 54.346 95.569 121.754 90.00 90.00 90.00 P 21 21 21 4 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 0.018401 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010464 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008213 0.00000