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 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- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : 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 RCSB ID CODE IS RCSB085960. 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 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 5CM C 7 -55.3 D D OUTSIDE RANGE 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 804 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 395 SG REMARK 620 2 CYS A 383 SG 114.5 REMARK 620 3 CYS A 389 SG 108.9 118.5 REMARK 620 4 CYS A 385 SG 94.5 101.2 116.7 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 425 SG REMARK 620 2 CYS A 431 SG 128.5 REMARK 620 3 CYS A 435 SG 116.8 105.4 REMARK 620 4 CYS A 389 SG 99.5 110.4 88.2 REMARK 620 N 1 2 3 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 429 SG REMARK 620 2 CYS A 383 SG 102.8 REMARK 620 3 CYS A 425 SG 115.7 118.7 REMARK 620 4 CYS A 397 SG 93.1 143.5 81.6 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 612 SG REMARK 620 2 CYS A 619 SG 109.7 REMARK 620 3 CYS A 614 SG 96.8 134.1 REMARK 620 4 CYS A 554 SG 110.9 117.2 84.9 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 REMARK 900 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 395 ZN ZN A 804 1555 1555 2.11 LINK SG CYS A 425 ZN ZN A 803 1555 1555 2.17 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 429 ZN ZN A 802 1555 1555 2.32 LINK SG CYS A 383 ZN ZN A 804 1555 1555 2.36 LINK SG CYS A 612 ZN ZN A 805 1555 1555 2.37 LINK SG CYS A 389 ZN ZN A 804 1555 1555 2.37 LINK SG CYS A 389 ZN ZN A 803 1555 1555 2.38 LINK SG CYS A 383 ZN ZN A 802 1555 1555 2.40 LINK SG CYS A 619 ZN ZN A 805 1555 1555 2.41 LINK SG CYS A 385 ZN ZN A 804 1555 1555 2.46 LINK SG CYS A 425 ZN ZN A 802 1555 1555 2.57 LINK SG CYS A 397 ZN ZN A 802 1555 1555 2.60 LINK SG CYS A 614 ZN ZN A 805 1555 1555 2.73 LINK SG CYS A 554 ZN ZN A 805 1555 1555 2.75 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 MASTER 536 0 6 10 28 0 9 6 0 0 0 45 END