PDB Short entry for 3Q0C HEADER TRANSFERASE/DNA 15-DEC-10 3Q0C TITLE CRYSTAL STRUCTURE OF SUVH5 SRA-FULLY METHYLATED CG DNA COMPLEX IN TITLE 2 SPACE GROUP P6122 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HISTONE-LYSINE N-METHYLTRANSFERASE, H3 LYSINE-9 SPECIFIC COMPND 3 SUVH5; COMPND 4 CHAIN: X, A; COMPND 5 FRAGMENT: SUVH5 SRA DOMAIN (UNP RESIDUES 362-528); COMPND 6 SYNONYM: HISTONE H3-K9 METHYLTRANSFERASE 5, H3-K9-HMTASE 5, PROTEIN COMPND 7 SET DOMAIN GROUP 9, SUPPRESSOR OF VARIEGATION 3-9 HOMOLOG PROTEIN 5, COMPND 8 SU(VAR)3-9 HOMOLOG PROTEIN 5; COMPND 9 EC: 2.1.1.43; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: DNA (5'-D(*AP*CP*TP*AP*(5CM)P*GP*TP*AP*GP*TP*T)-3'); COMPND 13 CHAIN: C, B; COMPND 14 ENGINEERED: YES; COMPND 15 OTHER_DETAILS: SELF COMPLEMENTARY FULLY METHYLATED CG DNA 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: AT2G35160, SDG9, SET9, SUVH5, T4C15.17; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA2(DE3); 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 OTHER_DETAILS: CHEMICALLY SYNTHESIZED KEYWDS SRA, FULLY METHYLATED CG, SUVH5, 5MC BINDING PROTEIN, FULLY KEYWDS 2 METHYLATED CG DNA DUPLEX, TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR R.EERAPPA,D.K.SIMANSHU,D.J.PATEL REVDAT 3 13-SEP-23 3Q0C 1 REMARK LINK REVDAT 2 08-NOV-17 3Q0C 1 REMARK REVDAT 1 02-FEB-11 3Q0C 0 JRNL AUTH E.RAJAKUMARA,J.A.LAW,D.K.SIMANSHU,P.VOIGT,L.M.JOHNSON, JRNL AUTH 2 D.REINBERG,D.J.PATEL,S.E.JACOBSEN JRNL TITL A DUAL FLIP-OUT MECHANISM FOR 5MC RECOGNITION BY THE JRNL TITL 2 ARABIDOPSIS SUVH5 SRA DOMAIN AND ITS IMPACT ON DNA JRNL TITL 3 METHYLATION AND H3K9 DIMETHYLATION IN VIVO. JRNL REF GENES DEV. V. 25 137 2011 JRNL REFN ISSN 0890-9369 JRNL PMID 21245167 JRNL DOI 10.1101/GAD.1980311 REMARK 2 REMARK 2 RESOLUTION. 2.66 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.66 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 17028 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.253 REMARK 3 R VALUE (WORKING SET) : 0.251 REMARK 3 FREE R VALUE : 0.303 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 862 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 19.8474 - 4.8084 1.00 2891 137 0.2188 0.2543 REMARK 3 2 4.8084 - 3.8255 1.00 2718 138 0.2219 0.2641 REMARK 3 3 3.8255 - 3.3445 1.00 2684 135 0.2554 0.3004 REMARK 3 4 3.3445 - 3.0399 1.00 2656 137 0.2761 0.3494 REMARK 3 5 3.0399 - 2.8227 1.00 2595 170 0.3135 0.3606 REMARK 3 6 2.8227 - 2.6567 1.00 2622 145 0.3244 0.3944 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 : 0.28 REMARK 3 B_SOL : 34.10 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.980 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.920 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) : 1.85560 REMARK 3 B22 (A**2) : 1.85560 REMARK 3 B33 (A**2) : -3.71130 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 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 2759 REMARK 3 ANGLE : 1.021 3817 REMARK 3 CHIRALITY : 0.056 412 REMARK 3 PLANARITY : 0.006 425 REMARK 3 DIHEDRAL : 19.914 1056 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 : 2 REMARK 3 NCS GROUP : 1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN X RESID 362:376 REMARK 3 SELECTION : CHAIN A AND RESID 362:376 REMARK 3 ATOM PAIRS NUMBER : 109 REMARK 3 RMSD : 0.024 REMARK 3 NCS GROUP : 2 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: CHAIN X RESID 380:524 REMARK 3 SELECTION : CHAIN A AND RESID 380:524 REMARK 3 ATOM PAIRS NUMBER : 952 REMARK 3 RMSD : 0.029 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3Q0C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-JAN-11. REMARK 100 THE DEPOSITION ID IS D_1000063034. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : CRYOGENICALLY-COOLED SINGLE REMARK 200 CRYSTAL SI(111) SIDE BOUNCE REMARK 200 MONOCHROMATOR. OPTIONAL SI(311) REMARK 200 TO ACHIVE 13.474 KEV. REMARK 200 OPTICS : CRYOGENICALLY-COOLED SINGLE REMARK 200 CRYSTAL SI(111) SIDE BOUNCE REMARK 200 MONOCHROMATOR. OPTIONAL SI(311) REMARK 200 TO ACHIVE 13.474 KEV REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17149 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 28.10 REMARK 200 R MERGE (I) : 0.13600 REMARK 200 R SYM (I) : 0.13400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 27.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 28.90 REMARK 200 R MERGE FOR SHELL (I) : 0.83000 REMARK 200 R SYM FOR SHELL (I) : 0.85000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP MR REMARK 200 STARTING MODEL: PDB ENTRY 3Q0B REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.32 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 23% PEG 3350, 100 MM BIS-TRISPROPANE, REMARK 280 PH 7.0, 80 MM MG-ACETATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+5/6 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 58.89700 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 117.79400 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 88.34550 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 147.24250 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 29.44850 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 58.89700 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 117.79400 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 147.24250 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 88.34550 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 29.44850 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5500 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15770 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: X, A, C, B 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 MG MG B 12 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 LYS X 437 REMARK 465 LYS X 438 REMARK 465 LYS X 439 REMARK 465 ASN X 440 REMARK 465 ASN X 441 REMARK 465 LYS X 473 REMARK 465 ASN X 474 REMARK 465 THR X 475 REMARK 465 THR X 476 REMARK 465 LEU X 477 REMARK 465 GLN X 478 REMARK 465 SER X 479 REMARK 465 SER X 480 REMARK 465 VAL X 481 REMARK 465 VAL X 482 REMARK 465 ALA X 483 REMARK 465 LYS X 525 REMARK 465 GLU X 526 REMARK 465 VAL X 527 REMARK 465 ALA X 528 REMARK 465 GLY A 436 REMARK 465 LYS A 437 REMARK 465 LYS A 438 REMARK 465 LYS A 439 REMARK 465 ASN A 440 REMARK 465 ASN A 441 REMARK 465 GLU A 442 REMARK 465 LYS A 473 REMARK 465 ASN A 474 REMARK 465 THR A 475 REMARK 465 THR A 476 REMARK 465 LEU A 477 REMARK 465 GLN A 478 REMARK 465 SER A 479 REMARK 465 SER A 480 REMARK 465 VAL A 481 REMARK 465 VAL A 482 REMARK 465 ALA A 483 REMARK 465 TRP A 524 REMARK 465 LYS A 525 REMARK 465 GLU A 526 REMARK 465 VAL A 527 REMARK 465 ALA A 528 REMARK 465 DT C 11 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 ASP X 401 CG OD1 OD2 REMARK 470 GLU X 404 CG CD OE1 OE2 REMARK 470 TRP X 524 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP X 524 CZ3 CH2 REMARK 470 LYS A 399 CG CD CE NZ REMARK 470 ASP A 400 CG OD1 OD2 REMARK 470 ASP A 401 CB CG OD1 OD2 REMARK 470 GLU A 404 CG CD OE1 OE2 REMARK 470 LEU A 522 CG CD1 CD2 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 DT C 3 O4' - C1' - N1 ANGL. DEV. = -5.8 DEGREES REMARK 500 DA C 4 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 DC B 2 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 DT B 3 C3' - C2' - C1' ANGL. DEV. = -5.9 DEGREES REMARK 500 DA B 4 C3' - C2' - C1' ANGL. DEV. = -5.4 DEGREES REMARK 500 DA B 4 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DG B 6 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG B 9 O4' - C1' - N9 ANGL. DEV. = 3.1 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 GLN X 392 -47.32 -136.74 REMARK 500 ASP X 421 -164.33 -66.06 REMARK 500 ASN X 422 57.90 -105.79 REMARK 500 ASN X 434 72.66 53.83 REMARK 500 THR X 451 -131.91 55.42 REMARK 500 GLN A 392 -46.34 -135.21 REMARK 500 ASP A 401 28.20 -69.73 REMARK 500 ASP A 421 -165.71 -68.17 REMARK 500 ASN A 422 58.64 -105.02 REMARK 500 ASN A 434 71.86 55.12 REMARK 500 THR A 451 -129.63 54.64 REMARK 500 PRO A 520 170.96 -54.39 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 MG B 12 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DT B 11 OP1 REMARK 620 2 DT B 11 OP2 54.5 REMARK 620 3 HOH B 32 O 119.2 66.8 REMARK 620 4 HOH B 33 O 88.3 82.1 68.2 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 MG B 12 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3Q0B RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SUVH5 SRA- FULLY METHYLATED CG DNA COMPLEX IN REMARK 900 SPACE GROUP P42212 REMARK 900 RELATED ID: 3Q0D RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SUVH5 SRA-HEMI METHYLATED CG COMPLEX REMARK 900 RELATED ID: 3Q0F RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF SUVH5 SRA-METHYLATED CHH DNA COMPLEX DBREF 3Q0C X 362 528 UNP O82175 SUVH5_ARATH 362 528 DBREF 3Q0C A 362 528 UNP O82175 SUVH5_ARATH 362 528 DBREF 3Q0C C 1 11 PDB 3Q0C 3Q0C 1 11 DBREF 3Q0C B 1 11 PDB 3Q0C 3Q0C 1 11 SEQRES 1 X 167 GLN ILE ILE GLY THR VAL PRO GLY VAL GLU VAL GLY ASP SEQRES 2 X 167 GLU PHE GLN TYR ARG MET GLU LEU ASN LEU LEU GLY ILE SEQRES 3 X 167 HIS ARG PRO SER GLN SER GLY ILE ASP TYR MET LYS ASP SEQRES 4 X 167 ASP GLY GLY GLU LEU VAL ALA THR SER ILE VAL SER SER SEQRES 5 X 167 GLY GLY TYR ASN ASP VAL LEU ASP ASN SER ASP VAL LEU SEQRES 6 X 167 ILE TYR THR GLY GLN GLY GLY ASN VAL GLY LYS LYS LYS SEQRES 7 X 167 ASN ASN GLU PRO PRO LYS ASP GLN GLN LEU VAL THR GLY SEQRES 8 X 167 ASN LEU ALA LEU LYS ASN SER ILE ASN LYS LYS ASN PRO SEQRES 9 X 167 VAL ARG VAL ILE ARG GLY ILE LYS ASN THR THR LEU GLN SEQRES 10 X 167 SER SER VAL VAL ALA LYS ASN TYR VAL TYR ASP GLY LEU SEQRES 11 X 167 TYR LEU VAL GLU GLU TYR TRP GLU GLU THR GLY SER HIS SEQRES 12 X 167 GLY LYS LEU VAL PHE LYS PHE LYS LEU ARG ARG ILE PRO SEQRES 13 X 167 GLY GLN PRO GLU LEU PRO TRP LYS GLU VAL ALA SEQRES 1 A 167 GLN ILE ILE GLY THR VAL PRO GLY VAL GLU VAL GLY ASP SEQRES 2 A 167 GLU PHE GLN TYR ARG MET GLU LEU ASN LEU LEU GLY ILE SEQRES 3 A 167 HIS ARG PRO SER GLN SER GLY ILE ASP TYR MET LYS ASP SEQRES 4 A 167 ASP GLY GLY GLU LEU VAL ALA THR SER ILE VAL SER SER SEQRES 5 A 167 GLY GLY TYR ASN ASP VAL LEU ASP ASN SER ASP VAL LEU SEQRES 6 A 167 ILE TYR THR GLY GLN GLY GLY ASN VAL GLY LYS LYS LYS SEQRES 7 A 167 ASN ASN GLU PRO PRO LYS ASP GLN GLN LEU VAL THR GLY SEQRES 8 A 167 ASN LEU ALA LEU LYS ASN SER ILE ASN LYS LYS ASN PRO SEQRES 9 A 167 VAL ARG VAL ILE ARG GLY ILE LYS ASN THR THR LEU GLN SEQRES 10 A 167 SER SER VAL VAL ALA LYS ASN TYR VAL TYR ASP GLY LEU SEQRES 11 A 167 TYR LEU VAL GLU GLU TYR TRP GLU GLU THR GLY SER HIS SEQRES 12 A 167 GLY LYS LEU VAL PHE LYS PHE LYS LEU ARG ARG ILE PRO SEQRES 13 A 167 GLY GLN PRO GLU LEU PRO TRP LYS GLU VAL ALA SEQRES 1 C 11 DA DC DT DA 5CM DG DT DA DG DT DT SEQRES 1 B 11 DA DC DT DA 5CM DG DT DA DG DT DT MODRES 3Q0C 5CM C 5 DC MODRES 3Q0C 5CM B 5 DC HET 5CM C 5 20 HET 5CM B 5 20 HET MG B 12 1 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 3 5CM 2(C10 H16 N3 O7 P) FORMUL 5 MG MG 2+ FORMUL 6 HOH *36(H2 O) HELIX 1 1 TYR X 378 GLY X 386 1 9 HELIX 2 2 VAL X 450 LYS X 463 1 14 HELIX 3 3 TYR A 378 LEU A 385 1 8 HELIX 4 4 VAL A 450 LYS A 463 1 14 SHEET 1 A 5 GLU X 375 PHE X 376 0 SHEET 2 A 5 TYR X 486 THR X 501 -1 O TYR X 486 N PHE X 376 SHEET 3 A 5 VAL X 466 GLY X 471 -1 N VAL X 468 O ASP X 489 SHEET 4 A 5 LEU X 405 SER X 412 1 N SER X 412 O GLY X 471 SHEET 5 A 5 ILE X 395 LYS X 399 -1 N ASP X 396 O THR X 408 SHEET 1 B 4 GLU X 375 PHE X 376 0 SHEET 2 B 4 TYR X 486 THR X 501 -1 O TYR X 486 N PHE X 376 SHEET 3 B 4 LEU X 507 ARG X 515 -1 O LYS X 512 N GLU X 495 SHEET 4 B 4 VAL X 425 THR X 429 -1 N TYR X 428 O PHE X 511 SHEET 1 C 5 GLU A 375 PHE A 376 0 SHEET 2 C 5 TYR A 486 THR A 501 -1 O TYR A 486 N PHE A 376 SHEET 3 C 5 VAL A 466 GLY A 471 -1 N VAL A 468 O ASP A 489 SHEET 4 C 5 LEU A 405 SER A 412 1 N SER A 412 O GLY A 471 SHEET 5 C 5 ILE A 395 LYS A 399 -1 N ASP A 396 O THR A 408 SHEET 1 D 4 GLU A 375 PHE A 376 0 SHEET 2 D 4 TYR A 486 THR A 501 -1 O TYR A 486 N PHE A 376 SHEET 3 D 4 LEU A 507 ARG A 515 -1 O LYS A 512 N GLU A 495 SHEET 4 D 4 VAL A 425 THR A 429 -1 N LEU A 426 O LEU A 513 LINK O3' DA C 4 P 5CM C 5 1555 1555 1.59 LINK O3' 5CM C 5 P DG C 6 1555 1555 1.61 LINK O3' DA B 4 P 5CM B 5 1555 1555 1.60 LINK O3' 5CM B 5 P DG B 6 1555 1555 1.61 LINK OP1 DT B 11 MG MG B 12 1555 1555 2.66 LINK OP2 DT B 11 MG MG B 12 1555 1555 2.89 LINK MG MG B 12 O HOH B 32 1555 1555 2.52 LINK MG MG B 12 O HOH B 33 1555 1555 2.32 SITE 1 AC1 3 DT B 11 HOH B 32 HOH B 33 CRYST1 104.462 104.462 176.691 90.00 90.00 120.00 P 61 2 2 24 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 0.009573 0.005527 0.000000 0.00000 SCALE2 0.000000 0.011054 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005660 0.00000