HEADER TRANSFERASE/DNA 13-JUL-15 5CIY TITLE STRUCTURAL BASIS OF THE RECOGNITION OF H3K36ME3 BY DNMT3B PWWP DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MODIFICATION METHYLASE HHAI; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: M.HHAI,CYTOSINE-SPECIFIC METHYLTRANSFERASE HHAI; COMPND 5 EC: 2.1.1.37; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'-D(P*CP*CP*AP*TP*GP*CP*GP*CP*TP*GP*AP*C)-3'); COMPND 9 CHAIN: C; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: DNA (5'-D(P*GP*TP*CP*AP*GP*(3DR)P*GP*CP*AP*TP*GP*G)-3'); COMPND 13 CHAIN: D; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HAEMOPHILUS PARAHAEMOLYTICUS; SOURCE 3 ORGANISM_TAXID: 735; SOURCE 4 GENE: HHAIM; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI K-12; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 7 EXPRESSION_SYSTEM_VARIANT: ER1727; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PUHE25HHAI; SOURCE 10 MOL_ID: 2; SOURCE 11 SYNTHETIC: YES; SOURCE 12 ORGANISM_SCIENTIFIC: HAEMOPHILUS HAEMOLYTICUS; SOURCE 13 ORGANISM_TAXID: 726; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: HAEMOPHILUS HAEMOLYTICUS; SOURCE 17 ORGANISM_TAXID: 726 KEYWDS CG-SPECIFICITY, CPG SEQUENCE, C5-METHYLCYTOSINE, NUCLEOTIDE FLIPPING, KEYWDS 2 S-ADENOSYL-L-HOMOCYSTEINE, COMPLEX (METHYLTRANSFERASE- DNA), KEYWDS 3 TRANSFERASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR G.RONDELET,T.DAL MASO,L.WILLEMS,J.WOUTERS REVDAT 4 10-JAN-24 5CIY 1 REMARK REVDAT 3 12-JUN-19 5CIY 1 AUTHOR REVDAT 2 04-MAY-16 5CIY 1 JRNL REVDAT 1 30-MAR-16 5CIY 0 JRNL AUTH G.RONDELET,T.DAL MASO,L.WILLEMS,J.WOUTERS JRNL TITL STRUCTURAL BASIS FOR RECOGNITION OF HISTONE H3K36ME3 JRNL TITL 2 NUCLEOSOME BY HUMAN DE NOVO DNA METHYLTRANSFERASES 3A AND JRNL TITL 3 3B. JRNL REF J.STRUCT.BIOL. V. 194 357 2016 JRNL REFN ESSN 1095-8657 JRNL PMID 26993463 JRNL DOI 10.1016/J.JSB.2016.03.013 REMARK 2 REMARK 2 RESOLUTION. 1.59 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.59 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 72699 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3634 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 36.5641 - 4.7191 0.97 2800 147 0.1602 0.1574 REMARK 3 2 4.7191 - 3.7469 0.99 2753 145 0.1248 0.1287 REMARK 3 3 3.7469 - 3.2736 1.00 2737 144 0.1324 0.1365 REMARK 3 4 3.2736 - 2.9745 1.00 2719 143 0.1548 0.1622 REMARK 3 5 2.9745 - 2.7613 1.00 2725 143 0.1632 0.1918 REMARK 3 6 2.7613 - 2.5986 1.00 2717 144 0.1640 0.1907 REMARK 3 7 2.5986 - 2.4685 1.00 2691 141 0.1623 0.1851 REMARK 3 8 2.4685 - 2.3610 1.00 2705 143 0.1609 0.1886 REMARK 3 9 2.3610 - 2.2702 1.00 2689 141 0.1581 0.1894 REMARK 3 10 2.2702 - 2.1918 1.00 2701 142 0.1546 0.1931 REMARK 3 11 2.1918 - 2.1233 1.00 2684 142 0.1527 0.2146 REMARK 3 12 2.1233 - 2.0626 1.00 2683 141 0.1531 0.2155 REMARK 3 13 2.0626 - 2.0083 1.00 2681 141 0.1533 0.1793 REMARK 3 14 2.0083 - 1.9593 1.00 2698 142 0.1528 0.2076 REMARK 3 15 1.9593 - 1.9148 1.00 2670 140 0.1562 0.1868 REMARK 3 16 1.9148 - 1.8740 1.00 2664 141 0.1510 0.2022 REMARK 3 17 1.8740 - 1.8366 1.00 2687 141 0.1604 0.1722 REMARK 3 18 1.8366 - 1.8019 1.00 2680 141 0.1565 0.1998 REMARK 3 19 1.8019 - 1.7697 1.00 2638 139 0.1868 0.2652 REMARK 3 20 1.7697 - 1.7397 0.99 2656 140 0.2305 0.2752 REMARK 3 21 1.7397 - 1.7117 0.99 2659 140 0.2905 0.3338 REMARK 3 22 1.7117 - 1.6853 0.98 2623 138 0.3085 0.3790 REMARK 3 23 1.6853 - 1.6605 0.97 2581 136 0.3444 0.3390 REMARK 3 24 1.6605 - 1.6372 0.95 2501 132 0.4177 0.4338 REMARK 3 25 1.6372 - 1.6150 0.93 2466 129 0.5107 0.4924 REMARK 3 26 1.6150 - 1.5941 0.84 2257 118 0.6495 0.7086 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.210 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.62 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.16 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 3262 REMARK 3 ANGLE : 1.161 4506 REMARK 3 CHIRALITY : 0.072 482 REMARK 3 PLANARITY : 0.005 495 REMARK 3 DIHEDRAL : 17.121 1255 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 5CIY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-JUL-15. REMARK 100 THE DEPOSITION ID IS D_1000211715. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9801 REMARK 200 MONOCHROMATOR : CRYOGENICALLY COOLED CHANNEL-CUT REMARK 200 SI[111] REMARK 200 OPTICS : X-RAY FLUORESCCENCE DETECTOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 72764 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.590 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.0500 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.59 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.69400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.080 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.2 REMARK 200 STARTING MODEL: 9MHT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE 1.8 M, CITRATE 50MM, REMARK 280 PH 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z REMARK 290 7555 X+2/3,Y+1/3,Z+1/3 REMARK 290 8555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 9555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 10555 Y+2/3,X+1/3,-Z+1/3 REMARK 290 11555 X-Y+2/3,-Y+1/3,-Z+1/3 REMARK 290 12555 -X+2/3,-X+Y+1/3,-Z+1/3 REMARK 290 13555 X+1/3,Y+2/3,Z+2/3 REMARK 290 14555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 15555 -X+Y+1/3,-X+2/3,Z+2/3 REMARK 290 16555 Y+1/3,X+2/3,-Z+2/3 REMARK 290 17555 X-Y+1/3,-Y+2/3,-Z+2/3 REMARK 290 18555 -X+1/3,-X+Y+2/3,-Z+2/3 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 47.66750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 27.52084 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 104.89600 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 47.66750 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 27.52084 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 104.89600 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 47.66750 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 27.52084 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 104.89600 REMARK 290 SMTRY1 10 -0.500000 0.866025 0.000000 47.66750 REMARK 290 SMTRY2 10 0.866025 0.500000 0.000000 27.52084 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 104.89600 REMARK 290 SMTRY1 11 1.000000 0.000000 0.000000 47.66750 REMARK 290 SMTRY2 11 0.000000 -1.000000 0.000000 27.52084 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 104.89600 REMARK 290 SMTRY1 12 -0.500000 -0.866025 0.000000 47.66750 REMARK 290 SMTRY2 12 -0.866025 0.500000 0.000000 27.52084 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 104.89600 REMARK 290 SMTRY1 13 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 55.04169 REMARK 290 SMTRY3 13 0.000000 0.000000 1.000000 209.79200 REMARK 290 SMTRY1 14 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 14 0.866025 -0.500000 0.000000 55.04169 REMARK 290 SMTRY3 14 0.000000 0.000000 1.000000 209.79200 REMARK 290 SMTRY1 15 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 15 -0.866025 -0.500000 0.000000 55.04169 REMARK 290 SMTRY3 15 0.000000 0.000000 1.000000 209.79200 REMARK 290 SMTRY1 16 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 16 0.866025 0.500000 0.000000 55.04169 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 209.79200 REMARK 290 SMTRY1 17 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 17 0.000000 -1.000000 0.000000 55.04169 REMARK 290 SMTRY3 17 0.000000 0.000000 -1.000000 209.79200 REMARK 290 SMTRY1 18 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 18 -0.866025 0.500000 0.000000 55.04169 REMARK 290 SMTRY3 18 0.000000 0.000000 -1.000000 209.79200 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -92.0 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 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 793 LIES ON A SPECIAL POSITION. 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 HOH A 512 O HOH A 690 2.11 REMARK 500 O HOH A 603 O HOH A 866 2.13 REMARK 500 O HOH A 721 O HOH A 755 2.15 REMARK 500 O HOH A 668 O HOH A 811 2.16 REMARK 500 O HOH A 814 O HOH A 881 2.17 REMARK 500 O HOH A 502 O HOH A 928 2.18 REMARK 500 O HOH A 603 O HOH A 878 2.18 REMARK 500 O HOH A 942 O HOH A 1008 2.18 REMARK 500 O HOH A 964 O HOH A 1010 2.19 REMARK 500 O HOH A 877 O HOH A 881 2.19 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 DA C 412 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DC D 424 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG D 426 C3' - C2' - C1' ANGL. DEV. = -5.1 DEGREES REMARK 500 DG D 433 O4' - C1' - N9 ANGL. DEV. = 2.7 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 ASP A 60 100.34 -9.66 REMARK 500 ASP A 144 40.36 74.97 REMARK 500 PHE A 259 46.30 -99.09 REMARK 500 LYS A 261 -30.03 75.79 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 A1015 DISTANCE = 6.00 ANGSTROMS 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 408 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 409 DBREF 5CIY A 1 327 UNP P05102 MTH1_HAEPH 1 327 DBREF 5CIY C 402 413 PDB 5CIY 5CIY 402 413 DBREF 5CIY D 422 433 PDB 5CIY 5CIY 422 433 SEQRES 1 A 327 MET ILE GLU ILE LYS ASP LYS GLN LEU THR GLY LEU ARG SEQRES 2 A 327 PHE ILE ASP LEU PHE ALA GLY LEU GLY GLY PHE ARG LEU SEQRES 3 A 327 ALA LEU GLU SER CYS GLY ALA GLU CYS VAL TYR SER ASN SEQRES 4 A 327 GLU TRP ASP LYS TYR ALA GLN GLU VAL TYR GLU MET ASN SEQRES 5 A 327 PHE GLY GLU LYS PRO GLU GLY ASP ILE THR GLN VAL ASN SEQRES 6 A 327 GLU LYS THR ILE PRO ASP HIS ASP ILE LEU CYS ALA GLY SEQRES 7 A 327 PHE PRO CYS GLN ALA PHE SER ILE SER GLY LYS GLN LYS SEQRES 8 A 327 GLY PHE GLU ASP SER ARG GLY THR LEU PHE PHE ASP ILE SEQRES 9 A 327 ALA ARG ILE VAL ARG GLU LYS LYS PRO LYS VAL VAL PHE SEQRES 10 A 327 MET GLU ASN VAL LYS ASN PHE ALA SER HIS ASP ASN GLY SEQRES 11 A 327 ASN THR LEU GLU VAL VAL LYS ASN THR MET ASN GLU LEU SEQRES 12 A 327 ASP TYR SER PHE HIS ALA LYS VAL LEU ASN ALA LEU ASP SEQRES 13 A 327 TYR GLY ILE PRO GLN LYS ARG GLU ARG ILE TYR MET ILE SEQRES 14 A 327 CYS PHE ARG ASN ASP LEU ASN ILE GLN ASN PHE GLN PHE SEQRES 15 A 327 PRO LYS PRO PHE GLU LEU ASN THR PHE VAL LYS ASP LEU SEQRES 16 A 327 LEU LEU PRO ASP SER GLU VAL GLU HIS LEU VAL ILE ASP SEQRES 17 A 327 ARG LYS ASP LEU VAL MET THR ASN GLN GLU ILE GLU GLN SEQRES 18 A 327 THR THR PRO LYS THR VAL ARG LEU GLY ILE VAL GLY LYS SEQRES 19 A 327 GLY GLY GLN GLY GLU ARG ILE TYR SER THR ARG GLY ILE SEQRES 20 A 327 ALA ILE THR LEU SER ALA TYR GLY GLY GLY ILE PHE ALA SEQRES 21 A 327 LYS THR GLY GLY TYR LEU VAL ASN GLY LYS THR ARG LYS SEQRES 22 A 327 LEU HIS PRO ARG GLU CYS ALA ARG VAL MET GLY TYR PRO SEQRES 23 A 327 ASP SER TYR LYS VAL HIS PRO SER THR SER GLN ALA TYR SEQRES 24 A 327 LYS GLN PHE GLY ASN SER VAL VAL ILE ASN VAL LEU GLN SEQRES 25 A 327 TYR ILE ALA TYR ASN ILE GLY SER SER LEU ASN PHE LYS SEQRES 26 A 327 PRO TYR SEQRES 1 C 12 DC DC DA DT DG DC DG DC DT DG DA DC SEQRES 1 D 12 DG DT DC DA DG 3DR DG DC DA DT DG DG HET 3DR D 427 11 HET SAH A 401 26 HET SO4 A 402 5 HET SO4 A 403 5 HET SO4 A 404 5 HET SO4 A 405 5 HET SO4 A 406 5 HET SO4 A 407 5 HET SO4 A 408 5 HET SO4 A 409 5 HETNAM 3DR 1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE HETNAM SAH S-ADENOSYL-L-HOMOCYSTEINE HETNAM SO4 SULFATE ION HETSYN 3DR ABASIC DIDEOXYRIBOSE FORMUL 3 3DR C5 H11 O6 P FORMUL 4 SAH C14 H20 N6 O5 S FORMUL 5 SO4 8(O4 S 2-) FORMUL 13 HOH *634(H2 O) HELIX 1 AA1 GLY A 22 CYS A 31 1 10 HELIX 2 AA2 ASP A 42 GLY A 54 1 13 HELIX 3 AA3 ASP A 60 VAL A 64 5 5 HELIX 4 AA4 ASN A 65 ILE A 69 5 5 HELIX 5 AA5 LYS A 91 GLY A 98 5 8 HELIX 6 AA6 THR A 99 LYS A 112 1 14 HELIX 7 AA7 ASN A 123 ASN A 129 5 7 HELIX 8 AA8 GLY A 130 LEU A 143 1 14 HELIX 9 AA9 LEU A 155 TYR A 157 5 3 HELIX 10 AB1 ASN A 173 ASN A 176 5 4 HELIX 11 AB2 PHE A 191 LEU A 195 5 5 HELIX 12 AB3 PRO A 198 HIS A 204 5 7 HELIX 13 AB4 HIS A 275 MET A 283 1 9 HELIX 14 AB5 SER A 294 SER A 305 1 12 HELIX 15 AB6 VAL A 307 PHE A 324 1 18 SHEET 1 AA1 6 GLU A 34 ASN A 39 0 SHEET 2 AA1 6 ARG A 13 LEU A 17 1 N ASP A 16 O TYR A 37 SHEET 3 AA1 6 ILE A 74 GLY A 78 1 O CYS A 76 N LEU A 17 SHEET 4 AA1 6 VAL A 115 VAL A 121 1 O PHE A 117 N LEU A 75 SHEET 5 AA1 6 GLU A 164 PHE A 171 -1 O MET A 168 N MET A 118 SHEET 6 AA1 6 HIS A 148 ASN A 153 -1 N HIS A 148 O ILE A 169 SHEET 1 AA2 6 VAL A 206 ILE A 207 0 SHEET 2 AA2 6 LYS A 270 ARG A 272 -1 O THR A 271 N ILE A 207 SHEET 3 AA2 6 GLY A 264 VAL A 267 -1 N VAL A 267 O LYS A 270 SHEET 4 AA2 6 ARG A 240 SER A 243 1 N TYR A 242 O GLY A 264 SHEET 5 AA2 6 ARG A 228 ILE A 231 -1 N LEU A 229 O ILE A 241 SHEET 6 AA2 6 VAL A 213 MET A 214 -1 N VAL A 213 O ILE A 231 LINK O3' DG D 426 P 3DR D 427 1555 1555 1.61 LINK O3' 3DR D 427 P DG D 428 1555 1555 1.62 SITE 1 AC1 24 PHE A 18 ALA A 19 GLY A 20 LEU A 21 SITE 2 AC1 24 GLY A 23 ASN A 39 GLU A 40 TRP A 41 SITE 3 AC1 24 ASP A 42 ASP A 60 ILE A 61 GLY A 78 SITE 4 AC1 24 PRO A 80 TYR A 285 ASN A 304 SER A 305 SITE 5 AC1 24 VAL A 306 HOH A 574 HOH A 621 HOH A 650 SITE 6 AC1 24 HOH A 665 HOH A 754 HOH A 783 HOH A 838 SITE 1 AC2 9 PRO A 198 ASP A 199 HOH A 513 HOH A 553 SITE 2 AC2 9 HOH A 636 HOH A 685 HOH A 686 HOH A 776 SITE 3 AC2 9 HOH A 780 SITE 1 AC3 10 LYS A 193 ARG A 245 LYS A 290 HOH A 532 SITE 2 AC3 10 HOH A 587 HOH A 608 HOH A 627 HOH A 666 SITE 3 AC3 10 HOH A 711 HOH A 791 SITE 1 AC4 6 PRO A 286 ASP A 287 SER A 288 HOH A 519 SITE 2 AC4 6 HOH A 547 HOH A 810 SITE 1 AC5 5 ILE A 219 GLU A 220 GLN A 221 HOH A 520 SITE 2 AC5 5 HOH A 746 SITE 1 AC6 3 LYS A 114 ARG A 172 HOH A 813 SITE 1 AC7 3 LEU A 196 PRO A 198 ARG A 281 SITE 1 AC8 6 ASN A 141 SER A 146 PHE A 147 HOH A 515 SITE 2 AC8 6 HOH A 573 HOH A 580 SITE 1 AC9 3 TRP A 41 HOH A 523 HOH A 691 CRYST1 95.335 95.335 314.688 90.00 90.00 120.00 H 3 2 18 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 0.010489 0.006056 0.000000 0.00000 SCALE2 0.000000 0.012112 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003178 0.00000