HEADER TRANSCRIPTION/DNA 15-AUG-13 4M9V TITLE ZFP57 MUTANT (E182Q) IN COMPLEX WITH 5-CARBOXYLCYTOSINE DNA CAVEAT 4M9V CHIRALITY ERROR AT C4 OF MPD B 101, C 203, E 101 AND F 203 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*TP*AP*TP*TP*GP*CP*(5CM)P*GP*CP*AP*G)-3'); COMPND 3 CHAIN: A, D; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*AP*CP*TP*GP*(1CC)P*GP*GP*CP*AP*AP*T)-3'); COMPND 7 CHAIN: B, E; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: ZINC FINGER PROTEIN 57; COMPND 11 CHAIN: C, F; COMPND 12 SYNONYM: ZFP-57; COMPND 13 ENGINEERED: YES; COMPND 14 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: DNA SYNTHESIS; SOURCE 4 MOL_ID: 2; SOURCE 5 SYNTHETIC: YES; SOURCE 6 OTHER_DETAILS: DNA SYNTHESIS; SOURCE 7 MOL_ID: 3; SOURCE 8 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 9 ORGANISM_COMMON: MOUSE; SOURCE 10 ORGANISM_TAXID: 10090; SOURCE 11 GENE: ZFP57; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 EXPRESSION_SYSTEM_PLASMID: PXC1158 KEYWDS EPIGENETICS, TRANSCRIPTION FACTOR, 5-CARBOXYLCYTOSINE, C2H2 ZINC KEYWDS 2 FINGER, DNA BINDING, TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIU,Y.O.OLANREWAJU,X.ZHANG,X.CHENG REVDAT 4 20-SEP-23 4M9V 1 REMARK LINK REVDAT 3 24-JUN-20 4M9V 1 REMARK SEQADV LINK ATOM REVDAT 2 22-JAN-14 4M9V 1 JRNL REVDAT 1 27-NOV-13 4M9V 0 JRNL AUTH Y.LIU,Y.O.OLANREWAJU,X.ZHANG,X.CHENG JRNL TITL DNA RECOGNITION OF 5-CARBOXYLCYTOSINE BY A ZFP57 MUTANT AT JRNL TITL 2 AN ATOMIC RESOLUTION OF 0.97 ANGSTROM. JRNL REF BIOCHEMISTRY V. 52 9310 2013 JRNL REFN ISSN 0006-2960 JRNL PMID 24236546 JRNL DOI 10.1021/BI401360N REMARK 2 REMARK 2 RESOLUTION. 0.97 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.1_1168) 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) : 0.97 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 129906 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.131 REMARK 3 R VALUE (WORKING SET) : 0.130 REMARK 3 FREE R VALUE : 0.143 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 6543 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 33.4792 - 3.0088 0.92 3996 224 0.1366 0.1451 REMARK 3 2 3.0088 - 2.3884 0.96 4182 215 0.1450 0.1345 REMARK 3 3 2.3884 - 2.0865 0.97 4203 199 0.1306 0.1507 REMARK 3 4 2.0865 - 1.8958 0.97 4125 249 0.1228 0.1333 REMARK 3 5 1.8958 - 1.7599 0.97 4187 209 0.1120 0.1284 REMARK 3 6 1.7599 - 1.6561 0.97 4121 244 0.1044 0.1161 REMARK 3 7 1.6561 - 1.5732 0.97 4186 226 0.0990 0.1239 REMARK 3 8 1.5732 - 1.5047 0.98 4213 198 0.1067 0.1201 REMARK 3 9 1.5047 - 1.4468 0.97 4168 256 0.1027 0.1150 REMARK 3 10 1.4468 - 1.3969 0.98 4222 203 0.1020 0.1433 REMARK 3 11 1.3969 - 1.3532 0.98 4208 220 0.1051 0.1265 REMARK 3 12 1.3532 - 1.3145 0.97 4182 258 0.1086 0.1253 REMARK 3 13 1.3145 - 1.2799 0.97 4169 216 0.1101 0.1288 REMARK 3 14 1.2799 - 1.2487 0.97 4127 235 0.1107 0.1253 REMARK 3 15 1.2487 - 1.2203 0.97 4122 248 0.1187 0.1453 REMARK 3 16 1.2203 - 1.1943 0.95 4153 211 0.1181 0.1361 REMARK 3 17 1.1943 - 1.1704 0.97 4124 200 0.1230 0.1399 REMARK 3 18 1.1704 - 1.1483 0.96 4128 215 0.1284 0.1502 REMARK 3 19 1.1483 - 1.1278 0.96 4144 211 0.1297 0.1493 REMARK 3 20 1.1278 - 1.1087 0.96 4104 213 0.1327 0.1444 REMARK 3 21 1.1087 - 1.0908 0.95 4145 207 0.1416 0.1527 REMARK 3 22 1.0908 - 1.0740 0.95 4064 221 0.1482 0.1596 REMARK 3 23 1.0740 - 1.0582 0.95 4086 205 0.1600 0.1670 REMARK 3 24 1.0582 - 1.0433 0.95 4122 185 0.1745 0.2038 REMARK 3 25 1.0433 - 1.0292 0.95 4035 209 0.1909 0.2224 REMARK 3 26 1.0292 - 1.0159 0.95 4071 226 0.2119 0.2305 REMARK 3 27 1.0159 - 1.0032 0.95 4025 220 0.2408 0.2518 REMARK 3 28 1.0032 - 0.9911 0.95 4125 204 0.2550 0.2703 REMARK 3 29 0.9911 - 0.9796 0.93 3945 207 0.2610 0.2862 REMARK 3 30 0.9796 - 0.9685 0.84 3681 209 0.2851 0.2821 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.63 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.70 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 : 0.009 2197 REMARK 3 ANGLE : 1.815 3190 REMARK 3 CHIRALITY : 0.085 338 REMARK 3 PLANARITY : 0.010 252 REMARK 3 DIHEDRAL : 26.406 919 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: FLAT BULK SOLVENT MODEL REMARK 4 REMARK 4 4M9V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000081648. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-DEC-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL - LIQUID NITROGEN REMARK 200 COOLED REMARK 200 OPTICS : SI 111. ROSENBAUM-ROCK DOUBLE REMARK 200 -CRYSTAL MONOCHROMATOR: LIQUID REMARK 200 NITROGEN COOLED; SAGITALLY REMARK 200 FOCUSING 2ND CRYSTAL, ROSENBAUM- REMARK 200 ROCK VERTICAL FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 129957 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.969 REMARK 200 RESOLUTION RANGE LOW (A) : 33.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 2.600 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.97 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.7 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.64800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 4GZN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 35% 2-METHYL-2,4-PENTANEDIOL, 15% REMARK 280 POLYETHYLENE GLYCOL 8000, 100 MM CACL2, AND 100 MM ACETATE, PH REMARK 280 4.2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 48.04650 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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: TRIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 350 REMARK 350 BIOMOLECULE: 2 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: 4780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: D, E, F 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 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13370 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -90.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F 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 LEU C 134 REMARK 465 GLY C 135 REMARK 465 ALA C 195 REMARK 465 LEU F 134 REMARK 465 GLY F 135 REMARK 465 ALA F 195 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 GLY C 132 N CA REMARK 470 SER C 136 OG REMARK 470 GLU C 137 CG CD OE1 OE2 REMARK 470 LYS C 193 CG CD CE NZ REMARK 470 PRO C 194 C O CB CG CD REMARK 470 GLY F 132 N CA REMARK 470 GLU F 137 CG CD OE1 OE2 REMARK 470 LYS F 193 CG CD CE NZ REMARK 470 PRO F 194 O CB CG CD 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 OP2 DC B 2 O HOH B 244 1.93 REMARK 500 O HOH B 238 O HOH C 336 1.94 REMARK 500 OP2 DC E 2 O HOH E 263 1.95 REMARK 500 O HOH E 250 O HOH F 342 1.95 REMARK 500 O HOH D 120 O HOH E 259 2.02 REMARK 500 O HOH E 250 O HOH E 278 2.05 REMARK 500 O HOH F 379 O HOH F 395 2.11 REMARK 500 O HOH C 338 O HOH C 391 2.12 REMARK 500 O HOH F 357 O HOH F 394 2.12 REMARK 500 OP1 DG A 5 O HOH A 145 2.15 REMARK 500 O HOH E 248 O HOH E 251 2.16 REMARK 500 OXT ACT B 102 O HOH B 265 2.18 REMARK 500 O HOH C 364 O HOH C 384 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE2 GLU C 172 O HOH F 393 1556 2.18 REMARK 500 REMARK 500 REMARK: NULL 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 DT A 3 O3' DT A 3 C3' -0.054 REMARK 500 DT A 4 O3' DT A 4 C3' -0.040 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 DT A 1 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DT A 3 O5' - C5' - C4' ANGL. DEV. = -4.9 DEGREES REMARK 500 DT A 3 O4' - C1' - C2' ANGL. DEV. = 3.7 DEGREES REMARK 500 DT A 4 C3' - C2' - C1' ANGL. DEV. = -7.7 DEGREES REMARK 500 DG A 11 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT B 11 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DT D 3 O4' - C4' - C3' ANGL. DEV. = 5.0 DEGREES REMARK 500 DT D 4 C3' - C2' - C1' ANGL. DEV. = -7.1 DEGREES REMARK 500 DT D 4 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 DT D 4 O4' - C1' - N1 ANGL. DEV. = -4.9 DEGREES REMARK 500 DG D 11 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT E 11 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 144 DISTANCE = 6.01 ANGSTROMS 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 CA B 103 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 159 O REMARK 620 2 HOH A 160 O 87.1 REMARK 620 3 HOH A 161 O 76.1 78.1 REMARK 620 4 HOH B 268 O 87.7 151.0 128.0 REMARK 620 5 HOH B 269 O 113.6 135.1 69.9 72.5 REMARK 620 6 HOH B 270 O 82.0 78.3 148.3 72.7 141.0 REMARK 620 7 HOH B 271 O 165.5 81.6 110.2 97.7 80.9 86.8 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 142 SG REMARK 620 2 CYS C 145 SG 118.4 REMARK 620 3 HIS C 158 NE2 105.6 105.2 REMARK 620 4 HIS C 162 NE2 107.2 122.0 94.2 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN C 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS C 170 SG REMARK 620 2 CYS C 173 SG 114.4 REMARK 620 3 HIS C 186 NE2 105.6 106.3 REMARK 620 4 HIS C 190 NE2 109.2 112.2 108.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA E 103 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH D 145 O REMARK 620 2 HOH D 146 O 77.0 REMARK 620 3 HOH D 147 O 78.3 87.3 REMARK 620 4 HOH E 206 O 128.5 87.0 150.2 REMARK 620 5 HOH E 279 O 69.9 114.6 134.9 73.4 REMARK 620 6 HOH E 280 O 148.3 81.2 77.9 72.3 141.2 REMARK 620 7 HOH E 281 O 109.9 165.4 81.7 97.7 80.0 87.0 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN F 202 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS F 142 SG REMARK 620 2 CYS F 145 SG 118.4 REMARK 620 3 HIS F 158 NE2 105.3 104.1 REMARK 620 4 HIS F 162 NE2 108.0 121.8 95.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN F 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS F 170 SG REMARK 620 2 CYS F 173 SG 114.8 REMARK 620 3 HIS F 186 NE2 105.3 106.7 REMARK 620 4 HIS F 190 NE2 109.1 112.8 107.5 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA B 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD C 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT C 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD E 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT E 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA E 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN F 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN F 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD F 203 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4GZN RELATED DB: PDB REMARK 900 MOUSE ZFP57 ZINC FINGERS IN COMPLEX WITH METHYLATED DNA DBREF 4M9V C 137 195 UNP Q8C6P8 ZFP57_MOUSE 137 195 DBREF 4M9V F 137 195 UNP Q8C6P8 ZFP57_MOUSE 137 195 DBREF 4M9V A 1 11 PDB 4M9V 4M9V 1 11 DBREF 4M9V D 1 11 PDB 4M9V 4M9V 1 11 DBREF 4M9V B 1 11 PDB 4M9V 4M9V 1 11 DBREF 4M9V E 1 11 PDB 4M9V 4M9V 1 11 SEQADV 4M9V GLY C 132 UNP Q8C6P8 EXPRESSION TAG SEQADV 4M9V PRO C 133 UNP Q8C6P8 EXPRESSION TAG SEQADV 4M9V LEU C 134 UNP Q8C6P8 EXPRESSION TAG SEQADV 4M9V GLY C 135 UNP Q8C6P8 EXPRESSION TAG SEQADV 4M9V SER C 136 UNP Q8C6P8 EXPRESSION TAG SEQADV 4M9V GLN C 182 UNP Q8C6P8 GLU 182 ENGINEERED MUTATION SEQADV 4M9V GLY F 132 UNP Q8C6P8 EXPRESSION TAG SEQADV 4M9V PRO F 133 UNP Q8C6P8 EXPRESSION TAG SEQADV 4M9V LEU F 134 UNP Q8C6P8 EXPRESSION TAG SEQADV 4M9V GLY F 135 UNP Q8C6P8 EXPRESSION TAG SEQADV 4M9V SER F 136 UNP Q8C6P8 EXPRESSION TAG SEQADV 4M9V GLN F 182 UNP Q8C6P8 GLU 182 ENGINEERED MUTATION SEQRES 1 A 11 DT DA DT DT DG DC 5CM DG DC DA DG SEQRES 1 B 11 DA DC DT DG 1CC DG DG DC DA DA DT SEQRES 1 C 64 GLY PRO LEU GLY SER GLU ARG PRO PHE PHE CYS ASN PHE SEQRES 2 C 64 CYS GLY LYS THR TYR ARG ASP ALA SER GLY LEU SER ARG SEQRES 3 C 64 HIS ARG ARG ALA HIS LEU GLY TYR ARG PRO ARG SER CYS SEQRES 4 C 64 PRO GLU CYS GLY LYS CYS PHE ARG ASP GLN SER GLN VAL SEQRES 5 C 64 ASN ARG HIS LEU LYS VAL HIS GLN ASN LYS PRO ALA SEQRES 1 D 11 DT DA DT DT DG DC 5CM DG DC DA DG SEQRES 1 E 11 DA DC DT DG 1CC DG DG DC DA DA DT SEQRES 1 F 64 GLY PRO LEU GLY SER GLU ARG PRO PHE PHE CYS ASN PHE SEQRES 2 F 64 CYS GLY LYS THR TYR ARG ASP ALA SER GLY LEU SER ARG SEQRES 3 F 64 HIS ARG ARG ALA HIS LEU GLY TYR ARG PRO ARG SER CYS SEQRES 4 F 64 PRO GLU CYS GLY LYS CYS PHE ARG ASP GLN SER GLN VAL SEQRES 5 F 64 ASN ARG HIS LEU LYS VAL HIS GLN ASN LYS PRO ALA MODRES 4M9V 5CM A 7 DC MODRES 4M9V 1CC B 5 DC MODRES 4M9V 5CM D 7 DC MODRES 4M9V 1CC E 5 DC HET 5CM A 7 33 HET 1CC B 5 32 HET 5CM D 7 33 HET 1CC E 5 32 HET MPD B 101 22 HET ACT B 102 7 HET CA B 103 1 HET ZN C 201 1 HET ZN C 202 1 HET MPD C 203 22 HET ACT C 204 7 HET ACT C 205 7 HET MPD E 101 22 HET ACT E 102 7 HET CA E 103 1 HET ZN F 201 1 HET ZN F 202 1 HET MPD F 203 22 HETNAM 5CM 5-METHYL-2'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE HETNAM 1CC 5-CARBOXY-2'-DEOXYCYTIDINE MONOPHOSPHATE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM ACT ACETATE ION HETNAM CA CALCIUM ION HETNAM ZN ZINC ION FORMUL 1 5CM 2(C10 H16 N3 O7 P) FORMUL 2 1CC 2(C10 H14 N3 O9 P) FORMUL 7 MPD 4(C6 H14 O2) FORMUL 8 ACT 4(C2 H3 O2 1-) FORMUL 9 CA 2(CA 2+) FORMUL 10 ZN 4(ZN 2+) FORMUL 21 HOH *472(H2 O) HELIX 1 1 ASP C 151 GLY C 164 1 14 HELIX 2 2 ASP C 179 LEU C 187 1 9 HELIX 3 3 LYS C 188 GLN C 191 5 4 HELIX 4 4 ASP F 151 GLY F 164 1 14 HELIX 5 5 ASP F 179 LEU F 187 1 9 HELIX 6 6 LYS F 188 GLN F 191 5 4 SHEET 1 A 2 PHE C 140 PHE C 141 0 SHEET 2 A 2 THR C 148 TYR C 149 -1 O TYR C 149 N PHE C 140 SHEET 1 B 2 ARG C 168 SER C 169 0 SHEET 2 B 2 CYS C 176 PHE C 177 -1 O PHE C 177 N ARG C 168 SHEET 1 C 2 PHE F 140 PHE F 141 0 SHEET 2 C 2 THR F 148 TYR F 149 -1 O TYR F 149 N PHE F 140 SHEET 1 D 2 ARG F 168 SER F 169 0 SHEET 2 D 2 CYS F 176 PHE F 177 -1 O PHE F 177 N ARG F 168 LINK O3' DC A 6 P 5CM A 7 1555 1555 1.60 LINK O3' 5CM A 7 P DG A 8 1555 1555 1.60 LINK O3' DG B 4 P 1CC B 5 1555 1555 1.61 LINK O3' 1CC B 5 P DG B 6 1555 1555 1.60 LINK O3' DC D 6 P 5CM D 7 1555 1555 1.60 LINK O3' 5CM D 7 P DG D 8 1555 1555 1.61 LINK O3' DG E 4 P 1CC E 5 1555 1555 1.61 LINK O3' 1CC E 5 P DG E 6 1555 1555 1.61 LINK O HOH A 159 CA CA B 103 1555 1555 2.38 LINK O HOH A 160 CA CA B 103 1555 1555 2.42 LINK O HOH A 161 CA CA B 103 1555 1555 2.43 LINK CA CA B 103 O HOH B 268 1555 1555 2.41 LINK CA CA B 103 O HOH B 269 1555 1555 2.45 LINK CA CA B 103 O HOH B 270 1555 1555 2.42 LINK CA CA B 103 O HOH B 271 1555 1555 2.34 LINK SG CYS C 142 ZN ZN C 202 1555 1555 2.32 LINK SG CYS C 145 ZN ZN C 202 1555 1555 2.26 LINK NE2 HIS C 158 ZN ZN C 202 1555 1555 2.03 LINK NE2 HIS C 162 ZN ZN C 202 1555 1555 2.03 LINK SG CYS C 170 ZN ZN C 201 1555 1555 2.31 LINK SG CYS C 173 ZN ZN C 201 1555 1555 2.30 LINK NE2 HIS C 186 ZN ZN C 201 1555 1555 2.04 LINK NE2 HIS C 190 ZN ZN C 201 1555 1555 2.04 LINK O HOH D 145 CA CA E 103 1555 1555 2.42 LINK O HOH D 146 CA CA E 103 1555 1555 2.38 LINK O HOH D 147 CA CA E 103 1555 1555 2.42 LINK CA CA E 103 O HOH E 206 1555 1555 2.40 LINK CA CA E 103 O HOH E 279 1555 1555 2.45 LINK CA CA E 103 O HOH E 280 1555 1555 2.43 LINK CA CA E 103 O HOH E 281 1555 1555 2.34 LINK SG CYS F 142 ZN ZN F 202 1555 1555 2.32 LINK SG CYS F 145 ZN ZN F 202 1555 1555 2.27 LINK NE2 HIS F 158 ZN ZN F 202 1555 1555 2.05 LINK NE2 HIS F 162 ZN ZN F 202 1555 1555 2.01 LINK SG CYS F 170 ZN ZN F 201 1555 1555 2.31 LINK SG CYS F 173 ZN ZN F 201 1555 1555 2.29 LINK NE2 HIS F 186 ZN ZN F 201 1555 1555 2.06 LINK NE2 HIS F 190 ZN ZN F 201 1555 1555 2.03 SITE 1 AC1 9 1CC B 5 HOH B 276 HIS C 158 ALA C 161 SITE 2 AC1 9 HOH C 350 MPD E 101 ALA F 161 HIS F 162 SITE 3 AC1 9 GLY F 164 SITE 1 AC2 9 HOH A 139 HOH A 158 DA B 10 DT B 11 SITE 2 AC2 9 HOH B 241 HOH B 243 HOH B 264 HOH B 265 SITE 3 AC2 9 HOH B 272 SITE 1 AC3 7 HOH A 159 HOH A 160 HOH A 161 HOH B 268 SITE 2 AC3 7 HOH B 269 HOH B 270 HOH B 271 SITE 1 AC4 4 CYS C 170 CYS C 173 HIS C 186 HIS C 190 SITE 1 AC5 5 CYS C 142 PHE C 144 CYS C 145 HIS C 158 SITE 2 AC5 5 HIS C 162 SITE 1 AC6 5 PHE C 141 ASN C 184 HOH C 344 HOH C 347 SITE 2 AC6 5 HOH C 358 SITE 1 AC7 6 HOH A 109 LEU C 163 TYR C 165 HOH C 390 SITE 2 AC7 6 HIS F 190 HOH F 372 SITE 1 AC8 5 HIS C 190 HOH C 388 HOH D 143 TYR F 165 SITE 2 AC8 5 HOH F 393 SITE 1 AC9 9 MPD B 101 ALA C 161 HIS C 162 GLY C 164 SITE 2 AC9 9 HOH C 385 HOH C 393 1CC E 5 HIS F 158 SITE 3 AC9 9 ALA F 161 SITE 1 BC1 5 HOH D 132 DA E 10 DT E 11 HOH E 256 SITE 2 BC1 5 HOH E 277 SITE 1 BC2 7 HOH D 145 HOH D 146 HOH D 147 HOH E 206 SITE 2 BC2 7 HOH E 279 HOH E 280 HOH E 281 SITE 1 BC3 4 CYS F 170 CYS F 173 HIS F 186 HIS F 190 SITE 1 BC4 5 CYS F 142 PHE F 144 CYS F 145 HIS F 158 SITE 2 BC4 5 HIS F 162 SITE 1 BC5 6 HOH D 133 PHE F 141 ASN F 184 HOH F 345 SITE 2 BC5 6 HOH F 360 HOH F 374 CRYST1 36.388 96.093 36.408 90.00 113.14 90.00 P 1 21 1 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 0.027482 0.000000 0.011745 0.00000 SCALE2 0.000000 0.010407 0.000000 0.00000 SCALE3 0.000000 0.000000 0.029870 0.00000