HEADER LIGASE/DNA 18-MAR-14 4PW5 TITLE STRUCTURE OF UHRF2-SRA IN COMPLEX WITH A 5HMC-CONTAINING DNA, COMPLEX TITLE 2 I COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE UHRF2; COMPND 3 CHAIN: A, B, E, F; COMPND 4 SYNONYM: NP95/ICBP90-LIKE RING FINGER PROTEIN, NP95-LIKE RING FINGER COMPND 5 PROTEIN, NUCLEAR PROTEIN 97, NUCLEAR ZINC FINGER PROTEIN NP97, RING COMPND 6 FINGER PROTEIN 107, UBIQUITIN-LIKE PHD AND RING FINGER DOMAIN- COMPND 7 CONTAINING PROTEIN 2, UBIQUITIN-LIKE-CONTAINING PHD AND RING FINGER COMPND 8 DOMAINS PROTEIN 2; COMPND 9 EC: 6.3.2.-; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 2; COMPND 12 MOLECULE: 5HMC-CONTAINING DNA1; COMPND 13 CHAIN: C, G; COMPND 14 ENGINEERED: YES; COMPND 15 MOL_ID: 3; COMPND 16 MOLECULE: 5HMC-CONTAINING DNA2; COMPND 17 CHAIN: D, H; COMPND 18 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: UHRF2, NIRF, RNF107; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) CODON PLUS RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A-SMT; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS SRA, 5HMC BINDING, 5HMC-CONTAINING DNA, HYDROXYMETHYLATION, NUCLEAR, KEYWDS 2 LIGASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.ZHOU,J.XIONG,M.WANG,N.YANG,J.WONG,B.ZHU,R.M.XU REVDAT 4 20-SEP-23 4PW5 1 LINK REVDAT 3 25-JUN-14 4PW5 1 JRNL REVDAT 2 21-MAY-14 4PW5 1 JRNL REVDAT 1 07-MAY-14 4PW5 0 JRNL AUTH T.ZHOU,J.XIONG,M.WANG,N.YANG,J.WONG,B.ZHU,R.M.XU JRNL TITL STRUCTURAL BASIS FOR HYDROXYMETHYLCYTOSINE RECOGNITION BY JRNL TITL 2 THE SRA DOMAIN OF UHRF2. JRNL REF MOL.CELL V. 54 879 2014 JRNL REFN ISSN 1097-2765 JRNL PMID 24813944 JRNL DOI 10.1016/J.MOLCEL.2014.04.003 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.4_1491) 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 54592 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 2739 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 41.4393 - 5.9773 0.99 2651 142 0.1689 0.1795 REMARK 3 2 5.9773 - 4.7465 0.94 2531 125 0.1608 0.1846 REMARK 3 3 4.7465 - 4.1472 0.95 2556 138 0.1262 0.1710 REMARK 3 4 4.1472 - 3.7683 0.97 2606 134 0.1297 0.1557 REMARK 3 5 3.7683 - 3.4983 0.97 2591 152 0.1329 0.1895 REMARK 3 6 3.4983 - 3.2922 0.97 2628 133 0.1374 0.1753 REMARK 3 7 3.2922 - 3.1273 0.96 2630 156 0.1532 0.2251 REMARK 3 8 3.1273 - 2.9913 0.98 2581 147 0.1577 0.2047 REMARK 3 9 2.9913 - 2.8761 0.97 2633 148 0.1669 0.1917 REMARK 3 10 2.8761 - 2.7769 0.98 2665 125 0.1785 0.2309 REMARK 3 11 2.7769 - 2.6901 0.97 2652 115 0.1744 0.2540 REMARK 3 12 2.6901 - 2.6132 0.97 2591 141 0.1797 0.2728 REMARK 3 13 2.6132 - 2.5444 0.96 2608 136 0.1798 0.2185 REMARK 3 14 2.5444 - 2.4824 0.97 2581 129 0.1872 0.2491 REMARK 3 15 2.4824 - 2.4259 0.96 2628 140 0.1940 0.2595 REMARK 3 16 2.4259 - 2.3743 0.97 2569 125 0.1993 0.2570 REMARK 3 17 2.3743 - 2.3268 0.96 2577 152 0.2124 0.3110 REMARK 3 18 2.3268 - 2.2829 0.96 2595 140 0.2041 0.2893 REMARK 3 19 2.2829 - 2.2421 0.96 2553 127 0.2136 0.2371 REMARK 3 20 2.2421 - 2.2041 0.90 2427 134 0.2096 0.2628 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) : 21.030 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.10 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 : 0.006 7308 REMARK 3 ANGLE : 0.952 10132 REMARK 3 CHIRALITY : 0.039 1050 REMARK 3 PLANARITY : 0.004 1172 REMARK 3 DIHEDRAL : 17.425 2797 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 4PW5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-MAR-14. REMARK 100 THE DEPOSITION ID IS D_1000085293. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9789 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS 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 : 54600 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 200 DATA REDUNDANCY : 2.100 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.48300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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 3OLN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% ETHANOL AND 0.1 M TRIS PH 8.5, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3790 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20500 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3760 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -25.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, G, H 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 419 REMARK 465 THR A 420 REMARK 465 GLU A 421 REMARK 465 SER A 422 REMARK 465 ARG A 423 REMARK 465 ARG A 424 REMARK 465 ASP A 425 REMARK 465 TRP A 426 REMARK 465 GLY A 427 REMARK 465 ARG A 428 REMARK 465 GLY A 429 REMARK 465 MET A 430 REMARK 465 ALA A 431 REMARK 465 CYS A 432 REMARK 465 VAL A 433 REMARK 465 GLY A 434 REMARK 465 ARG A 435 REMARK 465 THR A 436 REMARK 465 ARG A 437 REMARK 465 GLU A 438 REMARK 465 CYS A 439 REMARK 465 THR A 440 REMARK 465 LYS A 513 REMARK 465 ASN A 514 REMARK 465 LEU A 515 REMARK 465 ALA A 516 REMARK 465 GLY A 517 REMARK 465 ASN A 518 REMARK 465 LYS A 519 REMARK 465 ARG A 520 REMARK 465 ILE A 521 REMARK 465 GLY A 522 REMARK 465 ALA A 523 REMARK 465 PRO A 524 REMARK 465 PRO A 642 REMARK 465 SER A 643 REMARK 465 ASP A 644 REMARK 465 LYS A 645 REMARK 465 GLU A 646 REMARK 465 GLY A 647 REMARK 465 LYS A 648 REMARK 465 SER B 419 REMARK 465 THR B 420 REMARK 465 GLU B 421 REMARK 465 SER B 422 REMARK 465 ARG B 423 REMARK 465 ARG B 424 REMARK 465 ASP B 425 REMARK 465 TRP B 426 REMARK 465 GLY B 427 REMARK 465 ARG B 428 REMARK 465 GLY B 429 REMARK 465 MET B 430 REMARK 465 ALA B 431 REMARK 465 CYS B 432 REMARK 465 VAL B 433 REMARK 465 GLY B 434 REMARK 465 ARG B 435 REMARK 465 THR B 436 REMARK 465 ARG B 437 REMARK 465 GLU B 438 REMARK 465 CYS B 439 REMARK 465 THR B 440 REMARK 465 GLY B 512 REMARK 465 LYS B 513 REMARK 465 ASN B 514 REMARK 465 LEU B 515 REMARK 465 ALA B 516 REMARK 465 GLY B 517 REMARK 465 ASN B 518 REMARK 465 LYS B 519 REMARK 465 ARG B 520 REMARK 465 ILE B 521 REMARK 465 GLY B 522 REMARK 465 ALA B 523 REMARK 465 PRO B 524 REMARK 465 PRO B 642 REMARK 465 SER B 643 REMARK 465 ASP B 644 REMARK 465 LYS B 645 REMARK 465 GLU B 646 REMARK 465 GLY B 647 REMARK 465 LYS B 648 REMARK 465 DC D 1 REMARK 465 SER E 419 REMARK 465 THR E 420 REMARK 465 GLU E 421 REMARK 465 SER E 422 REMARK 465 ARG E 423 REMARK 465 ARG E 424 REMARK 465 ASP E 425 REMARK 465 TRP E 426 REMARK 465 GLY E 427 REMARK 465 ARG E 428 REMARK 465 GLY E 429 REMARK 465 MET E 430 REMARK 465 ALA E 431 REMARK 465 CYS E 432 REMARK 465 VAL E 433 REMARK 465 GLY E 434 REMARK 465 ARG E 435 REMARK 465 THR E 436 REMARK 465 ARG E 437 REMARK 465 GLU E 438 REMARK 465 CYS E 439 REMARK 465 THR E 440 REMARK 465 ILE E 441 REMARK 465 LYS E 513 REMARK 465 ASN E 514 REMARK 465 LEU E 515 REMARK 465 ALA E 516 REMARK 465 GLY E 517 REMARK 465 ASN E 518 REMARK 465 LYS E 519 REMARK 465 ARG E 520 REMARK 465 ILE E 521 REMARK 465 GLY E 522 REMARK 465 ALA E 523 REMARK 465 PRO E 524 REMARK 465 PRO E 642 REMARK 465 SER E 643 REMARK 465 ASP E 644 REMARK 465 LYS E 645 REMARK 465 GLU E 646 REMARK 465 GLY E 647 REMARK 465 LYS E 648 REMARK 465 SER F 419 REMARK 465 THR F 420 REMARK 465 GLU F 421 REMARK 465 SER F 422 REMARK 465 ARG F 423 REMARK 465 ARG F 424 REMARK 465 ASP F 425 REMARK 465 TRP F 426 REMARK 465 GLY F 427 REMARK 465 ARG F 428 REMARK 465 GLY F 429 REMARK 465 MET F 430 REMARK 465 ALA F 431 REMARK 465 CYS F 432 REMARK 465 VAL F 433 REMARK 465 GLY F 434 REMARK 465 ARG F 435 REMARK 465 THR F 436 REMARK 465 ARG F 437 REMARK 465 GLU F 438 REMARK 465 CYS F 439 REMARK 465 THR F 440 REMARK 465 ILE F 441 REMARK 465 GLY F 512 REMARK 465 LYS F 513 REMARK 465 ASN F 514 REMARK 465 LEU F 515 REMARK 465 ALA F 516 REMARK 465 GLY F 517 REMARK 465 ASN F 518 REMARK 465 LYS F 519 REMARK 465 ARG F 520 REMARK 465 ILE F 521 REMARK 465 GLY F 522 REMARK 465 ALA F 523 REMARK 465 PRO F 524 REMARK 465 PRO F 642 REMARK 465 SER F 643 REMARK 465 ASP F 644 REMARK 465 LYS F 645 REMARK 465 GLU F 646 REMARK 465 GLY F 647 REMARK 465 LYS F 648 REMARK 465 DC H 1 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG E 634 CD NE CZ NH1 NH2 REMARK 480 ARG F 634 CD NE CZ NH1 NH2 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 O6 DG C 12 N4 DC D 2 2.08 REMARK 500 O HOH C 134 O HOH C 135 2.09 REMARK 500 O HOH F 851 O HOH F 852 2.13 REMARK 500 O HOH G 128 O HOH G 129 2.14 REMARK 500 O HOH F 725 O HOH F 829 2.14 REMARK 500 O HOH B 808 O HOH B 809 2.15 REMARK 500 O HOH F 816 O HOH F 841 2.15 REMARK 500 O HOH A 840 O HOH F 850 2.17 REMARK 500 O HOH A 816 O HOH A 821 2.18 REMARK 500 O HOH A 828 O HOH A 829 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 DC C 6 O4' - C1' - N1 ANGL. DEV. = 1.9 DEGREES REMARK 500 DG C 12 C3' - C2' - C1' ANGL. DEV. = -4.8 DEGREES REMARK 500 DG C 12 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DC D 6 O4' - C1' - N1 ANGL. DEV. = 2.3 DEGREES REMARK 500 DC G 6 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG G 12 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG H 7 O4' - C1' - N9 ANGL. DEV. = 2.1 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 VAL A 475 -51.00 -127.87 REMARK 500 ASP A 484 -80.22 -128.30 REMARK 500 SER A 510 -164.53 -114.50 REMARK 500 ASN A 532 -125.19 44.82 REMARK 500 ASN B 445 30.85 -95.65 REMARK 500 VAL B 475 -51.90 -123.61 REMARK 500 ASP B 484 -69.57 -120.66 REMARK 500 ASN B 532 -125.71 46.26 REMARK 500 VAL E 475 -61.23 -121.00 REMARK 500 VAL E 475 -61.23 -133.09 REMARK 500 ASP E 484 -76.23 -128.50 REMARK 500 ASN E 532 -126.88 46.07 REMARK 500 VAL F 475 -53.97 -122.40 REMARK 500 ASP F 484 -71.73 -134.70 REMARK 500 ASN F 532 -126.05 50.14 REMARK 500 ALA F 639 106.69 -49.52 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4PW6 RELATED DB: PDB REMARK 900 RELATED ID: 4PW7 RELATED DB: PDB DBREF 4PW5 A 419 648 UNP Q96PU4 UHRF2_HUMAN 419 648 DBREF 4PW5 B 419 648 UNP Q96PU4 UHRF2_HUMAN 419 648 DBREF 4PW5 E 419 648 UNP Q96PU4 UHRF2_HUMAN 419 648 DBREF 4PW5 F 419 648 UNP Q96PU4 UHRF2_HUMAN 419 648 DBREF 4PW5 C 1 12 PDB 4PW5 4PW5 1 12 DBREF 4PW5 G 1 12 PDB 4PW5 4PW5 1 12 DBREF 4PW5 D 1 12 PDB 4PW5 4PW5 1 12 DBREF 4PW5 H 1 12 PDB 4PW5 4PW5 1 12 SEQRES 1 A 230 SER THR GLU SER ARG ARG ASP TRP GLY ARG GLY MET ALA SEQRES 2 A 230 CYS VAL GLY ARG THR ARG GLU CYS THR ILE VAL PRO SER SEQRES 3 A 230 ASN HIS TYR GLY PRO ILE PRO GLY ILE PRO VAL GLY SER SEQRES 4 A 230 THR TRP ARG PHE ARG VAL GLN VAL SER GLU ALA GLY VAL SEQRES 5 A 230 HIS ARG PRO HIS VAL GLY GLY ILE HIS GLY ARG SER ASN SEQRES 6 A 230 ASP GLY ALA TYR SER LEU VAL LEU ALA GLY GLY PHE ALA SEQRES 7 A 230 ASP GLU VAL ASP ARG GLY ASP GLU PHE THR TYR THR GLY SEQRES 8 A 230 SER GLY GLY LYS ASN LEU ALA GLY ASN LYS ARG ILE GLY SEQRES 9 A 230 ALA PRO SER ALA ASP GLN THR LEU THR ASN MET ASN ARG SEQRES 10 A 230 ALA LEU ALA LEU ASN CYS ASP ALA PRO LEU ASP ASP LYS SEQRES 11 A 230 ILE GLY ALA GLU SER ARG ASN TRP ARG ALA GLY LYS PRO SEQRES 12 A 230 VAL ARG VAL ILE ARG SER PHE LYS GLY ARG LYS ILE SER SEQRES 13 A 230 LYS TYR ALA PRO GLU GLU GLY ASN ARG TYR ASP GLY ILE SEQRES 14 A 230 TYR LYS VAL VAL LYS TYR TRP PRO GLU ILE SER SER SER SEQRES 15 A 230 HIS GLY PHE LEU VAL TRP ARG TYR LEU LEU ARG ARG ASP SEQRES 16 A 230 ASP VAL GLU PRO ALA PRO TRP THR SER GLU GLY ILE GLU SEQRES 17 A 230 ARG SER ARG ARG LEU CYS LEU ARG LEU GLN TYR PRO ALA SEQRES 18 A 230 GLY TYR PRO SER ASP LYS GLU GLY LYS SEQRES 1 B 230 SER THR GLU SER ARG ARG ASP TRP GLY ARG GLY MET ALA SEQRES 2 B 230 CYS VAL GLY ARG THR ARG GLU CYS THR ILE VAL PRO SER SEQRES 3 B 230 ASN HIS TYR GLY PRO ILE PRO GLY ILE PRO VAL GLY SER SEQRES 4 B 230 THR TRP ARG PHE ARG VAL GLN VAL SER GLU ALA GLY VAL SEQRES 5 B 230 HIS ARG PRO HIS VAL GLY GLY ILE HIS GLY ARG SER ASN SEQRES 6 B 230 ASP GLY ALA TYR SER LEU VAL LEU ALA GLY GLY PHE ALA SEQRES 7 B 230 ASP GLU VAL ASP ARG GLY ASP GLU PHE THR TYR THR GLY SEQRES 8 B 230 SER GLY GLY LYS ASN LEU ALA GLY ASN LYS ARG ILE GLY SEQRES 9 B 230 ALA PRO SER ALA ASP GLN THR LEU THR ASN MET ASN ARG SEQRES 10 B 230 ALA LEU ALA LEU ASN CYS ASP ALA PRO LEU ASP ASP LYS SEQRES 11 B 230 ILE GLY ALA GLU SER ARG ASN TRP ARG ALA GLY LYS PRO SEQRES 12 B 230 VAL ARG VAL ILE ARG SER PHE LYS GLY ARG LYS ILE SER SEQRES 13 B 230 LYS TYR ALA PRO GLU GLU GLY ASN ARG TYR ASP GLY ILE SEQRES 14 B 230 TYR LYS VAL VAL LYS TYR TRP PRO GLU ILE SER SER SER SEQRES 15 B 230 HIS GLY PHE LEU VAL TRP ARG TYR LEU LEU ARG ARG ASP SEQRES 16 B 230 ASP VAL GLU PRO ALA PRO TRP THR SER GLU GLY ILE GLU SEQRES 17 B 230 ARG SER ARG ARG LEU CYS LEU ARG LEU GLN TYR PRO ALA SEQRES 18 B 230 GLY TYR PRO SER ASP LYS GLU GLY LYS SEQRES 1 C 12 DC DT DG DG DT DC 5HC DG DG DA DT DG SEQRES 1 D 12 DC DC DA DT DC DC DG DG DA DC DC DA SEQRES 1 E 230 SER THR GLU SER ARG ARG ASP TRP GLY ARG GLY MET ALA SEQRES 2 E 230 CYS VAL GLY ARG THR ARG GLU CYS THR ILE VAL PRO SER SEQRES 3 E 230 ASN HIS TYR GLY PRO ILE PRO GLY ILE PRO VAL GLY SER SEQRES 4 E 230 THR TRP ARG PHE ARG VAL GLN VAL SER GLU ALA GLY VAL SEQRES 5 E 230 HIS ARG PRO HIS VAL GLY GLY ILE HIS GLY ARG SER ASN SEQRES 6 E 230 ASP GLY ALA TYR SER LEU VAL LEU ALA GLY GLY PHE ALA SEQRES 7 E 230 ASP GLU VAL ASP ARG GLY ASP GLU PHE THR TYR THR GLY SEQRES 8 E 230 SER GLY GLY LYS ASN LEU ALA GLY ASN LYS ARG ILE GLY SEQRES 9 E 230 ALA PRO SER ALA ASP GLN THR LEU THR ASN MET ASN ARG SEQRES 10 E 230 ALA LEU ALA LEU ASN CYS ASP ALA PRO LEU ASP ASP LYS SEQRES 11 E 230 ILE GLY ALA GLU SER ARG ASN TRP ARG ALA GLY LYS PRO SEQRES 12 E 230 VAL ARG VAL ILE ARG SER PHE LYS GLY ARG LYS ILE SER SEQRES 13 E 230 LYS TYR ALA PRO GLU GLU GLY ASN ARG TYR ASP GLY ILE SEQRES 14 E 230 TYR LYS VAL VAL LYS TYR TRP PRO GLU ILE SER SER SER SEQRES 15 E 230 HIS GLY PHE LEU VAL TRP ARG TYR LEU LEU ARG ARG ASP SEQRES 16 E 230 ASP VAL GLU PRO ALA PRO TRP THR SER GLU GLY ILE GLU SEQRES 17 E 230 ARG SER ARG ARG LEU CYS LEU ARG LEU GLN TYR PRO ALA SEQRES 18 E 230 GLY TYR PRO SER ASP LYS GLU GLY LYS SEQRES 1 F 230 SER THR GLU SER ARG ARG ASP TRP GLY ARG GLY MET ALA SEQRES 2 F 230 CYS VAL GLY ARG THR ARG GLU CYS THR ILE VAL PRO SER SEQRES 3 F 230 ASN HIS TYR GLY PRO ILE PRO GLY ILE PRO VAL GLY SER SEQRES 4 F 230 THR TRP ARG PHE ARG VAL GLN VAL SER GLU ALA GLY VAL SEQRES 5 F 230 HIS ARG PRO HIS VAL GLY GLY ILE HIS GLY ARG SER ASN SEQRES 6 F 230 ASP GLY ALA TYR SER LEU VAL LEU ALA GLY GLY PHE ALA SEQRES 7 F 230 ASP GLU VAL ASP ARG GLY ASP GLU PHE THR TYR THR GLY SEQRES 8 F 230 SER GLY GLY LYS ASN LEU ALA GLY ASN LYS ARG ILE GLY SEQRES 9 F 230 ALA PRO SER ALA ASP GLN THR LEU THR ASN MET ASN ARG SEQRES 10 F 230 ALA LEU ALA LEU ASN CYS ASP ALA PRO LEU ASP ASP LYS SEQRES 11 F 230 ILE GLY ALA GLU SER ARG ASN TRP ARG ALA GLY LYS PRO SEQRES 12 F 230 VAL ARG VAL ILE ARG SER PHE LYS GLY ARG LYS ILE SER SEQRES 13 F 230 LYS TYR ALA PRO GLU GLU GLY ASN ARG TYR ASP GLY ILE SEQRES 14 F 230 TYR LYS VAL VAL LYS TYR TRP PRO GLU ILE SER SER SER SEQRES 15 F 230 HIS GLY PHE LEU VAL TRP ARG TYR LEU LEU ARG ARG ASP SEQRES 16 F 230 ASP VAL GLU PRO ALA PRO TRP THR SER GLU GLY ILE GLU SEQRES 17 F 230 ARG SER ARG ARG LEU CYS LEU ARG LEU GLN TYR PRO ALA SEQRES 18 F 230 GLY TYR PRO SER ASP LYS GLU GLY LYS SEQRES 1 G 12 DC DT DG DG DT DC 5HC DG DG DA DT DG SEQRES 1 H 12 DC DC DA DT DC DC DG DG DA DC DC DA MODRES 4PW5 5HC C 7 DC MODRES 4PW5 5HC G 7 DC HET 5HC C 7 21 HET 5HC G 7 21 HETNAM 5HC 2'-DEOXY-5-(HYDROXYMETHYL)CYTIDINE 5'-(DIHYDROGEN HETNAM 2 5HC PHOSPHATE) FORMUL 3 5HC 2(C10 H16 N3 O8 P) FORMUL 9 HOH *609(H2 O) HELIX 1 1 PHE A 461 ALA A 468 1 8 HELIX 2 2 THR A 531 ASN A 540 1 10 HELIX 3 3 ASN A 555 GLY A 559 5 5 HELIX 4 4 LYS A 569 ILE A 573 5 5 HELIX 5 5 THR A 621 LEU A 631 1 11 HELIX 6 6 PHE B 461 ALA B 468 1 8 HELIX 7 7 THR B 531 ASN B 540 1 10 HELIX 8 8 ASN B 555 GLY B 559 5 5 HELIX 9 9 LYS B 569 ILE B 573 5 5 HELIX 10 10 THR B 621 LEU B 631 1 11 HELIX 11 11 PHE E 461 ALA E 468 1 8 HELIX 12 12 THR E 531 ASN E 540 1 10 HELIX 13 13 ASN E 555 GLY E 559 5 5 HELIX 14 14 LYS E 569 ILE E 573 5 5 HELIX 15 15 THR E 621 LEU E 631 1 11 HELIX 16 16 PHE F 461 ALA F 468 1 8 HELIX 17 17 THR F 531 ASN F 540 1 10 HELIX 18 18 ASN F 555 GLY F 559 5 5 HELIX 19 19 LYS F 569 ILE F 573 5 5 HELIX 20 20 THR F 621 LEU F 631 1 11 SHEET 1 A 5 ILE A 478 ARG A 481 0 SHEET 2 A 5 GLY A 485 LEU A 491 -1 O SER A 488 N HIS A 479 SHEET 3 A 5 VAL A 562 SER A 567 1 O ILE A 565 N LEU A 491 SHEET 4 A 5 ASN A 582 ILE A 597 -1 O ASP A 585 N VAL A 564 SHEET 5 A 5 ALA A 551 GLU A 552 -1 N ALA A 551 O TYR A 593 SHEET 1 B 5 GLU A 504 THR A 508 0 SHEET 2 B 5 LEU A 604 ARG A 612 -1 O LEU A 610 N PHE A 505 SHEET 3 B 5 ASN A 582 ILE A 597 -1 N GLU A 596 O VAL A 605 SHEET 4 B 5 THR A 458 TRP A 459 -1 N TRP A 459 O ASN A 582 SHEET 5 B 5 LEU A 635 GLN A 636 1 O GLN A 636 N THR A 458 SHEET 1 C 4 THR B 458 TRP B 459 0 SHEET 2 C 4 ASN B 582 ILE B 597 -1 O ASN B 582 N TRP B 459 SHEET 3 C 4 LEU B 604 ARG B 612 -1 O LEU B 609 N VAL B 591 SHEET 4 C 4 GLU B 504 THR B 508 -1 N TYR B 507 O TYR B 608 SHEET 1 D 5 ILE B 478 ARG B 481 0 SHEET 2 D 5 GLY B 485 LEU B 491 -1 O TYR B 487 N HIS B 479 SHEET 3 D 5 VAL B 562 SER B 567 1 O ILE B 565 N LEU B 491 SHEET 4 D 5 ASN B 582 ILE B 597 -1 O ASP B 585 N VAL B 564 SHEET 5 D 5 ALA B 551 GLU B 552 -1 N ALA B 551 O TYR B 593 SHEET 1 E 5 ILE E 478 ARG E 481 0 SHEET 2 E 5 GLY E 485 LEU E 491 -1 O SER E 488 N HIS E 479 SHEET 3 E 5 VAL E 562 SER E 567 1 O ILE E 565 N LEU E 491 SHEET 4 E 5 ASN E 582 ILE E 597 -1 O TYR E 588 N VAL E 562 SHEET 5 E 5 ALA E 551 GLU E 552 -1 N ALA E 551 O TYR E 593 SHEET 1 F 5 GLU E 504 THR E 508 0 SHEET 2 F 5 LEU E 604 ARG E 612 -1 O TYR E 608 N TYR E 507 SHEET 3 F 5 ASN E 582 ILE E 597 -1 N GLU E 596 O VAL E 605 SHEET 4 F 5 THR E 458 TRP E 459 -1 N TRP E 459 O ASN E 582 SHEET 5 F 5 LEU E 635 GLN E 636 1 O GLN E 636 N THR E 458 SHEET 1 G 4 THR F 458 TRP F 459 0 SHEET 2 G 4 ASN F 582 ILE F 597 -1 O ASN F 582 N TRP F 459 SHEET 3 G 4 LEU F 604 ARG F 612 -1 O VAL F 605 N GLU F 596 SHEET 4 G 4 GLU F 504 THR F 508 -1 N PHE F 505 O LEU F 610 SHEET 1 H 5 ILE F 478 ARG F 481 0 SHEET 2 H 5 GLY F 485 LEU F 491 -1 O TYR F 487 N HIS F 479 SHEET 3 H 5 VAL F 562 SER F 567 1 O ILE F 565 N LEU F 491 SHEET 4 H 5 ASN F 582 ILE F 597 -1 O ASP F 585 N VAL F 564 SHEET 5 H 5 ALA F 551 GLU F 552 -1 N ALA F 551 O TYR F 593 LINK O3' DC C 6 P 5HC C 7 1555 1555 1.61 LINK O3' 5HC C 7 P DG C 8 1555 1555 1.61 LINK O3' DC G 6 P 5HC G 7 1555 1555 1.61 LINK O3' 5HC G 7 P DG G 8 1555 1555 1.62 CRYST1 42.273 82.807 82.864 90.05 90.00 89.98 P 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 0.023656 -0.000006 0.000000 0.00000 SCALE2 0.000000 0.012076 0.000011 0.00000 SCALE3 0.000000 0.000000 0.012068 0.00000