HEADER HYDROLASE/RNA 07-FEB-20 6VRD TITLE CRYSTAL STRUCTURE OF RNASE H/RNA/PS-ASO COMPLEX AT AN ATOMIC LEVEL COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBONUCLEASE H1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNASE H1,RIBONUCLEASE H TYPE II; COMPND 5 EC: 3.1.26.4; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RNA (5'- COMPND 10 R(*UP*GP*GP*CP*GP*AP*GP*UP*GP*GP*GP*UP*GP*AP*GP*UP*GP*AP*GP*G)-3'); COMPND 11 CHAIN: B; COMPND 12 ENGINEERED: YES; COMPND 13 MOL_ID: 3; COMPND 14 MOLECULE: RNA (5'-R(*(OMC)P*(N7X)P*(T39)P*(C5L)P*(A2M))-D(P*(SC) COMPND 15 P*(PST)P*(SC)P*(AS)P*(SC)P*(SC)P*(SC)P*(AS)P*(SC)P*(PST))-R(P*(6OO) COMPND 16 P*(RFJ)P*(6OO)P*(6OO)P*(6NW))-3'); COMPND 17 CHAIN: C; 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: RNASEH1, RNH1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 SYNTHETIC: YES; SOURCE 11 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 12 ORGANISM_COMMON: HUMAN; SOURCE 13 ORGANISM_TAXID: 9606; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 17 ORGANISM_TAXID: 32630 KEYWDS RNASE H, COMPLEX, RNA, ASO, DNA, HYDROLASE, HYDROLASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Y.-J.CHO,D.BUTLER REVDAT 3 15-NOV-23 6VRD 1 AUTHOR JRNL REVDAT 2 11-OCT-23 6VRD 1 REMARK REVDAT 1 10-FEB-21 6VRD 0 JRNL AUTH Y.-J.CHO,D.BUTLER JRNL TITL CRYSTAL STRUCTURE OF RNASE H/RNA/PS-ASO COMPLEX AT AN ATOMIC JRNL TITL 2 LEVEL JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 65928 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 3320 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 35.1330 - 3.7459 1.00 2815 149 0.1568 0.1900 REMARK 3 2 3.7459 - 2.9737 1.00 2696 141 0.1583 0.1967 REMARK 3 3 2.9737 - 2.5979 1.00 2668 141 0.1820 0.2260 REMARK 3 4 2.5979 - 2.3605 1.00 2649 139 0.1834 0.2389 REMARK 3 5 2.3605 - 2.1913 1.00 2642 140 0.1804 0.2211 REMARK 3 6 2.1913 - 2.0621 1.00 2636 139 0.1790 0.2166 REMARK 3 7 2.0621 - 1.9589 1.00 2592 136 0.1889 0.2582 REMARK 3 8 1.9589 - 1.8736 1.00 2611 137 0.2029 0.2460 REMARK 3 9 1.8736 - 1.8015 1.00 2607 138 0.1850 0.2154 REMARK 3 10 1.8015 - 1.7393 1.00 2619 137 0.1775 0.2096 REMARK 3 11 1.7393 - 1.6849 1.00 2596 137 0.1816 0.2143 REMARK 3 12 1.6849 - 1.6368 1.00 2608 137 0.1896 0.2181 REMARK 3 13 1.6368 - 1.5937 1.00 2593 137 0.2058 0.2710 REMARK 3 14 1.5937 - 1.5548 1.00 2586 136 0.2179 0.2682 REMARK 3 15 1.5548 - 1.5195 1.00 2584 135 0.2233 0.2370 REMARK 3 16 1.5195 - 1.4871 1.00 2585 137 0.2362 0.2804 REMARK 3 17 1.4871 - 1.4574 1.00 2595 136 0.2620 0.3085 REMARK 3 18 1.4574 - 1.4299 1.00 2580 124 0.2811 0.2967 REMARK 3 19 1.4299 - 1.4043 1.00 2576 148 0.2891 0.3032 REMARK 3 20 1.4043 - 1.3805 1.00 2570 147 0.3136 0.3038 REMARK 3 21 1.3805 - 1.3583 1.00 2593 131 0.3250 0.3464 REMARK 3 22 1.3583 - 1.3374 1.00 2562 140 0.3381 0.3399 REMARK 3 23 1.3374 - 1.3177 1.00 2583 142 0.3503 0.3958 REMARK 3 24 1.3177 - 1.2991 0.96 2462 136 0.3687 0.3482 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.830 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.54 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6VRD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-FEB-20. REMARK 100 THE DEPOSITION ID IS D_1000245869. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS VJAN10,2014 REMARK 200 DATA SCALING SOFTWARE : AIMLESS V0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65937 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.299 REMARK 200 RESOLUTION RANGE LOW (A) : 35.133 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.6700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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 V2.8.3 REMARK 200 STARTING MODEL: 2QK9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): NULL REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): NULL REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8 M AMMONIUM SULPHATE, 0.1 M CITRATE REMARK 280 PH 4.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 23.38000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.23850 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.51500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.23850 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.38000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.51500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 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 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 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 HIS A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 TRP A 3 REMARK 465 LEU A 4 REMARK 465 LEU A 5 REMARK 465 PHE A 6 REMARK 465 LEU A 7 REMARK 465 ALA A 8 REMARK 465 HIS A 9 REMARK 465 ARG A 10 REMARK 465 VAL A 11 REMARK 465 ALA A 12 REMARK 465 LEU A 13 REMARK 465 ALA A 14 REMARK 465 ALA A 15 REMARK 465 LEU A 16 REMARK 465 PRO A 17 REMARK 465 CYS A 18 REMARK 465 ARG A 19 REMARK 465 ARG A 20 REMARK 465 GLY A 21 REMARK 465 SER A 22 REMARK 465 ARG A 23 REMARK 465 GLY A 24 REMARK 465 PHE A 25 REMARK 465 GLY A 26 REMARK 465 MET A 27 REMARK 465 PHE A 28 REMARK 465 TYR A 29 REMARK 465 ALA A 30 REMARK 465 VAL A 31 REMARK 465 ARG A 32 REMARK 465 ARG A 33 REMARK 465 GLY A 34 REMARK 465 ARG A 35 REMARK 465 LYS A 36 REMARK 465 THR A 37 REMARK 465 GLY A 38 REMARK 465 VAL A 39 REMARK 465 PHE A 40 REMARK 465 LEU A 41 REMARK 465 THR A 42 REMARK 465 TRP A 43 REMARK 465 ASN A 44 REMARK 465 GLU A 45 REMARK 465 CYS A 46 REMARK 465 ARG A 47 REMARK 465 ALA A 48 REMARK 465 GLN A 49 REMARK 465 VAL A 50 REMARK 465 ASP A 51 REMARK 465 ARG A 52 REMARK 465 PHE A 53 REMARK 465 PRO A 54 REMARK 465 ALA A 55 REMARK 465 ALA A 56 REMARK 465 ARG A 57 REMARK 465 PHE A 58 REMARK 465 LYS A 59 REMARK 465 LYS A 60 REMARK 465 PHE A 61 REMARK 465 ALA A 62 REMARK 465 THR A 63 REMARK 465 GLU A 64 REMARK 465 ASP A 65 REMARK 465 GLU A 66 REMARK 465 ALA A 67 REMARK 465 TRP A 68 REMARK 465 ALA A 69 REMARK 465 PHE A 70 REMARK 465 VAL A 71 REMARK 465 ARG A 72 REMARK 465 LYS A 73 REMARK 465 SER A 74 REMARK 465 ALA A 75 REMARK 465 SER A 76 REMARK 465 PRO A 77 REMARK 465 GLU A 78 REMARK 465 VAL A 79 REMARK 465 SER A 80 REMARK 465 GLU A 81 REMARK 465 GLY A 82 REMARK 465 HIS A 83 REMARK 465 GLU A 84 REMARK 465 ASN A 85 REMARK 465 GLN A 86 REMARK 465 HIS A 87 REMARK 465 GLY A 88 REMARK 465 GLN A 89 REMARK 465 GLU A 90 REMARK 465 SER A 91 REMARK 465 GLU A 92 REMARK 465 ALA A 93 REMARK 465 LYS A 94 REMARK 465 ALA A 95 REMARK 465 SER A 96 REMARK 465 LYS A 97 REMARK 465 ARG A 98 REMARK 465 LEU A 99 REMARK 465 ARG A 100 REMARK 465 GLU A 101 REMARK 465 PRO A 102 REMARK 465 LEU A 103 REMARK 465 ASP A 104 REMARK 465 GLY A 105 REMARK 465 ASP A 106 REMARK 465 GLY A 107 REMARK 465 HIS A 108 REMARK 465 GLU A 109 REMARK 465 SER A 110 REMARK 465 ALA A 111 REMARK 465 GLU A 112 REMARK 465 PRO A 113 REMARK 465 TYR A 114 REMARK 465 ALA A 115 REMARK 465 LYS A 116 REMARK 465 HIS A 117 REMARK 465 MET A 118 REMARK 465 LYS A 119 REMARK 465 PRO A 120 REMARK 465 SER A 121 REMARK 465 VAL A 122 REMARK 465 GLU A 123 REMARK 465 PRO A 124 REMARK 465 ALA A 125 REMARK 465 PRO A 126 REMARK 465 PRO A 127 REMARK 465 VAL A 128 REMARK 465 SER A 129 REMARK 465 ARG A 130 REMARK 465 ASP A 131 REMARK 465 THR A 132 REMARK 465 PHE A 133 REMARK 465 SER A 134 REMARK 465 TYR A 135 REMARK 465 MET A 136 REMARK 465 ASP A 286 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 O1 SO4 A 301 O HOH A 401 2.05 REMARK 500 O HOH A 417 O HOH A 537 2.09 REMARK 500 O HOH B 130 O HOH B 165 2.12 REMARK 500 O HOH A 518 O HOH A 565 2.14 REMARK 500 O GLY A 137 O HOH A 402 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 O HOH A 458 O HOH A 520 4455 2.08 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 ARG A 184 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 249 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 MET A 259 CG - SD - CE ANGL. DEV. = 9.7 DEGREES REMARK 500 U B 1 N3 - C4 - O4 ANGL. DEV. = 4.6 DEGREES REMARK 500 G B 13 C4 - C5 - N7 ANGL. DEV. = -3.0 DEGREES REMARK 500 G B 15 N7 - C8 - N9 ANGL. DEV. = -3.9 DEGREES REMARK 500 G B 15 C8 - N9 - C4 ANGL. DEV. = 2.6 DEGREES REMARK 500 T39 C 3 O3' - P - OP2 ANGL. DEV. = 8.2 DEGREES REMARK 500 SC C 6 O3' - P - OP1 ANGL. DEV. = 11.4 DEGREES REMARK 500 6OO C 16 O3' - P - OP2 ANGL. DEV. = 9.4 DEGREES REMARK 500 RFJ C 17 O3' - P - OP2 ANGL. DEV. = 6.9 DEGREES REMARK 500 6OO C 18 C3' - O3' - P ANGL. DEV. = -8.7 DEGREES REMARK 500 6OO C 19 O3' - P - OP2 ANGL. DEV. = 7.3 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 ASN A 220 -44.57 -130.46 REMARK 500 ASN A 240 32.93 -98.49 REMARK 500 ASN A 240 32.93 -92.87 REMARK 500 HIS A 264 -132.35 64.34 REMARK 500 SER A 265 -5.66 84.72 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 576 DISTANCE = 6.08 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 C 202 DBREF 6VRD A 1 286 UNP O60930 RNH1_HUMAN 1 286 DBREF 6VRD B 1 20 PDB 6VRD 6VRD 1 20 DBREF 6VRD C 1 20 PDB 6VRD 6VRD 1 20 SEQADV 6VRD HIS A -7 UNP O60930 EXPRESSION TAG SEQADV 6VRD HIS A -6 UNP O60930 EXPRESSION TAG SEQADV 6VRD HIS A -5 UNP O60930 EXPRESSION TAG SEQADV 6VRD HIS A -4 UNP O60930 EXPRESSION TAG SEQADV 6VRD HIS A -3 UNP O60930 EXPRESSION TAG SEQADV 6VRD HIS A -2 UNP O60930 EXPRESSION TAG SEQADV 6VRD HIS A -1 UNP O60930 EXPRESSION TAG SEQADV 6VRD HIS A 0 UNP O60930 EXPRESSION TAG SEQADV 6VRD ASN A 210 UNP O60930 ASP 210 ENGINEERED MUTATION SEQRES 1 A 294 HIS HIS HIS HIS HIS HIS HIS HIS MET SER TRP LEU LEU SEQRES 2 A 294 PHE LEU ALA HIS ARG VAL ALA LEU ALA ALA LEU PRO CYS SEQRES 3 A 294 ARG ARG GLY SER ARG GLY PHE GLY MET PHE TYR ALA VAL SEQRES 4 A 294 ARG ARG GLY ARG LYS THR GLY VAL PHE LEU THR TRP ASN SEQRES 5 A 294 GLU CYS ARG ALA GLN VAL ASP ARG PHE PRO ALA ALA ARG SEQRES 6 A 294 PHE LYS LYS PHE ALA THR GLU ASP GLU ALA TRP ALA PHE SEQRES 7 A 294 VAL ARG LYS SER ALA SER PRO GLU VAL SER GLU GLY HIS SEQRES 8 A 294 GLU ASN GLN HIS GLY GLN GLU SER GLU ALA LYS ALA SER SEQRES 9 A 294 LYS ARG LEU ARG GLU PRO LEU ASP GLY ASP GLY HIS GLU SEQRES 10 A 294 SER ALA GLU PRO TYR ALA LYS HIS MET LYS PRO SER VAL SEQRES 11 A 294 GLU PRO ALA PRO PRO VAL SER ARG ASP THR PHE SER TYR SEQRES 12 A 294 MET GLY ASP PHE VAL VAL VAL TYR THR ASP GLY CYS CYS SEQRES 13 A 294 SER SER ASN GLY ARG ARG ARG PRO ARG ALA GLY ILE GLY SEQRES 14 A 294 VAL TYR TRP GLY PRO GLY HIS PRO LEU ASN VAL GLY ILE SEQRES 15 A 294 ARG LEU PRO GLY ARG GLN THR ASN GLN ARG ALA GLU ILE SEQRES 16 A 294 HIS ALA ALA CYS LYS ALA ILE GLU GLN ALA LYS THR GLN SEQRES 17 A 294 ASN ILE ASN LYS LEU VAL LEU TYR THR ASN SER MET PHE SEQRES 18 A 294 THR ILE ASN GLY ILE THR ASN TRP VAL GLN GLY TRP LYS SEQRES 19 A 294 LYS ASN GLY TRP LYS THR SER ALA GLY LYS GLU VAL ILE SEQRES 20 A 294 ASN LYS GLU ASP PHE VAL ALA LEU GLU ARG LEU THR GLN SEQRES 21 A 294 GLY MET ASP ILE GLN TRP MET HIS VAL PRO GLY HIS SER SEQRES 22 A 294 GLY PHE ILE GLY ASN GLU GLU ALA ASP ARG LEU ALA ARG SEQRES 23 A 294 GLU GLY ALA LYS GLN SER GLU ASP SEQRES 1 B 20 U G G C G A G U G G G U G SEQRES 2 B 20 A G U G A G G SEQRES 1 C 20 OMC N7X T39 C5L A2M SC PST SC AS SC SC SC AS SEQRES 2 C 20 SC PST 6OO RFJ 6OO 6OO 6NW HET OMC C 1 18 HET N7X C 2 25 HET T39 C 3 25 HET C5L C 4 25 HET A2M C 5 23 HET SC C 6 19 HET PST C 7 20 HET SC C 8 19 HET AS C 9 21 HET SC C 10 19 HET SC C 11 19 HET SC C 12 19 HET AS C 13 21 HET SC C 14 19 HET PST C 15 20 HET 6OO C 16 21 HET RFJ C 17 24 HET 6OO C 18 21 HET 6OO C 19 21 HET 6NW C 20 23 HET SO4 A 301 5 HET SO4 A 302 5 HET GOL A 303 6 HET PEG C 201 7 HET SO4 C 202 5 HETNAM OMC O2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE HETNAM N7X 5'-O-[(R)-HYDROXY(SULFANYLIDENE)-LAMBDA~5~-PHOSPHANYL]- HETNAM 2 N7X 2'-O-(2-METHOXYETHYL)-5-METHYLCYTIDINE HETNAM T39 2'-O-METHOXYETHYLENE THYMIDINE 5'-MONOPHOSPHATE HETNAM C5L 2'-O-(2-METHOXYETHYL)-5-METHYLCYTIDINE 5'-(DIHYDROGEN HETNAM 2 C5L PHOSPHATE) HETNAM A2M 2'-O-METHYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE) HETNAM SC 2-DEOXY-CYTIDINE-5'-THIOPHOSPHORATE HETNAM PST THYMIDINE-5'-THIOPHOSPHATE HETNAM AS 2-DEOXY-ADENOSINE -5'-THIO-MONOPHOSPHATE HETNAM 6OO 2'-O-METHYL-5'-O-THIOPHOSPHONOCYTIDINE HETNAM RFJ 2'-O-METHYL-5'-O-THIOPHOSPHONOGUANOSINE HETNAM 6NW 2'-O-METHYL-5'-O-THIOPHOSPHONOADENOSINE HETNAM SO4 SULFATE ION HETNAM GOL GLYCEROL HETNAM PEG DI(HYDROXYETHYL)ETHER HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 OMC C10 H16 N3 O8 P FORMUL 3 N7X C13 H22 N3 O8 P S FORMUL 3 T39 C13 H21 N2 O10 P FORMUL 3 C5L C13 H22 N3 O9 P FORMUL 3 A2M C11 H16 N5 O7 P FORMUL 3 SC 6(C9 H14 N3 O6 P S) FORMUL 3 PST 2(C10 H15 N2 O7 P S) FORMUL 3 AS 2(C10 H14 N5 O5 P S) FORMUL 3 6OO 3(C10 H16 N3 O7 P S) FORMUL 3 RFJ C11 H16 N5 O7 P S FORMUL 3 6NW C11 H16 N5 O6 P S FORMUL 4 SO4 3(O4 S 2-) FORMUL 6 GOL C3 H8 O3 FORMUL 7 PEG C4 H10 O3 FORMUL 9 HOH *350(H2 O) HELIX 1 AA1 THR A 181 GLN A 200 1 20 HELIX 2 AA2 SER A 211 ASN A 220 1 10 HELIX 3 AA3 ASN A 220 GLY A 229 1 10 HELIX 4 AA4 ASN A 240 GLN A 252 1 13 HELIX 5 AA5 PHE A 267 LYS A 282 1 16 SHEET 1 AA1 5 VAL A 172 ARG A 175 0 SHEET 2 AA1 5 ARG A 157 TYR A 163 -1 N ILE A 160 O ILE A 174 SHEET 3 AA1 5 VAL A 140 SER A 149 -1 N TYR A 143 O TYR A 163 SHEET 4 AA1 5 LYS A 204 THR A 209 1 O VAL A 206 N VAL A 142 SHEET 5 AA1 5 ASP A 255 HIS A 260 1 O MET A 259 N LEU A 207 LINK O3' OMC C 1 P N7X C 2 1555 1555 1.57 LINK O3' N7X C 2 P T39 C 3 1555 1555 1.56 LINK O3' T39 C 3 P C5L C 4 1555 1555 1.60 LINK O3' C5L C 4 P A2M C 5 1555 1555 1.60 LINK O3' A2M C 5 P SC C 6 1555 1555 1.55 LINK O3' SC C 6 P PST C 7 1555 1555 1.57 LINK O3' PST C 7 P SC C 8 1555 1555 1.57 LINK O3' SC C 8 P AS C 9 1555 1555 1.59 LINK O3' AS C 9 P SC C 10 1555 1555 1.58 LINK O3' SC C 10 P SC C 11 1555 1555 1.58 LINK O3' SC C 11 P SC C 12 1555 1555 1.57 LINK O3' SC C 12 P AS C 13 1555 1555 1.56 LINK O3' AS C 13 P SC C 14 1555 1555 1.57 LINK O3' SC C 14 P PST C 15 1555 1555 1.56 LINK O3' PST C 15 P 6OO C 16 1555 1555 1.57 LINK O3' 6OO C 16 P RFJ C 17 1555 1555 1.56 LINK O3' RFJ C 17 P 6OO C 18 1555 1555 1.56 LINK O3' 6OO C 18 P 6OO C 19 1555 1555 1.56 LINK O3' 6OO C 19 P 6NW C 20 1555 1555 1.57 SITE 1 AC1 6 ARG A 153 ARG A 154 HOH A 401 HOH A 437 SITE 2 AC1 6 HOH A 480 HOH B 148 SITE 1 AC2 4 ARG A 153 HOH A 406 HOH A 444 HOH B 110 SITE 1 AC3 4 ARG A 157 ARG A 175 SER A 284 GLU A 285 SITE 1 AC4 7 SC C 10 SC C 11 SC C 12 HOH C 302 SITE 2 AC4 7 HOH C 328 HOH C 340 HOH C 344 SITE 1 AC5 6 A2M C 5 SC C 6 HOH C 308 HOH C 331 SITE 2 AC5 6 HOH C 339 HOH C 357 CRYST1 46.760 53.030 106.477 90.00 90.00 90.00 P 21 21 21 4 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.021386 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018857 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009392 0.00000