HEADER RNA 19-AUG-14 4R4V TITLE CRYSTAL STRUCTURE OF THE VS RIBOZYME - G638A MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: VS RIBOZYME RNA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: NEUROSPORA; SOURCE 4 ORGANISM_TAXID: 5140; SOURCE 5 OTHER_DETAILS: IN VITRO TRANSCRIPTION KEYWDS NA, DIMER, RNA EXPDTA X-RAY DIFFRACTION AUTHOR J.A.PICCIRILLI,N.B.SUSLOV,S.DASGUPTA,H.HUANG,D.M.J.LILLEY,P.A.RICE REVDAT 4 28-FEB-24 4R4V 1 REMARK REVDAT 3 08-JUN-22 4R4V 1 REMARK LINK ATOM REVDAT 2 04-NOV-15 4R4V 1 JRNL REVDAT 1 30-SEP-15 4R4V 0 JRNL AUTH N.B.SUSLOV,S.DASGUPTA,H.HUANG,J.R.FULLER,D.M.LILLEY, JRNL AUTH 2 P.A.RICE,J.A.PICCIRILLI JRNL TITL CRYSTAL STRUCTURE OF THE VARKUD SATELLITE RIBOZYME. JRNL REF NAT.CHEM.BIOL. V. 11 840 2015 JRNL REFN ISSN 1552-4450 JRNL PMID 26414446 JRNL DOI 10.1038/NCHEMBIO.1929 REMARK 2 REMARK 2 RESOLUTION. 3.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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) : 3.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.07 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 21788 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.180 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.870 REMARK 3 FREE R VALUE TEST SET COUNT : 1280 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 42.0761 - 6.3794 0.99 2470 154 0.1524 0.1719 REMARK 3 2 6.3794 - 5.0662 1.00 2348 147 0.1685 0.1803 REMARK 3 3 5.0662 - 4.4266 1.00 2310 145 0.1547 0.1747 REMARK 3 4 4.4266 - 4.0222 1.00 2285 143 0.1707 0.2176 REMARK 3 5 4.0222 - 3.7341 0.99 2264 139 0.1777 0.2161 REMARK 3 6 3.7341 - 3.5141 0.97 2201 136 0.2166 0.2451 REMARK 3 7 3.5141 - 3.3382 0.98 2210 139 0.2330 0.2563 REMARK 3 8 3.3382 - 3.1929 0.97 2197 137 0.2491 0.2688 REMARK 3 9 3.1929 - 3.0700 0.99 2223 140 0.2988 0.3583 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) : 0.360 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.230 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 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 4481 REMARK 3 ANGLE : 1.827 7007 REMARK 3 CHIRALITY : 0.061 929 REMARK 3 PLANARITY : 0.010 186 REMARK 3 DIHEDRAL : 13.811 2228 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 4R4V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000086901. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-NOV-11 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07812 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL 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 : 21788 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.070 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 (%) : 99.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 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: SAD REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 6.5 2.0 M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 107.51000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 51.11450 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 51.11450 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 161.26500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 51.11450 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 51.11450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 53.75500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 51.11450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.11450 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 161.26500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 51.11450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.11450 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 53.75500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 107.51000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9370 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 59190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -77.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 215.02000 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 C A 602 OP1 REMARK 470 G A 603 OP1 REMARK 470 C A 604 OP1 REMARK 470 U A 605 OP1 REMARK 470 G A 606 OP1 REMARK 470 U A 607 OP1 REMARK 470 G A 608 OP1 REMARK 470 U A 609 OP1 REMARK 470 C A 610 OP1 REMARK 470 G A 611 OP1 REMARK 470 C A 612 OP1 REMARK 470 A A 613 OP1 REMARK 470 A A 614 OP1 REMARK 470 U A 615 OP1 REMARK 470 C A 616 OP1 REMARK 470 U A 617 OP1 REMARK 470 G A 618 OP1 REMARK 470 C A 619 OP1 REMARK 470 G A 620 OP1 REMARK 470 A A 621 OP1 REMARK 470 A A 622 OP1 REMARK 470 G A 623 OP1 REMARK 470 G A 624 OP1 REMARK 470 G A 625 OP1 REMARK 470 C A 626 OP1 REMARK 470 G A 627 OP1 REMARK 470 U A 628 OP1 REMARK 470 C A 629 OP1 REMARK 470 G A 630 OP1 REMARK 470 U A 631 OP1 REMARK 470 C A 632 OP1 REMARK 470 G A 633 OP1 REMARK 470 G A 634 OP1 REMARK 470 C A 635 OP1 REMARK 470 C A 636 OP1 REMARK 470 C A 637 OP1 REMARK 470 A A 638 OP1 REMARK 470 A A 639 OP1 REMARK 470 G A 640 OP1 REMARK 470 C A 641 OP1 REMARK 470 G A 642 OP1 REMARK 470 G A 643 OP1 REMARK 470 U A 644 OP1 REMARK 470 A A 645 OP1 REMARK 470 G A 646 OP1 REMARK 470 U A 647 OP1 REMARK 470 A A 648 OP1 REMARK 470 A A 649 OP1 REMARK 470 G A 650 OP1 REMARK 470 C A 651 OP1 REMARK 470 A A 652 OP1 REMARK 470 G A 653 OP1 REMARK 470 G A 654 OP1 REMARK 470 G A 655 OP1 REMARK 470 A A 656 OP1 REMARK 470 A A 657 OP1 REMARK 470 C A 658 OP1 REMARK 470 U A 659 OP1 REMARK 470 C A 660 OP1 REMARK 470 A A 661 OP1 REMARK 470 C A 662 OP1 REMARK 470 C A 663 OP1 REMARK 470 U A 664 OP1 REMARK 470 C A 665 OP1 REMARK 470 C A 666 OP1 REMARK 470 A A 667 OP1 REMARK 470 A A 668 OP1 REMARK 470 U A 669 OP1 REMARK 470 G A 670 OP1 REMARK 470 A A 671 OP1 REMARK 470 A A 672 OP1 REMARK 470 A A 673 OP1 REMARK 470 C A 674 OP1 REMARK 470 A A 675 OP1 REMARK 470 C A 676 OP1 REMARK 470 A A 677 OP1 REMARK 470 U A 678 OP1 REMARK 470 U A 679 OP1 REMARK 470 G A 680 OP1 REMARK 470 U A 681 OP1 REMARK 470 C A 682 OP1 REMARK 470 G A 683 OP1 REMARK 470 U A 684 OP1 REMARK 470 A A 685 OP1 REMARK 470 G A 686 OP1 REMARK 470 C A 687 OP1 REMARK 470 A A 688 OP1 REMARK 470 G A 689 OP1 REMARK 470 U A 690 OP1 REMARK 470 U A 691 OP1 REMARK 470 G A 692 OP1 REMARK 470 A A 693 OP1 REMARK 470 C A 694 OP1 REMARK 470 U A 695 OP1 REMARK 470 A A 696 OP1 REMARK 470 C A 697 OP1 REMARK 470 U A 698 OP1 REMARK 470 G A 699 OP1 REMARK 470 U A 700 OP1 REMARK 470 U A 701 OP1 REMARK 470 A A 702 OP1 REMARK 470 U A 703 OP1 REMARK 470 G A 704 OP1 REMARK 470 U A 705 OP1 REMARK 470 G A 706 OP1 REMARK 470 A A 707 OP1 REMARK 470 U A 708 OP1 REMARK 470 U A 709 OP1 REMARK 470 G A 710 OP1 REMARK 470 G A 711 OP1 REMARK 470 U A 712 OP1 REMARK 470 A A 713 OP1 REMARK 470 G A 714 OP1 REMARK 470 A A 715 OP1 REMARK 470 G A 716 OP1 REMARK 470 G A 717 OP1 REMARK 470 C A 718 OP1 REMARK 470 U A 719 OP1 REMARK 470 A A 720 OP1 REMARK 470 A A 721 OP1 REMARK 470 G A 722 OP1 REMARK 470 U A 723 OP1 REMARK 470 G A 724 OP1 REMARK 470 A A 725 OP1 REMARK 470 C A 726 OP1 REMARK 470 G A 727 OP1 REMARK 470 G A 728 OP1 REMARK 470 U A 729 OP1 REMARK 470 A A 730 OP1 REMARK 470 U A 731 OP1 REMARK 470 U A 732 OP1 REMARK 470 G A 733 OP1 REMARK 470 G A 734 OP1 REMARK 470 C A 735 OP1 REMARK 470 G A 736 OP1 REMARK 470 U A 737 OP1 REMARK 470 A A 738 OP1 REMARK 470 A A 739 OP1 REMARK 470 G A 740 OP1 REMARK 470 C A 741 OP1 REMARK 470 C A 742 OP1 REMARK 470 A A 743 OP1 REMARK 470 A A 744 OP1 REMARK 470 U A 745 OP1 REMARK 470 A A 746 OP1 REMARK 470 C A 747 OP1 REMARK 470 C A 748 OP1 REMARK 470 G A 749 OP1 REMARK 470 C A 750 OP1 REMARK 470 A A 751 OP1 REMARK 470 G A 752 OP1 REMARK 470 C A 753 OP1 REMARK 470 A A 754 OP1 REMARK 470 C A 755 OP1 REMARK 470 A A 756 OP1 REMARK 470 G A 757 OP1 REMARK 470 C A 758 OP1 REMARK 470 A A 759 OP1 REMARK 470 C A 760 OP1 REMARK 470 A A 761 OP1 REMARK 470 A A 762 OP1 REMARK 470 G A 763 OP1 REMARK 470 C A 764 OP1 REMARK 470 C A 765 OP1 REMARK 470 C A 766 OP1 REMARK 470 G A 767 OP1 REMARK 470 C A 768 OP1 REMARK 470 U A 769 OP1 REMARK 470 U A 770 OP1 REMARK 470 G A 771 OP1 REMARK 470 C A 772 OP1 REMARK 470 G A 773 OP1 REMARK 470 A A 774 OP1 REMARK 470 G A 775 OP1 REMARK 470 A A 776 OP1 REMARK 470 U A 777 OP1 REMARK 470 U A 778 OP1 REMARK 470 A A 779 OP1 REMARK 470 C A 780 OP1 REMARK 470 A A 781 OP1 REMARK 470 G A 782 OP1 REMARK 470 C A 783 OP1 REMARK 470 G A 784 OP1 REMARK 470 C A 785 OP1 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 906 O HOH A 907 2.08 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 C A 651 N1 C A 651 C6 -0.038 REMARK 500 A A 671 N9 A A 671 C4 -0.050 REMARK 500 G A 749 C5 G A 749 N7 -0.038 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 U A 644 O3' - P - OP2 ANGL. DEV. = 10.8 DEGREES REMARK 500 G A 650 C5 - C6 - O6 ANGL. DEV. = -3.9 DEGREES REMARK 500 G A 654 C6 - C5 - N7 ANGL. DEV. = -4.8 DEGREES REMARK 500 G A 654 N1 - C6 - O6 ANGL. DEV. = 4.1 DEGREES REMARK 500 G A 654 C5 - C6 - O6 ANGL. DEV. = -4.7 DEGREES REMARK 500 G A 655 N1 - C2 - N2 ANGL. DEV. = -5.5 DEGREES REMARK 500 A A 656 C8 - N9 - C4 ANGL. DEV. = 2.5 DEGREES REMARK 500 C A 660 C6 - N1 - C2 ANGL. DEV. = 3.4 DEGREES REMARK 500 C A 660 C2 - N3 - C4 ANGL. DEV. = -3.6 DEGREES REMARK 500 C A 660 N3 - C4 - C5 ANGL. DEV. = 2.7 DEGREES REMARK 500 C A 660 C5 - C6 - N1 ANGL. DEV. = -3.8 DEGREES REMARK 500 C A 662 N3 - C4 - C5 ANGL. DEV. = 2.6 DEGREES REMARK 500 C A 662 C5 - C4 - N4 ANGL. DEV. = -4.6 DEGREES REMARK 500 G A 670 C5 - C6 - O6 ANGL. DEV. = -4.3 DEGREES REMARK 500 A A 672 N1 - C2 - N3 ANGL. DEV. = 3.1 DEGREES REMARK 500 A A 672 C2 - N3 - C4 ANGL. DEV. = -4.3 DEGREES REMARK 500 A A 672 C8 - N9 - C4 ANGL. DEV. = -2.6 DEGREES REMARK 500 A A 677 C5 - C6 - N6 ANGL. DEV. = -5.2 DEGREES REMARK 500 C A 682 C6 - N1 - C2 ANGL. DEV. = 3.3 DEGREES REMARK 500 U A 709 O5' - P - OP2 ANGL. DEV. = 7.3 DEGREES REMARK 500 G A 722 C5 - C6 - N1 ANGL. DEV. = 3.8 DEGREES REMARK 500 G A 722 C4 - C5 - N7 ANGL. DEV. = 2.9 DEGREES REMARK 500 G A 722 C5 - C6 - O6 ANGL. DEV. = -5.5 DEGREES REMARK 500 G A 724 N1 - C2 - N3 ANGL. DEV. = 4.8 DEGREES REMARK 500 G A 724 C6 - C5 - N7 ANGL. DEV. = -5.0 DEGREES REMARK 500 G A 724 N1 - C2 - N2 ANGL. DEV. = -6.1 DEGREES REMARK 500 G A 724 C8 - N9 - C1' ANGL. DEV. = -7.9 DEGREES REMARK 500 C A 726 O3' - P - OP2 ANGL. DEV. = 9.0 DEGREES REMARK 500 C A 726 C2 - N3 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 C A 726 N3 - C4 - C5 ANGL. DEV. = 2.5 DEGREES REMARK 500 U A 732 O3' - P - OP2 ANGL. DEV. = 6.7 DEGREES REMARK 500 A A 738 C2 - N3 - C4 ANGL. DEV. = -3.3 DEGREES REMARK 500 C A 741 C6 - N1 - C2 ANGL. DEV. = 3.9 DEGREES REMARK 500 A A 743 O3' - P - OP2 ANGL. DEV. = 8.0 DEGREES REMARK 500 C A 748 C6 - N1 - C2 ANGL. DEV. = 2.6 DEGREES REMARK 500 C A 748 N1 - C2 - O2 ANGL. DEV. = -3.7 DEGREES REMARK 500 G A 749 C6 - C5 - N7 ANGL. DEV. = -4.4 DEGREES REMARK 500 A A 754 C8 - N9 - C4 ANGL. DEV. = 2.5 DEGREES REMARK 500 A A 754 C5 - C6 - N6 ANGL. DEV. = -4.9 DEGREES REMARK 500 C A 755 C2 - N3 - C4 ANGL. DEV. = -3.6 DEGREES REMARK 500 C A 755 N1 - C2 - O2 ANGL. DEV. = -3.6 DEGREES REMARK 500 G A 757 N1 - C2 - N3 ANGL. DEV. = 3.8 DEGREES REMARK 500 G A 757 C4 - C5 - N7 ANGL. DEV. = 3.0 DEGREES REMARK 500 C A 758 O5' - P - OP2 ANGL. DEV. = 7.7 DEGREES REMARK 500 C A 760 O3' - P - OP2 ANGL. DEV. = 7.6 DEGREES REMARK 500 C A 768 C6 - N1 - C2 ANGL. DEV. = 2.8 DEGREES REMARK 500 C A 768 N1 - C2 - O2 ANGL. DEV. = -4.1 DEGREES REMARK 500 C A 768 N3 - C2 - O2 ANGL. DEV. = 4.9 DEGREES REMARK 500 C A 768 C5 - C4 - N4 ANGL. DEV. = -6.4 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 809 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 704 O2' REMARK 620 2 HOH A 901 O 137.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 801 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 906 O REMARK 620 2 HOH A 907 O 47.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 803 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 911 O REMARK 620 2 HOH A 912 O 177.9 REMARK 620 3 HOH A 913 O 85.3 92.8 REMARK 620 4 HOH A 914 O 92.0 87.1 91.1 REMARK 620 5 HOH A 915 O 93.8 87.2 91.9 173.7 REMARK 620 6 HOH A 916 O 92.4 89.6 176.2 92.0 85.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 805 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 917 O REMARK 620 2 HOH A 918 O 178.0 REMARK 620 3 HOH A 919 O 89.0 92.0 REMARK 620 4 HOH A 920 O 87.6 90.8 88.3 REMARK 620 5 HOH A 921 O 92.0 89.6 91.9 179.6 REMARK 620 6 HOH A 922 O 89.9 89.1 178.8 91.5 88.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 806 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 923 O REMARK 620 2 HOH A 924 O 176.0 REMARK 620 3 HOH A 925 O 86.3 95.4 REMARK 620 4 HOH A 926 O 89.3 86.9 96.0 REMARK 620 5 HOH A 927 O 90.2 93.5 86.2 177.7 REMARK 620 6 HOH A 928 O 94.7 83.8 177.0 86.8 91.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 807 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 929 O REMARK 620 2 HOH A 930 O 178.6 REMARK 620 3 HOH A 931 O 91.9 87.7 REMARK 620 4 HOH A 932 O 89.2 92.2 91.4 REMARK 620 5 HOH A 933 O 88.3 90.3 85.6 176.1 REMARK 620 6 HOH A 934 O 89.2 91.2 177.4 90.9 92.0 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 808 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 909 O REMARK 620 2 HOH A 910 O 101.8 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 805 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 806 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 807 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 808 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 809 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 810 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE K A 811 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 813 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4R4P RELATED DB: PDB DBREF 4R4V A 600 785 PDB 4R4V 4R4V 600 785 SEQRES 1 A 186 GDP G C G C U G U G U C G C SEQRES 2 A 186 A A U C U G C G A A G G G SEQRES 3 A 186 C G U C G U C G G C C C A SEQRES 4 A 186 A G C G G U A G U A A G C SEQRES 5 A 186 A G G G A A C U C A C C U SEQRES 6 A 186 C C A A U G A A A C A C A SEQRES 7 A 186 U U G U C G U A G C A G U SEQRES 8 A 186 U G A C U A C U G U U A U SEQRES 9 A 186 G U G A U U G G U A G A G SEQRES 10 A 186 G C U A A G U G A C G G U SEQRES 11 A 186 A U U G G C G U A A G C C SEQRES 12 A 186 A A U A C C G C A G C A C SEQRES 13 A 186 A G C A C A A G C C C G C SEQRES 14 A 186 U U G C G A G A U U A C A SEQRES 15 A 186 G C G C MODRES 4R4V GDP A 600 G GUANOSINE-5'-DIPHOSPHATE HET GDP A 600 37 HET MG A 801 1 HET K A 802 1 HET MG A 803 1 HET K A 804 1 HET MG A 805 1 HET MG A 806 1 HET MG A 807 1 HET MG A 808 1 HET K A 809 1 HET K A 810 1 HET K A 811 1 HET MG A 812 1 HET MG A 813 1 HET MG A 814 1 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION FORMUL 1 GDP C10 H15 N5 O11 P2 FORMUL 2 MG 9(MG 2+) FORMUL 3 K 5(K 1+) FORMUL 16 HOH *35(H2 O) LINK O3' GDP A 600 P G A 601 1555 1555 1.60 LINK O4 U A 669 K K A 804 1555 1555 2.66 LINK O2' G A 704 K K A 809 1555 1555 3.19 LINK MG MG A 801 O HOH A 906 1555 1555 2.80 LINK MG MG A 801 O HOH A 907 1555 1555 2.24 LINK K K A 802 O HOH A 902 1555 1555 3.40 LINK MG MG A 803 O HOH A 911 1555 1555 2.20 LINK MG MG A 803 O HOH A 912 1555 1555 2.16 LINK MG MG A 803 O HOH A 913 1555 1555 2.20 LINK MG MG A 803 O HOH A 914 1555 1555 2.20 LINK MG MG A 803 O HOH A 915 1555 1555 2.18 LINK MG MG A 803 O HOH A 916 1555 1555 2.18 LINK MG MG A 805 O HOH A 917 1555 1555 2.17 LINK MG MG A 805 O HOH A 918 1555 1555 2.19 LINK MG MG A 805 O HOH A 919 1555 1555 2.21 LINK MG MG A 805 O HOH A 920 1555 1555 2.17 LINK MG MG A 805 O HOH A 921 1555 1555 2.19 LINK MG MG A 805 O HOH A 922 1555 1555 2.18 LINK MG MG A 806 O HOH A 923 1555 1555 2.19 LINK MG MG A 806 O HOH A 924 1555 1555 2.18 LINK MG MG A 806 O HOH A 925 1555 1555 2.21 LINK MG MG A 806 O HOH A 926 1555 1555 2.17 LINK MG MG A 806 O HOH A 927 1555 1555 2.20 LINK MG MG A 806 O HOH A 928 1555 1555 2.16 LINK MG MG A 807 O HOH A 929 1555 1555 2.17 LINK MG MG A 807 O HOH A 930 1555 1555 2.20 LINK MG MG A 807 O HOH A 931 1555 1555 2.17 LINK MG MG A 807 O HOH A 932 1555 1555 2.18 LINK MG MG A 807 O HOH A 933 1555 1555 2.18 LINK MG MG A 807 O HOH A 934 1555 1555 2.20 LINK MG MG A 808 O HOH A 909 1555 1555 2.66 LINK MG MG A 808 O HOH A 910 1555 1555 2.30 LINK K K A 809 O HOH A 901 1555 1555 2.82 SITE 1 AC1 2 HOH A 906 HOH A 907 SITE 1 AC2 6 HOH A 911 HOH A 912 HOH A 913 HOH A 914 SITE 2 AC2 6 HOH A 915 HOH A 916 SITE 1 AC3 1 U A 669 SITE 1 AC4 7 C A 758 HOH A 917 HOH A 918 HOH A 919 SITE 2 AC4 7 HOH A 920 HOH A 921 HOH A 922 SITE 1 AC5 6 HOH A 923 HOH A 924 HOH A 925 HOH A 926 SITE 2 AC5 6 HOH A 927 HOH A 928 SITE 1 AC6 6 HOH A 929 HOH A 930 HOH A 931 HOH A 932 SITE 2 AC6 6 HOH A 933 HOH A 934 SITE 1 AC7 2 HOH A 909 HOH A 910 SITE 1 AC8 3 G A 704 U A 705 HOH A 901 SITE 1 AC9 2 G A 740 C A 741 SITE 1 BC1 1 C A 764 SITE 1 BC2 1 C A 674 CRYST1 102.229 102.229 215.020 90.00 90.00 90.00 P 43 21 2 8 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 0.009782 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009782 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004651 0.00000 HETATM 1 PB GDP A 600 -2.981 72.309 122.482 1.00139.82 P HETATM 2 O1B GDP A 600 -4.133 71.579 121.814 1.00120.90 O HETATM 3 O2B GDP A 600 -2.948 71.982 123.963 1.00125.94 O HETATM 4 O3B GDP A 600 -3.164 73.804 122.307 1.00108.52 O HETATM 5 O3A GDP A 600 -1.562 71.873 121.829 1.00127.75 O HETATM 6 PA GDP A 600 -1.300 71.678 120.240 1.00119.95 P HETATM 7 O1A GDP A 600 -0.124 70.747 120.058 1.00105.96 O HETATM 8 O2A GDP A 600 -2.515 71.196 119.468 1.00111.89 O HETATM 9 O5' GDP A 600 -0.870 73.144 119.746 1.00102.76 O HETATM 10 C5' GDP A 600 -1.173 73.558 118.423 1.00 96.08 C HETATM 11 C4' GDP A 600 -0.766 75.015 118.239 1.00 94.91 C HETATM 12 O4' GDP A 600 -1.142 75.804 119.380 1.00 99.11 O HETATM 13 C3' GDP A 600 0.739 75.227 118.070 1.00 90.39 C HETATM 14 O3' GDP A 600 1.223 75.025 116.733 1.00 90.05 O HETATM 15 C2' GDP A 600 0.896 76.661 118.516 1.00 84.66 C HETATM 16 O2' GDP A 600 0.522 77.572 117.470 1.00 76.34 O HETATM 17 C1' GDP A 600 -0.077 76.718 119.692 1.00 92.08 C HETATM 18 N9 GDP A 600 0.612 76.249 120.917 1.00 82.57 N HETATM 19 C8 GDP A 600 0.220 75.227 121.709 1.00 93.47 C HETATM 20 N7 GDP A 600 1.090 75.036 122.730 1.00 85.80 N HETATM 21 C5 GDP A 600 2.066 75.946 122.583 1.00 73.22 C HETATM 22 C6 GDP A 600 3.300 76.291 123.315 1.00 66.38 C HETATM 23 O6 GDP A 600 3.637 75.662 124.341 1.00 70.28 O HETATM 24 N1 GDP A 600 4.039 77.292 122.849 1.00 60.77 N HETATM 25 C2 GDP A 600 3.707 77.982 121.745 1.00 65.83 C HETATM 26 N2 GDP A 600 4.523 78.981 121.348 1.00 57.87 N HETATM 27 N3 GDP A 600 2.587 77.726 121.016 1.00 66.73 N HETATM 28 C4 GDP A 600 1.749 76.737 121.388 1.00 71.13 C HETATM 29 H4' GDP A 600 -1.272 75.404 117.344 1.00113.89 H HETATM 30 H3' GDP A 600 1.274 74.573 118.772 1.00108.47 H HETATM 31 H2' GDP A 600 1.923 76.841 118.862 1.00101.59 H HETATM 32 HO2' GDP A 600 1.123 77.465 116.720 1.00 91.61 H HETATM 33 H1' GDP A 600 -0.457 77.742 119.817 1.00110.50 H HETATM 34 H8 GDP A 600 -0.678 74.643 121.554 1.00112.16 H HETATM 35 HN1 GDP A 600 4.911 77.548 123.355 1.00 72.92 H HETATM 36 HN21 GDP A 600 4.298 79.519 120.523 1.00 69.45 H HETATM 37 HN22 GDP A 600 5.358 79.191 121.875 1.00 69.45 H