PDB Short entry for 5DH7 HEADER RNA 29-AUG-15 5DH7 TITLE TWO DIVALENT METAL IONS AND CONFORMATIONAL CHANGES PLAY ROLES IN THE TITLE 2 HAMMERHEAD RIBOZYME CLEAVAGE REACTION-G12A MUTANT IN MN2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: RNA (48-MER); COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-R(*GP*GP*GP*CP*GP*UP*DC*UP*GP*GP*GP*CP*AP*GP*UP*AP*CP*CP COMPND 8 *CP*A)-3'; COMPND 9 CHAIN: B; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 4 ORGANISM_TAXID: 32630; SOURCE 5 OTHER_DETAILS: THIS RNA WAS MADE BY IN VITRO TRANSCRIPTION; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 9 ORGANISM_TAXID: 32630; SOURCE 10 OTHER_DETAILS: SYNTHESIZED OLIGONUCLEOTIDE KEYWDS RIBOZYME, HAMMERHEAD, RNA EXPDTA X-RAY DIFFRACTION AUTHOR A.MIR,J.CHEN,D.NEAU,B.L.GOLDEN REVDAT 5 25-DEC-19 5DH7 1 REMARK REVDAT 4 27-SEP-17 5DH7 1 REMARK REVDAT 3 20-JUL-16 5DH7 1 REMARK REVDAT 2 04-NOV-15 5DH7 1 JRNL REVDAT 1 07-OCT-15 5DH7 0 JRNL AUTH A.MIR,J.CHEN,K.ROBINSON,E.LENDY,J.GOODMAN,D.NEAU,B.L.GOLDEN JRNL TITL TWO DIVALENT METAL IONS AND CONFORMATIONAL CHANGES PLAY JRNL TITL 2 ROLES IN THE HAMMERHEAD RIBOZYME CLEAVAGE REACTION. JRNL REF BIOCHEMISTRY V. 54 6369 2015 JRNL REFN ISSN 0006-2960 JRNL PMID 26398724 JRNL DOI 10.1021/ACS.BIOCHEM.5B00824 REMARK 2 REMARK 2 RESOLUTION. 3.06 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 3.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 12124 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.950 REMARK 3 FREE R VALUE TEST SET COUNT : 1206 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 40.6581 - 6.3669 0.96 1280 133 0.2047 0.2778 REMARK 3 2 6.3669 - 5.0566 0.98 1291 140 0.1843 0.2391 REMARK 3 3 5.0566 - 4.4183 0.98 1302 137 0.1852 0.2044 REMARK 3 4 4.4183 - 4.0148 0.98 1256 147 0.1834 0.2523 REMARK 3 5 4.0148 - 3.7272 0.98 1286 141 0.1887 0.2404 REMARK 3 6 3.7272 - 3.5076 0.95 1231 152 0.2121 0.2162 REMARK 3 7 3.5076 - 3.3320 0.92 1219 133 0.2174 0.2591 REMARK 3 8 3.3320 - 3.1870 0.86 1139 127 0.2504 0.3120 REMARK 3 9 3.1870 - 3.0644 0.70 914 96 0.2661 0.3362 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) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.050 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 : 0.001 1626 REMARK 3 ANGLE : 0.376 2532 REMARK 3 CHIRALITY : 0.022 338 REMARK 3 PLANARITY : 0.002 68 REMARK 3 DIHEDRAL : 10.115 807 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 5DH7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000213197. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.8923 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12239 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.9 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.13500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.25200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 70.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 33 % MPD, 0.4 M POTASSIUM CHLORIDE, 50 REMARK 280 MM POTASSIUM ACETATE PH 5.0, 10 MM MGCL2, AND 0.5MM SPERMINE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 51.76400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 51.76400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 40.65450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.91250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.65450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.91250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.76400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.65450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 42.91250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.76400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.65450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 42.91250 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3290 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -60.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 MN A 101 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 1 N7 REMARK 620 2 G A 1 N7 0.0 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 MN A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 103 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 105 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 106 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 107 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 108 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DH6 RELATED DB: PDB REMARK 900 RELATED ID: 5DH8 RELATED DB: PDB REMARK 900 RELATED ID: 5DI2 RELATED DB: PDB REMARK 900 RELATED ID: 5DI4 RELATED DB: PDB DBREF 5DH7 A 1 48 PDB 5DH7 5DH7 1 48 DBREF 5DH7 B 1 19 PDB 5DH7 5DH7 1 19 SEQRES 1 A 48 G G G U A C U U A A G C C SEQRES 2 A 48 C A C U G A U G A G U C G SEQRES 3 A 48 C U G G G A U G C G A C A SEQRES 4 A 48 A A A C G C C C A SEQRES 1 B 20 G G G C G U DC U G G G C A SEQRES 2 B 20 G U A C C C A HET MN A 101 1 HET MN A 102 1 HET MN A 103 1 HET MN A 104 1 HET MN A 105 1 HET MN A 106 1 HET MN A 107 1 HET MN A 108 1 HET MN A 109 1 HET MN B 101 1 HET MN B 102 1 HETNAM MN MANGANESE (II) ION FORMUL 3 MN 11(MN 2+) LINK N7 G A 1 MN MN A 101 1555 1555 2.69 LINK N7 G A 18 MN MN A 105 1555 1555 2.40 LINK N7 G A 30 MN MN A 107 1555 1555 2.27 LINK OP2 A A 41 MN MN A 103 1555 1555 2.30 LINK N7 G B 10 MN MN B 101 1555 1555 2.73 LINK N7 G A 1 MN MN A 101 1555 3655 2.45 SITE 1 AC1 1 G A 1 SITE 1 AC2 1 G A 2 SITE 1 AC3 1 A A 41 SITE 1 AC4 1 G A 29 SITE 1 AC5 1 G A 18 SITE 1 AC6 1 A A 48 SITE 1 AC7 1 G A 30 SITE 1 AC8 2 A A 22 G A 23 SITE 1 AC9 1 G B 10 SITE 1 AD1 2 G B 2 G B 3 CRYST1 81.309 85.825 103.528 90.00 90.00 90.00 C 2 2 21 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 0.012299 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011652 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009659 0.00000