HEADER RNA 05-JUN-18 6DMD TITLE PPGPP RIBOSWITCH BOUND TO PPGPP, MANGANESE CHLORIDE STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PPGPP RIBOSWITCH; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOBACILLUS ACIDOPHILUS DSM 10332; SOURCE 3 ORGANISM_TAXID: 679936; SOURCE 4 EXPRESSION_SYSTEM: IN VITRO TRANSCRIPTION VECTOR PT7-TP(DELTAI); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 905931 KEYWDS RIBOSWITCH, NON-CODING, RNA, YKKC EXPDTA X-RAY DIFFRACTION AUTHOR A.PESELIS,A.SERGANOV REVDAT 3 27-APR-22 6DMD 1 SPRSDE HETSYN LINK REVDAT 2 01-JAN-20 6DMD 1 SPRSDE REVDAT 1 14-NOV-18 6DMD 0 JRNL AUTH A.PESELIS,A.SERGANOV JRNL TITL YKKC RIBOSWITCHES EMPLOY AN ADD-ON HELIX TO ADJUST JRNL TITL 2 SPECIFICITY FOR POLYANIONIC LIGANDS. JRNL REF NAT. CHEM. BIOL. V. 14 887 2018 JRNL REFN ESSN 1552-4469 JRNL PMID 30120360 JRNL DOI 10.1038/S41589-018-0114-4 REMARK 2 REMARK 2 RESOLUTION. 2.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 16626 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.220 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.272 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 850 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.72 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1044 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.4280 REMARK 3 BIN FREE R VALUE SET COUNT : 60 REMARK 3 BIN FREE R VALUE : 0.4460 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 4414 REMARK 3 HETEROGEN ATOMS : 99 REMARK 3 SOLVENT ATOMS : 43 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -4.30000 REMARK 3 B22 (A**2) : 3.65000 REMARK 3 B33 (A**2) : 0.47000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.62000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.734 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.388 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.309 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.617 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.893 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5020 ; 0.005 ; 0.011 REMARK 3 BOND LENGTHS OTHERS (A): 2020 ; 0.004 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7842 ; 1.223 ; 1.327 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4864 ; 1.595 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 824 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2510 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1104 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 6DMD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-18. REMARK 100 THE DEPOSITION ID IS D_1000234921. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-FEB-18 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 : NSLS-II REMARK 200 BEAMLINE : 17-ID-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.105 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16626 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.650 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.10700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.45500 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: NULL REMARK 200 SOFTWARE USED: REFMAC REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.68 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.075 M MGCL2, 0.1 M NA-ACETATE PH REMARK 280 4.2, AND 21% PEG400 (V/V), VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K 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 24.79750 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 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MG A 218 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GTP A 1 O2G REMARK 620 2 G4P A 201 O2B 81.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 202 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 3 N7 REMARK 620 2 G4P A 201 O1B 88.0 REMARK 620 3 G4P A 201 O2A 166.0 87.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 203 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 13 OP2 REMARK 620 2 G A 14 N7 84.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 204 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 13 OP1 REMARK 620 2 G A 14 OP2 79.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 205 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 43 OP1 REMARK 620 2 A A 87 OP1 85.4 REMARK 620 3 C A 88 OP2 76.5 79.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 214 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 43 OP2 REMARK 620 2 C A 88 OP1 83.5 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 207 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 44 O2 REMARK 620 2 C A 72 OP2 79.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 212 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 U A 81 O4 REMARK 620 2 A A 84 OP2 62.6 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 217 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A A 96 OP1 REMARK 620 2 A A 97 OP2 95.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 210 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GTP B 1 O2A REMARK 620 2 G4P B 201 O2B 140.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 202 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 A B 3 N7 REMARK 620 2 G4P B 201 O1B 97.6 REMARK 620 3 G4P B 201 O2A 162.9 73.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 203 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 43 OP1 REMARK 620 2 A B 87 OP1 76.7 REMARK 620 3 C B 88 OP2 81.5 79.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 205 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G B 43 OP2 REMARK 620 2 C B 88 OP1 83.3 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 204 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C B 44 O2 REMARK 620 2 C B 72 OP2 80.9 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 G4P A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 212 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 218 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue K A 219 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue G4P B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 210 REMARK 800 REMARK 800 SITE_IDENTIFIER: AE6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-nucleotide GTP B 1 and G B 2 DBREF 6DMD A 1 102 PDB 6DMD 6DMD 1 102 DBREF 6DMD B 1 102 PDB 6DMD 6DMD 1 102 SEQRES 1 A 102 GTP G A A G U G U A C C U A SEQRES 2 A 102 G G G A U C C A C C U C G SEQRES 3 A 102 A G A G A G G A A G G A C SEQRES 4 A 102 C A A G C G G U A C A G G SEQRES 5 A 102 C C U A C U U C G G U A G SEQRES 6 A 102 G U U A C A C C G U G G G SEQRES 7 A 102 G A U A A A A G A C C C G SEQRES 8 A 102 U G G C A A G U U U CCC SEQRES 1 B 102 GTP G A A G U G U A C C U A SEQRES 2 B 102 G G G A U C C A C C U C G SEQRES 3 B 102 A G A G A G G A A G G A C SEQRES 4 B 102 C A A G C G G U A C A G G SEQRES 5 B 102 C C U A C U U C G G U A G SEQRES 6 B 102 G U U A C A C C G U G G G SEQRES 7 B 102 G A U A A A A G A C C C G SEQRES 8 B 102 U G G C A A G U U U CCC HET GTP A 1 32 HET CCC A 102 23 HET GTP B 1 32 HET CCC B 102 23 HET G4P A 201 36 HET MN A 202 1 HET MN A 203 1 HET MN A 204 1 HET MN A 205 1 HET MN A 206 1 HET MN A 207 1 HET NA A 208 1 HET NA A 209 1 HET NA A 210 1 HET NA A 211 1 HET NA A 212 1 HET MG A 213 1 HET MG A 214 1 HET MG A 215 1 HET MG A 216 1 HET MG A 217 1 HET MG A 218 1 HET K A 219 1 HET G4P B 201 36 HET MN B 202 1 HET MN B 203 1 HET MN B 204 1 HET MN B 205 1 HET NA B 206 1 HET NA B 207 1 HET NA B 208 1 HET MG B 209 1 HET MG B 210 1 HETNAM GTP GUANOSINE-5'-TRIPHOSPHATE HETNAM CCC CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE HETNAM G4P GUANOSINE-5',3'-TETRAPHOSPHATE HETNAM MN MANGANESE (II) ION HETNAM NA SODIUM ION HETNAM MG MAGNESIUM ION HETNAM K POTASSIUM ION HETSYN G4P GUANOSINE TETRAPHOSPHATE;PPGPP FORMUL 1 GTP 2(C10 H16 N5 O14 P3) FORMUL 1 CCC 2(C9 H13 N3 O10 P2) FORMUL 3 G4P 2(C10 H17 N5 O17 P4) FORMUL 4 MN 10(MN 2+) FORMUL 10 NA 8(NA 1+) FORMUL 15 MG 8(MG 2+) FORMUL 21 K K 1+ FORMUL 32 HOH *43(H2 O) LINK O3' GTP A 1 P G A 2 1555 1555 1.62 LINK O3' U A 101 P CCC A 102 1555 1555 1.59 LINK O3' GTP B 1 P G B 2 1555 1555 1.59 LINK O3' U B 101 P CCC B 102 1555 1555 1.60 LINK O2G GTP A 1 MG MG A 218 1555 1555 2.52 LINK N7 A A 3 MN MN A 202 1555 1555 2.59 LINK OP2 C A 11 NA NA A 208 1555 1555 3.01 LINK OP2 A A 13 MN MN A 203 1555 1555 2.12 LINK OP1 A A 13 MN MN A 204 1555 1555 2.37 LINK N7 G A 14 MN MN A 203 1555 1555 2.35 LINK OP2 G A 14 MN MN A 204 1555 1555 2.39 LINK OP2 G A 37 MG MG A 216 1555 1555 2.21 LINK OP1 G A 43 MN MN A 205 1555 1555 2.23 LINK OP2 G A 43 MG MG A 214 1555 1555 2.22 LINK O2 C A 44 MN MN A 207 1555 1555 2.32 LINK OP2 C A 72 MN MN A 207 1555 1555 2.39 LINK O4 U A 81 NA NA A 212 1555 1555 3.10 LINK OP2 A A 84 NA NA A 212 1555 1555 2.54 LINK OP1 A A 87 MN MN A 205 1555 1555 2.08 LINK OP2 C A 88 MN MN A 205 1555 1555 2.41 LINK OP1 C A 88 MG MG A 214 1555 1555 2.14 LINK OP1 A A 96 MG MG A 217 1555 1555 2.17 LINK OP2 A A 97 MG MG A 217 1555 1555 2.03 LINK O1B G4P A 201 MN MN A 202 1555 1555 2.12 LINK O2A G4P A 201 MN MN A 202 1555 1555 2.20 LINK O1C G4P A 201 MG MG A 215 1555 1555 2.27 LINK O2B G4P A 201 MG MG A 218 1555 1555 2.71 LINK NA NA A 210 O HOH A 316 1555 1555 2.57 LINK O2A GTP B 1 MG MG B 210 1555 1555 1.95 LINK N7 A B 3 MN MN B 202 1555 1555 2.59 LINK OP1 G B 43 MN MN B 203 1555 1555 2.29 LINK OP2 G B 43 MN MN B 205 1555 1555 2.28 LINK O2 C B 44 MN MN B 204 1555 1555 2.44 LINK OP1 G B 66 NA NA B 208 1555 1555 2.28 LINK OP2 C B 72 MN MN B 204 1555 1555 2.36 LINK OP1 A B 87 MN MN B 203 1555 1555 2.34 LINK OP2 C B 88 MN MN B 203 1555 1555 2.21 LINK OP1 C B 88 MN MN B 205 1555 1555 2.06 LINK O1B G4P B 201 MN MN B 202 1555 1555 2.33 LINK O2A G4P B 201 MN MN B 202 1555 1555 2.39 LINK O1C G4P B 201 MG MG B 209 1555 1555 2.64 LINK O2B G4P B 201 MG MG B 210 1555 1555 1.99 SITE 1 AC1 15 GTP A 1 A A 3 A A 4 G A 5 SITE 2 AC1 15 G A 43 C A 70 A A 71 C A 72 SITE 3 AC1 15 A A 96 G A 98 MN A 202 MG A 215 SITE 4 AC1 15 MG A 218 HOH A 304 HOH A 307 SITE 1 AC2 2 A A 3 G4P A 201 SITE 1 AC3 2 A A 13 G A 14 SITE 1 AC4 2 A A 13 G A 14 SITE 1 AC5 3 G A 43 A A 87 C A 88 SITE 1 AC6 2 C A 44 C A 72 SITE 1 AC7 2 C A 11 A A 41 SITE 1 AC8 1 HOH A 316 SITE 1 AC9 3 A A 80 U A 81 A A 84 SITE 1 AD1 2 G A 43 C A 88 SITE 1 AD2 1 G4P A 201 SITE 1 AD3 1 G A 37 SITE 1 AD4 2 A A 96 A A 97 SITE 1 AD5 2 GTP A 1 G4P A 201 SITE 1 AD6 4 A A 17 G A 36 G A 37 A A 38 SITE 1 AD7 12 GTP B 1 A B 3 A B 4 G B 5 SITE 2 AD7 12 G B 43 C B 70 A B 71 C B 72 SITE 3 AD7 12 G B 98 MN B 202 MG B 209 MG B 210 SITE 1 AD8 2 A B 3 G4P B 201 SITE 1 AD9 3 G B 43 A B 87 C B 88 SITE 1 AE1 2 C B 44 C B 72 SITE 1 AE2 2 G B 43 C B 88 SITE 1 AE3 1 G B 66 SITE 1 AE4 1 G4P B 201 SITE 1 AE5 3 GTP B 1 G B 2 G4P B 201 SITE 1 AE6 8 GTP A 1 U A 101 CCC A 102 A B 3 SITE 2 AE6 8 U B 101 CCC B 102 G4P B 201 MG B 210 CRYST1 78.741 49.595 79.365 90.00 97.29 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 0.012700 0.000000 0.001624 0.00000 SCALE2 0.000000 0.020163 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012703 0.00000 HETATM 1 PG GTP A 1 -59.719 -0.587 17.765 1.00 84.24 P HETATM 2 O1G GTP A 1 -60.985 -1.067 17.081 1.00 77.30 O HETATM 3 O2G GTP A 1 -58.509 -1.351 17.246 1.00 76.13 O HETATM 4 O3G GTP A 1 -59.539 0.901 17.567 1.00 89.62 O HETATM 5 O3B GTP A 1 -59.854 -0.761 19.361 1.00 81.82 O HETATM 6 PB GTP A 1 -58.629 -0.412 20.356 1.00 76.98 P HETATM 7 O1B GTP A 1 -58.477 1.104 20.472 1.00 70.75 O HETATM 8 O2B GTP A 1 -58.934 -1.121 21.666 1.00 64.07 O HETATM 9 O3A GTP A 1 -57.364 -1.079 19.590 1.00 63.01 O HETATM 10 PA GTP A 1 -56.337 -2.088 20.298 1.00 57.98 P HETATM 11 O1A GTP A 1 -55.001 -2.104 19.574 1.00 59.33 O HETATM 12 O2A GTP A 1 -56.113 -1.682 21.734 1.00 64.92 O HETATM 13 O5' GTP A 1 -57.046 -3.529 20.332 1.00 46.38 O HETATM 14 C5' GTP A 1 -56.334 -4.624 20.848 1.00 39.34 C HETATM 15 C4' GTP A 1 -57.018 -5.935 20.477 1.00 35.73 C HETATM 16 O4' GTP A 1 -58.412 -5.798 20.553 1.00 33.51 O HETATM 17 C3' GTP A 1 -56.790 -6.412 19.050 1.00 34.05 C HETATM 18 O3' GTP A 1 -55.535 -7.070 18.880 1.00 31.75 O HETATM 19 C2' GTP A 1 -57.982 -7.326 18.810 1.00 32.62 C HETATM 20 O2' GTP A 1 -57.846 -8.545 19.500 1.00 32.74 O HETATM 21 C1' GTP A 1 -59.058 -6.496 19.508 1.00 31.44 C HETATM 22 N9 GTP A 1 -59.758 -5.569 18.580 1.00 28.93 N HETATM 23 C8 GTP A 1 -59.814 -4.208 18.606 1.00 26.70 C HETATM 24 N7 GTP A 1 -60.570 -3.789 17.564 1.00 25.90 N HETATM 25 C5 GTP A 1 -61.011 -4.851 16.879 1.00 26.00 C HETATM 26 C6 GTP A 1 -61.814 -5.004 15.757 1.00 26.35 C HETATM 27 O6 GTP A 1 -62.273 -4.030 15.175 1.00 25.94 O HETATM 28 N1 GTP A 1 -62.088 -6.266 15.271 1.00 26.66 N HETATM 29 C2 GTP A 1 -61.585 -7.374 15.922 1.00 27.73 C HETATM 30 N2 GTP A 1 -61.838 -8.599 15.469 1.00 27.91 N HETATM 31 N3 GTP A 1 -60.801 -7.211 17.044 1.00 28.05 N HETATM 32 C4 GTP A 1 -60.517 -5.971 17.513 1.00 27.39 C