HEADER RNA 23-OCT-07 3B4A TITLE T. TENGCONGENSIS GLMS RIBOZYME WITH G40A MUTATION, BOUND TO TITLE 2 GLUCOSAMINE-6-PHOSPHATE CAVEAT 3B4A C B 57 HAS WRONG CHIRALITY AT ATOM C3' COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLMS RIBOZYME SUBSTRATE RNA; COMPND 3 CHAIN: A; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: GLMS RIBOZYME RNA; COMPND 6 CHAIN: B; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOANAEROBACTER TENGCONGENSIS; SOURCE 3 ORGANISM_TAXID: 119072; SOURCE 4 MOL_ID: 2; SOURCE 5 ORGANISM_SCIENTIFIC: THERMOANAEROBACTER TENGCONGENSIS; SOURCE 6 ORGANISM_TAXID: 119072 KEYWDS RIBOZYME, RIBOSWITCH, GLUCOSAMINE-6-PHOSPHATE, RNA EXPDTA X-RAY DIFFRACTION AUTHOR D.J.KLEIN,A.R.FERRE-D'AMARE REVDAT 4 21-FEB-24 3B4A 1 HETSYN REVDAT 3 29-JUL-20 3B4A 1 CAVEAT COMPND REMARK DBREF REVDAT 3 2 1 HETNAM LINK SITE REVDAT 2 24-FEB-09 3B4A 1 VERSN REVDAT 1 11-DEC-07 3B4A 0 JRNL AUTH D.J.KLEIN,M.D.BEEN,A.R.FERRE-D'AMARE JRNL TITL ESSENTIAL ROLE OF AN ACTIVE-SITE GUANINE IN GLMS RIBOZYME JRNL TITL 2 CATALYSIS. JRNL REF J.AM.CHEM.SOC. V. 129 14858 2007 JRNL REFN ISSN 0002-7863 JRNL PMID 17990888 JRNL DOI 10.1021/JA0768441 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.8 REMARK 3 NUMBER OF REFLECTIONS : 15548 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.246 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1514 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 0 REMARK 3 NUCLEIC ACID ATOMS : 3078 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 3 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.40 REMARK 3 ESD FROM SIGMAA (A) : 0.48 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.47 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.54 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3B4A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-NOV-07. REMARK 100 THE DEPOSITION ID IS D_1000045060. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-SEP-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16141 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 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 (%) : 97.2 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : 0.08300 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.40 REMARK 200 R MERGE FOR SHELL (I) : 0.93300 REMARK 200 R SYM FOR SHELL (I) : 0.93300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: GROWN FROM: 12% PEG 4000, 1M LICL, REMARK 280 100MM MES-NAOH PH 5.4, 5MM MGCL2, STABILIZED IN: 24% PEG 4000, REMARK 280 1.5M LICL, 30MM MGCL2, 100MM MES-NAOH PH 5.5, 20MM GLUCOSAMINE-6- REMARK 280 PHOSPHATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 88.57700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.84600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 88.57700 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.84600 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A MONOMER 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: 4370 ANGSTROM**2 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 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 U A 21 REMARK 465 G A 22 REMARK 465 C A 23 REMARK 465 A A 24 REMARK 465 C A 25 REMARK 465 U A 26 REMARK 465 C B 21 REMARK 465 C B 22 REMARK 465 U B 79 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 U A 6 N1 C2 O2 N3 C4 O4 C5 REMARK 470 U A 6 C6 REMARK 470 U B 103 N1 C2 O2 N3 C4 O4 C5 REMARK 470 U B 103 C6 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 B 49 C2' - C3' - O3' ANGL. DEV. = 11.4 DEGREES REMARK 500 G B 55 N9 - C1' - C2' ANGL. DEV. = 8.6 DEGREES REMARK 500 C B 57 C2' - C3' - O3' ANGL. DEV. = 15.3 DEGREES REMARK 500 U B 103 C2' - C3' - O3' ANGL. DEV. = 13.1 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 G B 55 0.06 SIDE CHAIN REMARK 500 G B 114 0.06 SIDE CHAIN REMARK 500 A B 127 0.05 SIDE CHAIN 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 MG B 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 2 OP2 REMARK 620 2 HOH A 301 O 93.9 REMARK 620 3 HOH A 302 O 80.6 164.8 REMARK 620 4 C B 36 OP2 165.0 91.4 90.7 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2Z74 RELATED DB: PDB REMARK 900 RELATED ID: 2Z75 RELATED DB: PDB REMARK 900 RELATED ID: 2HO7 RELATED DB: PDB REMARK 900 RELATED ID: 3B4B RELATED DB: PDB REMARK 900 RELATED ID: 3B4C RELATED DB: PDB DBREF 3B4A A -2 26 PDB 3B4A 3B4A -2 26 DBREF 3B4A B 21 145 PDB 3B4A 3B4A 21 145 SEQRES 1 A 28 A A G C G C C U G G A C U SEQRES 2 A 28 U A A A G C C A U U G C A SEQRES 3 A 28 C U SEQRES 1 B 125 C C G G C U U U A A G U U SEQRES 2 B 125 G A C G A G A G C A G G G SEQRES 3 B 125 U U U A U C G A G A C A U SEQRES 4 B 125 C G G C G G G U G C C C U SEQRES 5 B 125 G C G G U C U U C C U G C SEQRES 6 B 125 G A C C G U U A G A G G A SEQRES 7 B 125 C U G G U A A A A C C A C SEQRES 8 B 125 A G G C G A C U G U G G C SEQRES 9 B 125 A U A G A G C A G U C C G SEQRES 10 B 125 G G C A G G A A23 MODRES 3B4A A23 B 145 A HET A23 B 145 25 HET GLP A 401 16 HET MG A 204 1 HET MG B 201 1 HET MG B 202 1 HET MG B 203 1 HET MG B 205 1 HET MG B 206 1 HETNAM A23 ADENOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE HETNAM GLP 2-AMINO-2-DEOXY-6-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE HETNAM MG MAGNESIUM ION HETSYN GLP GLUCOSAMINE 6-PHOSPHATE; 6-O-PHOSPHONO-ALPHA-D- HETSYN 2 GLP GLUCOSAMINE; 2-AMINO-2-DEOXY-6-O-PHOSPHONO-ALPHA-D- HETSYN 3 GLP GLUCOSE; 2-AMINO-2-DEOXY-6-O-PHOSPHONO-D-GLUCOSE; 2- HETSYN 4 GLP AMINO-2-DEOXY-6-O-PHOSPHONO-GLUCOSE FORMUL 2 A23 C10 H13 N5 O9 P2 FORMUL 3 GLP C6 H14 N O8 P FORMUL 4 MG 6(MG 2+) FORMUL 10 HOH *3(H2 O) LINK O3' A B 144 P A23 B 145 1555 1555 1.61 LINK OP2 C A 2 MG MG B 201 1555 1555 2.40 LINK O HOH A 301 MG MG B 201 1555 1555 2.02 LINK O HOH A 302 MG MG B 201 1555 1555 1.84 LINK OP2 C B 36 MG MG B 201 1555 1555 2.42 CRYST1 177.154 41.692 77.699 90.00 90.00 90.00 P 21 21 2 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 0.005645 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023985 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012870 0.00000