HEADER RNA 23-OCT-07 3B4B TITLE T. TENGCONGENSIS GLMS RIBOZYME WITH G40A MUTATION, BOUND TO TITLE 2 GLUCOSAMINE-6-PHOSPHATE AND A SUBSTRATE RNA WITH A 2'5'- TITLE 3 PHOSPHODIESTER LINKAGE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLMS RIBOZYME SUBSTRATE WITH 2'5'-PHOSPHODIESTER LINKAGE; 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 3B4B 1 HETSYN REVDAT 3 29-JUL-20 3B4B 1 COMPND REMARK DBREF HETNAM REVDAT 3 2 1 LINK SITE REVDAT 2 24-FEB-09 3B4B 1 VERSN REVDAT 1 11-DEC-07 3B4B 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) (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 13960 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) : 0.216 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1377 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 : 3054 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 5 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) : 0.38 REMARK 3 ESD FROM SIGMAA (A) : 0.59 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) : 0.45 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.64 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 3B4B COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-NOV-07. REMARK 100 THE DEPOSITION ID IS D_1000045061. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUL-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14336 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 (%) : 97.4 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.12500 REMARK 200 R SYM (I) : 0.12500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.5000 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 (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.61400 REMARK 200 R SYM FOR SHELL (I) : 0.61400 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: FOURIER SYNTHESIS 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 (%): 52.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: GROWN FROM: 12% PEG 4000, 1M LICL, REMARK 280 100MM MES-NAOH PH 5.4, 5MM MGCL2, 4MM GLUCOSAMINE-6-P, REMARK 280 STABILIZED IN: 24% PEG 4000, 1.5M LICL, 30MM MGCL2, 100MM MES- REMARK 280 NAOH PH 5.5, 20MM GLUCOSE-6-PHOSPHATE, VAPOR DIFFUSION, SITTING REMARK 280 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 90.49600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.84300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 90.49600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.84300 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4160 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 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 G B 41 N9 - C1' - C2' ANGL. DEV. = 9.8 DEGREES REMARK 500 U B 48 N1 - C1' - C2' ANGL. DEV. = 9.9 DEGREES REMARK 500 U B 48 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 G B 55 N9 - C1' - C2' ANGL. DEV. = 8.7 DEGREES REMARK 500 C B 57 C2' - C3' - O3' ANGL. DEV. = 14.8 DEGREES REMARK 500 A B 58 N9 - C1' - C2' ANGL. DEV. = 8.3 DEGREES REMARK 500 G B 94 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 U B 103 C2' - C3' - O3' ANGL. DEV. = 13.6 DEGREES REMARK 500 G B 130 N9 - C1' - C2' ANGL. DEV. = 9.5 DEGREES REMARK 500 G B 130 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 G B 138 N9 - C1' - C2' ANGL. DEV. = 8.0 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 MG B 301 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 C A 2 OP2 REMARK 620 2 C B 36 OP2 176.1 REMARK 620 3 G B 37 OP2 86.6 95.8 REMARK 620 4 HOH B 405 O 103.5 73.6 86.7 REMARK 620 N 1 2 3 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3B4A RELATED DB: PDB REMARK 900 RELATED ID: 3B4C RELATED DB: PDB DBREF 3B4B A 1 26 PDB 3B4B 3B4B 1 26 DBREF 3B4B B 21 145 PDB 3B4B 3B4B 21 145 SEQRES 1 A 26 G C G C C U G G A C U U A SEQRES 2 A 26 A A G C C A U U G C A 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 A HET GLP A 201 16 HET 3AD A -1 18 HET MG B 301 1 HET MG B 302 1 HET MG B 303 1 HETNAM GLP 2-AMINO-2-DEOXY-6-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE HETNAM 3AD 3'-DEOXYADENOSINE 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 3 GLP C6 H14 N O8 P FORMUL 4 3AD C10 H13 N5 O3 FORMUL 5 MG 3(MG 2+) FORMUL 8 HOH *5(H2 O) LINK O2' 3AD A -1 P G A 1 1555 1555 1.60 LINK OP2 C A 2 MG MG B 301 1555 1555 2.34 LINK OP2 C B 36 MG MG B 301 1555 1555 2.44 LINK OP2 G B 37 MG MG B 301 1555 1555 2.21 LINK OP2 A B 38 MG MG B 302 1555 1555 2.21 LINK MG MG B 301 O HOH B 405 1555 1555 1.91 CRYST1 180.992 39.686 70.968 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 0.005525 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025198 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014091 0.00000