HEADER RNA 15-MAY-06 2H0Z TITLE PRE-CLEAVAGE STATE OF THE THERMOANAEROBACTER TENGCONGENSIS GLMS TITLE 2 RIBOZYME BOUND TO GLUCOSE-6-PHOSPHATE CAVEAT 2H0Z C A 5 HAS WRONG CHIRALITY AT ATOM C3' COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLMS RIBOZYME DEOXY RNA INHIBITOR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: ADENOSINE 0 IS DEOXY, ITS O2* IS NOT MISSING; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: GLMS RIBOZYME RNA; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN THERMOANAEROBACTER SOURCE 4 TENGCONGENSIS; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 OTHER_DETAILS: RNA PRODUCED BY IN VITRO TRANSCRIPTION. THIS SEQUENCE SOURCE 8 OCCURS NATURALLY IN THERMOANAEROBACTER TENGCONGENSIS KEYWDS RNA, RIBOZYME, PSEUDOKNOT, HELIX EXPDTA X-RAY DIFFRACTION AUTHOR D.J.KLEIN,A.R.FERRE-D'AMARE REVDAT 5 14-FEB-24 2H0Z 1 HETSYN REVDAT 4 29-JUL-20 2H0Z 1 CAVEAT COMPND REMARK SEQADV REVDAT 4 2 1 HETNAM LINK SITE REVDAT 3 24-FEB-09 2H0Z 1 VERSN REVDAT 2 03-OCT-06 2H0Z 1 JRNL REVDAT 1 26-SEP-06 2H0Z 0 JRNL AUTH D.J.KLEIN,A.R.FERRE-D'AMARE JRNL TITL STRUCTURAL BASIS OF GLMS RIBOZYME ACTIVATION BY JRNL TITL 2 GLUCOSAMINE-6-PHOSPHATE JRNL REF SCIENCE V. 313 1752 2006 JRNL REFN ISSN 0036-8075 JRNL PMID 16990543 JRNL DOI 10.1126/SCIENCE.1129666 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) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 13530 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1328 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 : 3073 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 15 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) : 0.36 REMARK 3 ESD FROM SIGMAA (A) : 0.54 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) : 0.41 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.69 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.210 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 : A SOLVENT DENSITY LEVEL OF 0.35 AND SOLVENT B REMARK 3 -FACTOR OF 20 WERE USED FOR THE BULK SOLVENT REMARK 3 DURING REFINEMENT 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 2H0Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-MAY-06. REMARK 100 THE DEPOSITION ID IS D_1000037793. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-APR-06 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 : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14171 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL 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 (%) : 96.9 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR 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 (%): 52.18 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.57 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 GLUCOSE-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 90.43850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.90450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 90.43850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.90450 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 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 C A 5 C2' - C3' - O3' ANGL. DEV. = 17.2 DEGREES REMARK 500 U B 49 C2' - C3' - O3' ANGL. DEV. = 10.2 DEGREES REMARK 500 C B 57 C2' - C3' - O3' ANGL. DEV. = 14.7 DEGREES REMARK 500 A B 58 N9 - C1' - C2' ANGL. DEV. = 8.2 DEGREES REMARK 500 G B 94 N9 - C1' - C2' ANGL. DEV. = 7.9 DEGREES REMARK 500 G B 94 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 U B 103 C2' - C3' - O3' ANGL. DEV. = 12.1 DEGREES REMARK 500 G B 130 N9 - C1' - C2' ANGL. DEV. = 8.9 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 A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 G A 1 O3' REMARK 620 2 C A 2 OP2 55.6 REMARK 620 3 C B 36 OP2 142.6 134.7 REMARK 620 4 HOH B 201 O 84.1 104.1 59.0 REMARK 620 5 HOH B 202 O 139.8 86.0 57.6 95.5 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2GCS RELATED DB: PDB REMARK 900 RELATED ID: 2GCV RELATED DB: PDB REMARK 900 RELATED ID: 2H0S RELATED DB: PDB REMARK 900 RELATED ID: 2H0W RELATED DB: PDB REMARK 900 RELATED ID: 2H0X RELATED DB: PDB DBREF 2H0Z B 23 145 GB 20517198 AE013165 2582 2704 DBREF 2H0Z A 0 26 PDB 2H0Z 2H0Z 0 26 SEQADV 2H0Z C B 21 GB 20517198 INSERTION SEQADV 2H0Z C B 22 GB 20517198 INSERTION SEQRES 1 A 27 DA G C G C C U G G A C U U SEQRES 2 A 27 A A A G C C A U U G C A C SEQRES 3 A 27 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 G 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 G6P A 301 16 HET MG A 401 1 HET MG B 402 1 HET MG B 403 1 HET MG B 404 1 HET MG B 405 1 HET MG B 406 1 HET MG B 407 1 HET MG B 408 1 HETNAM G6P 6-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE HETNAM MG MAGNESIUM ION HETSYN G6P ALPHA-D-GLUCOSE-6-PHOSPHATE; 6-O-PHOSPHONO-ALPHA-D- HETSYN 2 G6P GLUCOSE; 6-O-PHOSPHONO-D-GLUCOSE; 6-O-PHOSPHONO- HETSYN 3 G6P GLUCOSE FORMUL 3 G6P C6 H13 O9 P FORMUL 4 MG 8(MG 2+) FORMUL 12 HOH *15(H2 O) LINK O3' G A 1 MG MG A 401 1555 1555 2.90 LINK OP2 C A 2 MG MG A 401 1555 1555 2.22 LINK O2P G6P A 301 MG MG B 406 1555 1555 2.44 LINK MG MG A 401 OP2 C B 36 1555 1555 3.03 LINK MG MG A 401 O HOH B 201 1555 1555 1.99 LINK MG MG A 401 O HOH B 202 1555 1555 1.91 LINK O2' A B 56 MG MG B 402 1555 1555 2.96 LINK O2 U B 79 MG MG B 403 1555 1555 2.88 LINK N2 G B 86 MG MG B 407 1555 1555 3.11 CRYST1 180.877 39.809 70.226 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 0.005529 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025120 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014240 0.00000