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 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 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 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 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 MASTER 285 0 9 0 0 0 0 6 0 0 0 13 END