HEADER TRANSCRIPTION 20-APR-12 4ERL TITLE CRYSTAL STRUCTURE OF THE LYSINE RIBOSWITCH BOUND TO A LYSINE-GLYCINE TITLE 2 DIPEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE RIBOSWITCH RNA; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: LYSINE RIBOSWITCH APTAMER DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 2336; SOURCE 4 GENE: ASD KEYWDS RIBOSWITCH APTAMER DOMAIN, REGULATORY MRNA, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR A.D.GARST,E.PORTER,R.T.BATEY REVDAT 3 13-SEP-23 4ERL 1 REMARK LINK REVDAT 2 03-OCT-12 4ERL 1 JRNL REVDAT 1 18-JUL-12 4ERL 0 JRNL AUTH A.D.GARST,E.B.PORTER,R.T.BATEY JRNL TITL INSIGHTS INTO THE REGULATORY LANDSCAPE OF THE LYSINE JRNL TITL 2 RIBOSWITCH. JRNL REF J.MOL.BIOL. V. 423 17 2012 JRNL REFN ISSN 0022-2836 JRNL PMID 22771573 JRNL DOI 10.1016/J.JMB.2012.06.038 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.970 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 18687 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 965 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 19.6201 - 5.6994 1.00 2552 135 0.1405 0.1643 REMARK 3 2 5.6994 - 4.5423 1.00 2512 158 0.1576 0.1899 REMARK 3 3 4.5423 - 3.9735 1.00 2564 129 0.1742 0.2228 REMARK 3 4 3.9735 - 3.6127 0.99 2517 130 0.2079 0.2602 REMARK 3 5 3.6127 - 3.3551 0.99 2532 159 0.2330 0.3093 REMARK 3 6 3.3551 - 3.1582 0.99 2508 118 0.2634 0.2910 REMARK 3 7 3.1582 - 3.0000 0.98 2537 136 0.3191 0.3725 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.25 REMARK 3 B_SOL : 11.90 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.430 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.540 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.24 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.59350 REMARK 3 B22 (A**2) : 2.59350 REMARK 3 B33 (A**2) : 10.43170 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 3910 REMARK 3 ANGLE : 0.933 6101 REMARK 3 CHIRALITY : 0.060 805 REMARK 3 PLANARITY : 0.008 162 REMARK 3 DIHEDRAL : 13.848 1941 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -23.1393 45.42691264.8736 REMARK 3 T TENSOR REMARK 3 T11: 0.0362 T22: 0.0814 REMARK 3 T33: 0.0730 T12: -0.0029 REMARK 3 T13: -0.1095 T23: 0.0996 REMARK 3 L TENSOR REMARK 3 L11: 0.5450 L22: 0.2064 REMARK 3 L33: 0.3659 L12: -0.1584 REMARK 3 L13: 0.2187 L23: -0.1208 REMARK 3 S TENSOR REMARK 3 S11: 0.0491 S12: -0.0440 S13: -0.0035 REMARK 3 S21: 0.0085 S22: 0.0701 S23: 0.0342 REMARK 3 S31: -0.0629 S32: 0.1073 S33: 0.0133 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4ERL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-MAY-12. REMARK 100 THE DEPOSITION ID IS D_1000071981. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-APR-10 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 7.0 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 RU300 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 19.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 1.920 REMARK 200 R MERGE (I) : 0.11300 REMARK 200 R SYM (I) : 0.11300 REMARK 200 FOR THE DATA SET : 5.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.5 REMARK 200 DATA REDUNDANCY IN SHELL : 1.93 REMARK 200 R MERGE FOR SHELL (I) : 0.32100 REMARK 200 R SYM FOR SHELL (I) : 0.32100 REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 3D0U) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10 MM NA-HEPES PH 7.0, 2 M LI2SO4, AND REMARK 280 5 MM MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 303K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.16200 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 19.58100 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: 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O2' G A 9 OP2 G A 11 1.90 REMARK 500 O2 C A 81 N2 G A 108 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 G A 1 P G A 1 OP3 -0.117 REMARK 500 REMARK 500 REMARK: NULL 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 A 65 C6 - N1 - C2 ANGL. DEV. = 4.0 DEGREES REMARK 500 G A 65 C8 - N9 - C4 ANGL. DEV. = 2.5 DEGREES REMARK 500 C A 81 N1 - C2 - O2 ANGL. DEV. = 4.4 DEGREES REMARK 500 C A 81 N3 - C2 - O2 ANGL. DEV. = -6.8 DEGREES REMARK 500 A A 83 N1 - C6 - N6 ANGL. DEV. = 4.3 DEGREES REMARK 500 U A 105 C2 - N3 - C4 ANGL. DEV. = -3.6 DEGREES REMARK 500 G A 107 C8 - N9 - C1' ANGL. DEV. = -7.8 DEGREES REMARK 500 G A 107 C4 - N9 - C1' ANGL. DEV. = 9.4 DEGREES REMARK 500 G A 108 C4 - C5 - N7 ANGL. DEV. = 3.2 DEGREES REMARK 500 G A 108 N9 - C4 - C5 ANGL. DEV. = -2.9 DEGREES REMARK 500 G A 108 C6 - C5 - N7 ANGL. DEV. = -4.2 DEGREES REMARK 500 G A 108 N1 - C6 - O6 ANGL. DEV. = 6.3 DEGREES REMARK 500 G A 108 C5 - C6 - O6 ANGL. DEV. = -6.8 DEGREES REMARK 500 A A 118 N1 - C6 - N6 ANGL. DEV. = 3.7 DEGREES REMARK 500 A A 123 C2 - N3 - C4 ANGL. DEV. = -3.7 DEGREES REMARK 500 A A 123 C4 - C5 - N7 ANGL. DEV. = 3.3 DEGREES REMARK 500 A A 123 C5 - N7 - C8 ANGL. DEV. = -3.5 DEGREES REMARK 500 A A 161 C8 - N9 - C4 ANGL. DEV. = -2.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE LYS A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLY A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3D0U RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE LYSINE RIBOSWITCH BOUND TO LYSINE REMARK 900 RELATED ID: 3D0X RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE UNLIGANDED LYSINE RIBOSWITCH REMARK 900 RELATED ID: 4ERJ RELATED DB: PDB DBREF 4ERL A 1 161 PDB 4ERL 4ERL 1 161 SEQRES 1 A 161 G G A C G G A G G C G C G SEQRES 2 A 161 C C C G A G A U G A G U A SEQRES 3 A 161 G G C U G U C C C A U C A SEQRES 4 A 161 G G G G A G G A A U C G G SEQRES 5 A 161 G G A C G G C U G A A A G SEQRES 6 A 161 G C G A G G G C G C C G A SEQRES 7 A 161 A G C G A G C A G A G U U SEQRES 8 A 161 C C U C C C G C U C U G C SEQRES 9 A 161 U U G G C U G G G G G U G SEQRES 10 A 161 A G G G G A A U A C C C U SEQRES 11 A 161 U A C C A C U G U C G C G SEQRES 12 A 161 A A A G C G G A G A G C C SEQRES 13 A 161 G U C C A HET LYS A 201 9 HET GLY A 202 5 HETNAM LYS LYSINE HETNAM GLY GLYCINE FORMUL 2 LYS C6 H15 N2 O2 1+ FORMUL 3 GLY C2 H5 N O2 FORMUL 4 HOH *10(H2 O) LINK C LYS A 201 N GLY A 202 1555 1555 1.44 SITE 1 AC1 9 G A 8 G A 9 G A 11 G A 77 SITE 2 AC1 9 A A 78 G A 111 G A 112 GLY A 202 SITE 3 AC1 9 HOH A 310 SITE 1 AC2 6 G A 8 G A 9 G A 11 G A 111 SITE 2 AC2 6 G A 112 LYS A 201 CRYST1 119.878 119.878 58.743 90.00 90.00 120.00 P 32 3 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 0.008342 0.004816 0.000000 0.00000 SCALE2 0.000000 0.009632 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017023 0.00000