HEADER TRANSCRIPTION TERMINATION 05-MAR-98 1A62 TITLE CRYSTAL STRUCTURE OF THE RNA-BINDING DOMAIN OF THE TRANSCRIPTIONAL TITLE 2 TERMINATOR PROTEIN RHO COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHO; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RNA BINDING DOMAIN, RESIDUES 1 - 130; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI BL21(DE3); SOURCE 3 ORGANISM_TAXID: 469008; SOURCE 4 STRAIN: BL21 (DE3); SOURCE 5 CELL_LINE: BL21; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: T7; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET11A; SOURCE 12 EXPRESSION_SYSTEM_GENE: RHO KEYWDS TRANSCRIPTION TERMINATION, TERMINATION, RNA BINDING DOMAIN, KEYWDS 2 TRANSCRIPTION REGULATION, OB FOLD, F1-ATPASE EXPDTA X-RAY DIFFRACTION AUTHOR T.J.ALLISON,T.C.WOOD,D.M.BRIERCHECK,F.RASTINEJAD,J.P.RICHARDSON, AUTHOR 2 G.S.RULE REVDAT 4 30-OCT-24 1A62 1 REMARK REVDAT 3 05-JUN-24 1A62 1 SEQADV LINK REVDAT 2 24-FEB-09 1A62 1 VERSN REVDAT 1 17-JUN-98 1A62 0 JRNL AUTH T.J.ALLISON,T.C.WOOD,D.M.BRIERCHECK,F.RASTINEJAD, JRNL AUTH 2 J.P.RICHARDSON,G.S.RULE JRNL TITL CRYSTAL STRUCTURE OF THE RNA-BINDING DOMAIN FROM JRNL TITL 2 TRANSCRIPTION TERMINATION FACTOR RHO. JRNL REF NAT.STRUCT.BIOL. V. 5 352 1998 JRNL REFN ISSN 1072-8368 JRNL PMID 9586995 JRNL DOI 10.1038/NSB0598-352 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.M.BRIERCHECK,T.C.WOOD,T.J.ALLISON,J.P.RICHARDSON,G.S.RULE REMARK 1 TITL THE NMR STRUCTURE OF THE RNA BINDING DOMAIN OF E. COLI RHO REMARK 1 TITL 2 FACTOR SUGGESTS POSSIBLE RNA-PROTEIN INTERACTIONS REMARK 1 REF NAT.STRUCT.BIOL. V. 5 393 1998 REMARK 1 REFN ISSN 1072-8368 REMARK 1 REFERENCE 2 REMARK 1 AUTH D.M.BRIERCHECK,T.J.ALLISON,J.P.RICHARDSON,J.F.ELLENA, REMARK 1 AUTH 2 T.C.WOOD,G.S.RULE REMARK 1 TITL 1H, 15N AND 13C RESONANCE ASSIGNMENTS AND SECONDARY REMARK 1 TITL 2 STRUCTURE DETERMINATION OF THE RNA-BINDING DOMAIN OF E.COLI REMARK 1 TITL 3 RHO PROTEIN REMARK 1 REF J.BIOMOL.NMR V. 8 429 1996 REMARK 1 REFN ISSN 0925-2738 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.010 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.0 REMARK 3 NUMBER OF REFLECTIONS : 16360 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) : 0.216 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1636 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 : 987 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 115 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.10 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.011 REMARK 3 BOND ANGLES (DEGREES) : 1.320 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED 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 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 : PARAM19X.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPH19X.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1A62 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000170437. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : MAY-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 4 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.969, 0.978, 0.979, 0.984 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : FUJI REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16360 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.010 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : 0.04000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 22.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 67.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.27000 REMARK 200 R SYM FOR SHELL (I) : 0.26000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.0 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 28.00500 REMARK 290 SMTRY3 2 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: MONOMERIC 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 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 ASN A 126 REMARK 465 ALA A 127 REMARK 465 ARG A 128 REMARK 465 ASN A 129 REMARK 465 LYS A 130 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 MSE A 21 CG MSE A 21 SE -0.252 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 TYR A 72 17.83 84.52 REMARK 500 PHE A 121 15.30 59.77 REMARK 500 PRO A 124 14.21 -54.43 REMARK 500 REMARK 500 REMARK: NULL DBREF 1A62 A 2 130 UNP P03002 RHO_ECOLI 2 130 SEQADV 1A62 MSE A 21 UNP P03002 MET 21 MODIFIED RESIDUE SEQADV 1A62 MSE A 29 UNP P03002 MET 29 MODIFIED RESIDUE SEQRES 1 A 130 MSE ASN LEU THR GLU LEU LYS ASN THR PRO VAL SER GLU SEQRES 2 A 130 LEU ILE THR LEU GLY GLU ASN MSE GLY LEU GLU ASN LEU SEQRES 3 A 130 ALA ARG MSE ARG LYS GLN ASP ILE ILE PHE ALA ILE LEU SEQRES 4 A 130 LYS GLN HIS ALA LYS SER GLY GLU ASP ILE PHE GLY ASP SEQRES 5 A 130 GLY VAL LEU GLU ILE LEU GLN ASP GLY PHE GLY PHE LEU SEQRES 6 A 130 ARG SER ALA ASP SER SER TYR LEU ALA GLY PRO ASP ASP SEQRES 7 A 130 ILE TYR VAL SER PRO SER GLN ILE ARG ARG PHE ASN LEU SEQRES 8 A 130 ARG THR GLY ASP THR ILE SER GLY LYS ILE ARG PRO PRO SEQRES 9 A 130 LYS GLU GLY GLU ARG TYR PHE ALA LEU LEU LYS VAL ASN SEQRES 10 A 130 GLU VAL ASN PHE ASP LYS PRO GLU ASN ALA ARG ASN LYS MODRES 1A62 MSE A 1 MET SELENOMETHIONINE MODRES 1A62 MSE A 21 MET SELENOMETHIONINE MODRES 1A62 MSE A 29 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 21 8 HET MSE A 29 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 HOH *115(H2 O) HELIX 1 1 LEU A 3 LYS A 7 1 5 HELIX 2 2 VAL A 11 MSE A 21 1 11 HELIX 3 3 LYS A 31 SER A 45 1 15 HELIX 4 4 ALA A 68 SER A 70 5 3 HELIX 5 5 PRO A 83 ARG A 88 1 6 SHEET 1 A 5 ILE A 79 VAL A 81 0 SHEET 2 A 5 GLY A 63 ARG A 66 -1 N LEU A 65 O ILE A 79 SHEET 3 A 5 ILE A 49 ILE A 57 -1 N GLU A 56 O PHE A 64 SHEET 4 A 5 THR A 96 ILE A 101 -1 N ILE A 101 O ILE A 49 SHEET 5 A 5 LYS A 115 VAL A 119 -1 N GLU A 118 O SER A 98 LINK C MSE A 1 N ASN A 2 1555 1555 1.33 LINK C ASN A 20 N MSE A 21 1555 1555 1.34 LINK C MSE A 21 N GLY A 22 1555 1555 1.34 LINK C ARG A 28 N MSE A 29 1555 1555 1.33 LINK C MSE A 29 N ARG A 30 1555 1555 1.33 CRYST1 25.950 56.010 42.920 90.00 99.35 90.00 P 1 21 1 2 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 0.038536 0.000000 0.006345 0.00000 SCALE2 0.000000 0.017854 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023613 0.00000 HETATM 1 N MSE A 1 21.403 -20.945 -2.823 1.00 26.95 N HETATM 2 CA MSE A 1 20.871 -21.439 -4.117 1.00 24.20 C HETATM 3 C MSE A 1 20.532 -20.299 -5.054 1.00 20.83 C HETATM 4 O MSE A 1 19.954 -19.297 -4.629 1.00 17.01 O HETATM 5 CB MSE A 1 19.631 -22.270 -3.871 1.00 23.98 C HETATM 6 CG MSE A 1 19.516 -23.445 -4.813 1.00 31.88 C HETATM 7 SE MSE A 1 17.706 -24.281 -4.281 1.00 40.09 SE HETATM 8 CE MSE A 1 18.342 -25.482 -3.128 1.00 33.94 C