HEADER LIGASE 29-AUG-11 3TL4 TITLE CRYSTAL STRUCTURE OF THE TRNA BINDING DOMAIN OF GLUTAMINYL-TRNA TITLE 2 SYNTHETASE FROM SACCHAROMYCES CEREVISIAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUTAMINYL-TRNA SYNTHETASE; COMPND 3 CHAIN: X; COMPND 4 FRAGMENT: TRNA BINDING DOMAIN (UNP RESIDUES 1-187); COMPND 5 SYNONYM: GLUTAMINE--TRNA LIGASE, GLNRS; COMPND 6 EC: 6.1.1.18; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROMYCES CEREVISIAE; SOURCE 3 ORGANISM_COMMON: BAKER'S YEAST; SOURCE 4 ORGANISM_TAXID: 559292; SOURCE 5 STRAIN: ATCC 204508 / S288C; SOURCE 6 GENE: GLN4, O3601, YOR168W; SOURCE 7 EXPRESSION_SYSTEM: SACCHAROMYCES CEREVISIAE; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 4932; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BCY123; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: BG2483 KEYWDS GLUTAMINE, TRNA SYNTHETASE, APPENDED DOMAIN, HINGE, TRNA LIGASE, KEYWDS 2 AMIDOTRANSFERASE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR T.D.GRANT,E.H.SNELL REVDAT 3 13-JUN-12 3TL4 1 JRNL REVDAT 2 28-DEC-11 3TL4 1 JRNL REVDAT 1 30-NOV-11 3TL4 0 JRNL AUTH T.D.GRANT,E.H.SNELL,J.R.LUFT,E.QUARTLEY,S.CORRETORE, JRNL AUTH 2 J.R.WOLFLEY,M.E.SNELL,A.HADD,J.J.PERONA,E.M.PHIZICKY, JRNL AUTH 3 E.J.GRAYHACK JRNL TITL STRUCTURAL CONSERVATION OF AN ANCIENT TRNA SENSOR IN JRNL TITL 2 EUKARYOTIC GLUTAMINYL-TRNA SYNTHETASE. JRNL REF NUCLEIC ACIDS RES. V. 40 3723 2012 JRNL REFN ISSN 0305-1048 JRNL PMID 22180531 JRNL DOI 10.1093/NAR/GKR1223 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.1_743) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VICENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.30 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 9385 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.770 REMARK 3 FREE R VALUE TEST SET COUNT : 448 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 26.3011 - 3.3159 1.00 3029 164 0.1606 0.1702 REMARK 3 2 3.3159 - 2.6327 1.00 2972 142 0.1949 0.2837 REMARK 3 3 2.6327 - 2.3001 1.00 2936 142 0.2314 0.2616 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.95 REMARK 3 K_SOL : 0.35 REMARK 3 B_SOL : 31.40 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.600 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.430 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.62160 REMARK 3 B22 (A**2) : -0.87090 REMARK 3 B33 (A**2) : 4.91430 REMARK 3 B12 (A**2) : -0.00000 REMARK 3 B13 (A**2) : 2.69020 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 1511 REMARK 3 ANGLE : 1.034 2033 REMARK 3 CHIRALITY : 0.077 231 REMARK 3 PLANARITY : 0.004 259 REMARK 3 DIHEDRAL : 14.390 587 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 3TL4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-SEP-11. REMARK 100 THE RCSB ID CODE IS RCSB067612. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUL-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97904, 0.91162, 0.97937 REMARK 200 MONOCHROMATOR : SIDE SCATTERING BENT CUBE-ROOT I REMARK 200 -BEAM SINGLE CRYSTAL; ASYMMETRIC REMARK 200 CUT 4.965 DEGS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9393 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 73.615 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.10000 REMARK 200 FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.42 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : 0.49000 REMARK 200 R SYM FOR SHELL (I) : 0.49000 REMARK 200 FOR SHELL : 1.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM KCL, 100MM TRIS, 20% (W/V) PEG REMARK 280 4000, PH 8.0, MICROBATCH UNDER OIL, TEMPERATURE 295K 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 17.31000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: X 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 MSE X 1 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 O HOH X 241 O HOH X 265 2.16 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 GLU X 40 30.89 -99.45 REMARK 500 LYS X 63 59.90 38.67 REMARK 500 ARG X 141 -138.53 60.38 REMARK 500 REMARK 500 REMARK: NULL DBREF 3TL4 X 1 187 UNP P13188 SYQ_YEAST 1 187 SEQRES 1 X 187 MSE SER SER VAL GLU GLU LEU THR GLN LEU PHE SER GLN SEQRES 2 X 187 VAL GLY PHE GLU ASP LYS LYS VAL LYS GLU ILE VAL LYS SEQRES 3 X 187 ASN LYS LYS VAL SER ASP SER LEU TYR LYS LEU ILE LYS SEQRES 4 X 187 GLU THR PRO SER ASP TYR GLN TRP ASN LYS SER THR ARG SEQRES 5 X 187 ALA LEU VAL HIS ASN LEU ALA SER PHE VAL LYS GLY THR SEQRES 6 X 187 ASP LEU PRO LYS SER GLU LEU ILE VAL ASN GLY ILE ILE SEQRES 7 X 187 ASN GLY ASP LEU LYS THR SER LEU GLN VAL ASP ALA ALA SEQRES 8 X 187 PHE LYS TYR VAL LYS ALA ASN GLY GLU ALA SER THR LYS SEQRES 9 X 187 MSE GLY MSE ASN GLU ASN SER GLY VAL GLY ILE GLU ILE SEQRES 10 X 187 THR GLU ASP GLN VAL ARG ASN TYR VAL MSE GLN TYR ILE SEQRES 11 X 187 GLN GLU ASN LYS GLU ARG ILE LEU THR GLU ARG TYR LYS SEQRES 12 X 187 LEU VAL PRO GLY ILE PHE ALA ASP VAL LYS ASN LEU LYS SEQRES 13 X 187 GLU LEU LYS TRP ALA ASP PRO ARG SER PHE LYS PRO ILE SEQRES 14 X 187 ILE ASP GLN GLU VAL LEU LYS LEU LEU GLY PRO LYS ASP SEQRES 15 X 187 GLU ARG ASP LEU ILE MODRES 3TL4 MSE X 105 MET SELENOMETHIONINE MODRES 3TL4 MSE X 107 MET SELENOMETHIONINE MODRES 3TL4 MSE X 127 MET SELENOMETHIONINE HET MSE X 105 8 HET MSE X 107 8 HET MSE X 127 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 HOH *82(H2 O) HELIX 1 1 SER X 3 VAL X 14 1 12 HELIX 2 2 GLU X 17 VAL X 25 1 9 HELIX 3 3 ASN X 27 GLU X 40 1 14 HELIX 4 4 ASN X 48 LYS X 63 1 16 HELIX 5 5 LYS X 69 ASN X 79 1 11 HELIX 6 6 THR X 84 GLY X 99 1 16 HELIX 7 7 GLU X 100 SER X 102 5 3 HELIX 8 8 THR X 103 ASN X 110 1 8 HELIX 9 9 THR X 118 ASN X 133 1 16 HELIX 10 10 ASN X 133 ARG X 141 1 9 HELIX 11 11 LEU X 144 ASN X 154 1 11 HELIX 12 12 LEU X 155 LYS X 159 5 5 HELIX 13 13 SER X 165 GLY X 179 1 15 HELIX 14 14 ASP X 182 LEU X 186 5 5 LINK C LYS X 104 N MSE X 105 1555 1555 1.34 LINK C MSE X 105 N GLY X 106 1555 1555 1.33 LINK C GLY X 106 N MSE X 107 1555 1555 1.32 LINK C MSE X 107 N ASN X 108 1555 1555 1.33 LINK C VAL X 126 N MSE X 127 1555 1555 1.33 LINK C MSE X 127 N GLN X 128 1555 1555 1.32 CRYST1 40.800 34.620 74.269 90.00 97.61 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 0.024510 0.000000 0.003276 0.00000 SCALE2 0.000000 0.028885 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013584 0.00000