HEADER TRANSFERASE/RNA 16-MAY-13 4KR7 TITLE CRYSTAL STRUCTURE OF A 4-THIOURIDINE SYNTHETASE - RNA COMPLEX WITH TITLE 2 BOUND ATP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE TRNA SULFURTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SULFUR CARRIER PROTEIN THIS SULFURTRANSFERASE, THIAMINE COMPND 5 BIOSYNTHESIS PROTEIN THII, TRNA 4-THIOURIDINE SYNTHASE; COMPND 6 EC: 2.8.1.4; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES; COMPND 9 MOL_ID: 2; COMPND 10 MOLECULE: RNA (39-MER); COMPND 11 CHAIN: M, X; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOTOGA MARITIMA; SOURCE 3 ORGANISM_TAXID: 243274; SOURCE 4 STRAIN: ATCC 43589; SOURCE 5 GENE: AAD36761, THII, TM_1694; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS TRNA MODIFICATION, THIOURIDINE, SULFURTRANSFERASE, ADENYLATION, THUMP KEYWDS 2 DOMAIN, PP-LOOP MOTIF, 4-THIOURIDINE SYNTHESIS, TRANSFERASE-RNA KEYWDS 3 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR P.NEUMANN,R.FICNER,K.LAKOMEK REVDAT 3 04-SEP-19 4KR7 1 REMARK REVDAT 2 16-JUL-14 4KR7 1 JRNL REVDAT 1 23-APR-14 4KR7 0 JRNL AUTH P.NEUMANN,K.LAKOMEK,P.T.NAUMANN,W.M.ERWIN,C.T.LAUHON, JRNL AUTH 2 R.FICNER JRNL TITL CRYSTAL STRUCTURE OF A 4-THIOURIDINE SYNTHETASE-RNA COMPLEX JRNL TITL 2 REVEALS SPECIFICITY OF TRNA U8 MODIFICATION. JRNL REF NUCLEIC ACIDS RES. V. 42 6673 2014 JRNL REFN ISSN 0305-1048 JRNL PMID 24705700 JRNL DOI 10.1093/NAR/GKU249 REMARK 2 REMARK 2 RESOLUTION. 3.42 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.2_1309 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) : 3.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 21154 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.233 REMARK 3 R VALUE (WORKING SET) : 0.230 REMARK 3 FREE R VALUE : 0.274 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1058 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 29.3927 - 6.8173 0.95 2581 136 0.1825 0.2015 REMARK 3 2 6.8173 - 5.4222 0.99 2567 135 0.2323 0.3016 REMARK 3 3 5.4222 - 4.7400 1.00 2550 134 0.2115 0.2659 REMARK 3 4 4.7400 - 4.3081 1.00 2555 135 0.2026 0.2604 REMARK 3 5 4.3081 - 4.0001 1.00 2543 133 0.2447 0.2986 REMARK 3 6 4.0001 - 3.7648 1.00 2525 133 0.2683 0.3367 REMARK 3 7 3.7648 - 3.5766 1.00 2511 132 0.3093 0.3702 REMARK 3 8 3.5766 - 3.4211 0.90 2264 120 0.3858 0.4123 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.600 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.470 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 76.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 103.0 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 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 : 0.010 8243 REMARK 3 ANGLE : 0.968 11510 REMARK 3 CHIRALITY : 0.062 1350 REMARK 3 PLANARITY : 0.004 1164 REMARK 3 DIHEDRAL : 18.736 3386 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 77:162 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.4714 43.5177 7.4757 REMARK 3 T TENSOR REMARK 3 T11: 0.5873 T22: 0.7037 REMARK 3 T33: 0.7217 T12: 0.0133 REMARK 3 T13: -0.0265 T23: -0.0303 REMARK 3 L TENSOR REMARK 3 L11: 4.9021 L22: 4.6657 REMARK 3 L33: 3.6315 L12: 0.0357 REMARK 3 L13: 1.2797 L23: 0.9878 REMARK 3 S TENSOR REMARK 3 S11: -0.3683 S12: 0.2748 S13: 0.7367 REMARK 3 S21: 0.2875 S22: 0.2888 S23: 0.5244 REMARK 3 S31: 0.1692 S32: 0.2400 S33: -0.0142 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN A AND RESID 3:76 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.5845 21.4078 8.9659 REMARK 3 T TENSOR REMARK 3 T11: 0.6038 T22: 0.8090 REMARK 3 T33: 0.5532 T12: 0.0678 REMARK 3 T13: 0.0261 T23: 0.0228 REMARK 3 L TENSOR REMARK 3 L11: 2.2226 L22: 3.1300 REMARK 3 L33: 2.5365 L12: 1.1503 REMARK 3 L13: 0.5248 L23: 0.4312 REMARK 3 S TENSOR REMARK 3 S11: 0.1443 S12: -0.4283 S13: -0.0019 REMARK 3 S21: 0.4365 S22: -0.2105 S23: 0.2182 REMARK 3 S31: 0.3808 S32: 0.0091 S33: 0.2264 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND ( RESID 163:388 OR RESID 401:402 ) ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.3591 -4.0758 -13.0931 REMARK 3 T TENSOR REMARK 3 T11: 0.6142 T22: 0.5002 REMARK 3 T33: 0.7202 T12: 0.1067 REMARK 3 T13: 0.1565 T23: -0.0364 REMARK 3 L TENSOR REMARK 3 L11: 2.2377 L22: 1.9178 REMARK 3 L33: 1.7256 L12: -0.2469 REMARK 3 L13: -0.3170 L23: 0.7180 REMARK 3 S TENSOR REMARK 3 S11: -0.3180 S12: -0.0681 S13: -0.6696 REMARK 3 S21: -0.0458 S22: 0.2062 S23: -0.1204 REMARK 3 S31: 0.4575 S32: 0.2692 S33: 0.1850 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN B AND RESID 77:162 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.2871 34.0806 -43.9568 REMARK 3 T TENSOR REMARK 3 T11: 1.1188 T22: 0.9314 REMARK 3 T33: 1.0566 T12: -0.2799 REMARK 3 T13: 0.3975 T23: -0.0238 REMARK 3 L TENSOR REMARK 3 L11: 2.3852 L22: 2.5571 REMARK 3 L33: 2.0577 L12: 0.3946 REMARK 3 L13: 0.2019 L23: -0.0624 REMARK 3 S TENSOR REMARK 3 S11: -0.0170 S12: 0.3145 S13: 0.6991 REMARK 3 S21: -0.8362 S22: 0.3896 S23: -0.5281 REMARK 3 S31: -0.4293 S32: -0.6460 S33: -0.1834 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN B AND RESID 3:76 ) REMARK 3 ORIGIN FOR THE GROUP (A): -22.5231 17.7906 -41.8930 REMARK 3 T TENSOR REMARK 3 T11: 0.9019 T22: 0.8902 REMARK 3 T33: 0.6254 T12: -0.1346 REMARK 3 T13: 0.0819 T23: 0.0030 REMARK 3 L TENSOR REMARK 3 L11: 2.6199 L22: 2.6879 REMARK 3 L33: 2.6478 L12: -0.4742 REMARK 3 L13: -0.0339 L23: -0.8187 REMARK 3 S TENSOR REMARK 3 S11: -0.3487 S12: 0.6154 S13: -0.0656 REMARK 3 S21: -0.6977 S22: 0.3209 S23: 0.0463 REMARK 3 S31: 0.4283 S32: -0.3022 S33: 0.0947 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN B AND ( RESID 163:388 OR RESID 401:402 ) ) REMARK 3 ORIGIN FOR THE GROUP (A): -42.1475 5.6828 -16.7423 REMARK 3 T TENSOR REMARK 3 T11: 0.4994 T22: 0.5233 REMARK 3 T33: 0.7036 T12: -0.0137 REMARK 3 T13: 0.1088 T23: -0.1146 REMARK 3 L TENSOR REMARK 3 L11: 2.8305 L22: 2.3792 REMARK 3 L33: 3.1514 L12: 0.2179 REMARK 3 L13: -0.7782 L23: -0.4635 REMARK 3 S TENSOR REMARK 3 S11: -0.2891 S12: 0.0143 S13: -0.1441 REMARK 3 S21: 0.0225 S22: 0.1195 S23: 0.4076 REMARK 3 S31: 0.0551 S32: -0.3726 S33: 0.1857 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN M AND RESID 1:39 ) REMARK 3 ORIGIN FOR THE GROUP (A): -42.3671 27.6458 7.4265 REMARK 3 T TENSOR REMARK 3 T11: 1.0780 T22: 1.0341 REMARK 3 T33: 1.0572 T12: -0.1424 REMARK 3 T13: 0.0356 T23: 0.1204 REMARK 3 L TENSOR REMARK 3 L11: 3.6852 L22: 2.2613 REMARK 3 L33: 1.1569 L12: 0.3928 REMARK 3 L13: 0.7005 L23: -0.1836 REMARK 3 S TENSOR REMARK 3 S11: -0.3791 S12: -0.3562 S13: 0.5581 REMARK 3 S21: -0.2849 S22: 0.4197 S23: 0.8661 REMARK 3 S31: 0.2805 S32: -0.0618 S33: -0.0426 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: ( CHAIN X AND RESID 1:39 ) REMARK 3 ORIGIN FOR THE GROUP (A): 0.5291 7.5867 -39.2507 REMARK 3 T TENSOR REMARK 3 T11: 1.5949 T22: 1.3155 REMARK 3 T33: 1.2365 T12: -0.2233 REMARK 3 T13: 0.0768 T23: -0.1781 REMARK 3 L TENSOR REMARK 3 L11: 0.5427 L22: 5.8860 REMARK 3 L33: 0.1251 L12: -0.1804 REMARK 3 L13: 0.0982 L23: 0.8721 REMARK 3 S TENSOR REMARK 3 S11: 0.3712 S12: 0.3642 S13: -0.0585 REMARK 3 S21: 1.1270 S22: -0.0397 S23: -1.8844 REMARK 3 S31: 0.2418 S32: -0.3010 S33: -0.3465 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: REFINEMENT WAS BASED ON SIMULATED REMARK 3 ANNEALING IN TORSION ANGLE SPACE AND GROUPED B-FACTORS. REMARK 4 REMARK 4 4KR7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000079692. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAR-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.814000 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21271 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.420 REMARK 200 RESOLUTION RANGE LOW (A) : 35.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.52 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.67000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 MICRO-LITER OF THII-RNA COMPLEX REMARK 280 SOLUTION AT 10 MG/ML IN A BUFFER CONSISTING OF 150 MM AMMONIUM REMARK 280 SULFATE, 20MM TRIS/HCL PH 7.5 WAS MIXED WITH 3 MICRO-LITER OF REMARK 280 FRESHLY PREPARED RESERVOIR SOLUTION (2.0 M SODIUM FORMATE, 100 REMARK 280 MM SODIUM CITRATE, 2 MM DTT), VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 292K, PH 4.6 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 51.58500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.59000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 56.61000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 66.59000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 51.58500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 56.61000 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: BIOLOGICAL UNIT IS A HOMODIMER. THERE IS 1 BIOLOGICAL REMARK 300 UNIT IN THE ASYMMETRIC UNIT (CHAINS A & B) 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, M, 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 MET A 1 REMARK 465 GLU A 2 REMARK 465 MET B 1 REMARK 465 GLU B 2 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 LEU B 180 O2' ATP B 401 2.08 REMARK 500 O ILE A 32 OG1 THR A 36 2.16 REMARK 500 O ILE B 32 OG1 THR B 36 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NZ LYS A 350 O2' C X 38 3544 2.08 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 LEU B 181 CA - CB - CG ANGL. DEV. = 14.4 DEGREES REMARK 500 A M 23 C1' - O4' - C4' ANGL. DEV. = -4.8 DEGREES REMARK 500 A M 23 O4' - C1' - N9 ANGL. DEV. = 12.9 DEGREES REMARK 500 G X 10 O3' - P - OP2 ANGL. DEV. = 6.8 DEGREES REMARK 500 U X 13 N1 - C2 - O2 ANGL. DEV. = 5.0 DEGREES REMARK 500 U X 13 N3 - C2 - O2 ANGL. DEV. = -4.7 DEGREES REMARK 500 U X 13 C2 - N1 - C1' ANGL. DEV. = 8.7 DEGREES REMARK 500 C X 14 C6 - N1 - C2 ANGL. DEV. = -2.6 DEGREES REMARK 500 C X 14 C5 - C6 - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 C X 14 C6 - N1 - C1' ANGL. DEV. = -9.3 DEGREES REMARK 500 C X 14 C2 - N1 - C1' ANGL. DEV. = 12.0 DEGREES REMARK 500 C X 15 N1 - C2 - O2 ANGL. DEV. = 4.0 DEGREES REMARK 500 C X 15 C2 - N1 - C1' ANGL. DEV. = 7.3 DEGREES 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 11 53.34 -143.59 REMARK 500 SER A 12 106.55 -17.34 REMARK 500 PHE A 24 -72.12 -53.15 REMARK 500 ASN A 54 10.21 59.48 REMARK 500 ASP A 79 102.19 -55.72 REMARK 500 GLN A 106 77.02 -119.83 REMARK 500 PRO A 210 38.34 -92.75 REMARK 500 SER A 213 -173.88 -66.98 REMARK 500 GLU A 214 -86.72 -63.85 REMARK 500 PRO A 255 -174.49 -58.51 REMARK 500 SER A 343 -177.72 58.64 REMARK 500 PHE A 346 -88.21 -59.27 REMARK 500 HIS A 357 130.97 -179.96 REMARK 500 LEU B 16 13.01 57.79 REMARK 500 LYS B 17 -77.41 -52.32 REMARK 500 ASN B 20 94.63 -60.17 REMARK 500 PHE B 24 -71.87 -54.38 REMARK 500 ASP B 79 104.98 -59.97 REMARK 500 ARG B 197 20.05 -78.31 REMARK 500 PRO B 255 -177.10 -59.48 REMARK 500 GLN B 291 -33.12 -138.45 REMARK 500 GLN B 295 43.15 -152.28 REMARK 500 ILE B 337 44.20 38.55 REMARK 500 LYS B 338 159.69 69.65 REMARK 500 PHE B 346 -17.32 86.00 REMARK 500 SER B 356 -158.64 -154.06 REMARK 500 HIS B 357 132.06 178.73 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 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ATP A 401 O3B REMARK 620 2 ATP A 401 O3G 52.8 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ATP B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4KR6 RELATED DB: PDB REMARK 900 RELATED ID: 4KR9 RELATED DB: PDB DBREF 4KR7 A 1 388 UNP Q9X220 THII_THEMA 1 388 DBREF 4KR7 B 1 388 UNP Q9X220 THII_THEMA 1 388 DBREF 4KR7 M 1 39 PDB 4KR7 4KR7 1 39 DBREF 4KR7 X 1 39 PDB 4KR7 4KR7 1 39 SEQADV 4KR7 GLU A 2 UNP Q9X220 LYS 2 ENGINEERED MUTATION SEQADV 4KR7 GLU B 2 UNP Q9X220 LYS 2 ENGINEERED MUTATION SEQRES 1 A 388 MET GLU GLU LEU ARG VAL TYR ILE VAL ARG TYR SER GLU SEQRES 2 A 388 ILE GLY LEU LYS GLY LYS ASN ARG LYS ASP PHE GLU GLU SEQRES 3 A 388 ALA LEU ARG ARG ASN ILE GLU ARG VAL THR GLY MET LYS SEQRES 4 A 388 VAL LYS ARG GLN TRP GLY ARG PHE LEU ILE PRO ILE ASP SEQRES 5 A 388 GLU ASN VAL THR LEU ASP ASP LYS LEU LYS LYS ILE PHE SEQRES 6 A 388 GLY ILE GLN ASN PHE SER LYS GLY PHE LEU VAL SER HIS SEQRES 7 A 388 ASP PHE GLU GLU VAL LYS LYS TYR SER LEU ILE ALA VAL SEQRES 8 A 388 LYS GLU LYS LEU GLU LYS GLY ASN TYR ARG THR PHE LYS SEQRES 9 A 388 VAL GLN ALA LYS LYS ALA TYR LYS GLU TYR LYS LYS GLY SEQRES 10 A 388 VAL TYR GLU ILE ASN SER GLU LEU GLY ALA LEU ILE LEU SEQRES 11 A 388 LYS ASN PHE LYS GLU LEU SER VAL ASP VAL ARG ASN PRO SEQRES 12 A 388 ASP PHE VAL LEU GLY VAL GLU VAL ARG PRO GLU GLY VAL SEQRES 13 A 388 LEU ILE PHE THR ASP ARG VAL GLU CYS TYR GLY GLY LEU SEQRES 14 A 388 PRO VAL GLY THR GLY GLY LYS ALA VAL LEU LEU LEU SER SEQRES 15 A 388 GLY GLY ILE ASP SER PRO VAL ALA GLY TRP TYR ALA LEU SEQRES 16 A 388 LYS ARG GLY VAL LEU ILE GLU SER VAL THR PHE VAL SER SEQRES 17 A 388 PRO PRO PHE THR SER GLU GLY ALA VAL GLU LYS VAL ARG SEQRES 18 A 388 ASP ILE LEU ARG VAL LEU ARG GLU PHE SER GLY GLY HIS SEQRES 19 A 388 PRO LEU ARG LEU HIS ILE VAL ASN LEU THR LYS LEU GLN SEQRES 20 A 388 LEU GLU VAL LYS LYS ARG VAL PRO ASP LYS TYR SER LEU SEQRES 21 A 388 ILE MET TYR ARG ARG SER MET PHE ARG ILE ALA GLU LYS SEQRES 22 A 388 ILE ALA GLU GLU THR GLY ALA VAL ALA PHE TYR THR GLY SEQRES 23 A 388 GLU ASN ILE GLY GLN VAL ALA SER GLN THR LEU GLU ASN SEQRES 24 A 388 LEU TRP SER ILE GLU SER VAL THR THR ARG PRO VAL ILE SEQRES 25 A 388 ARG PRO LEU SER GLY PHE ASP LYS THR GLU ILE VAL GLU SEQRES 26 A 388 LYS ALA LYS GLU ILE GLY THR TYR GLU ILE SER ILE LYS SEQRES 27 A 388 PRO TYR GLN ASP SER CYS VAL PHE PHE ALA PRO LYS ASN SEQRES 28 A 388 PRO ALA THR ARG SER HIS PRO SER ILE LEU GLU LYS LEU SEQRES 29 A 388 GLU GLN GLN VAL PRO ASP LEU PRO VAL LEU GLU GLU GLU SEQRES 30 A 388 ALA PHE THR SER ARG LYS VAL GLU VAL ILE GLU SEQRES 1 B 388 MET GLU GLU LEU ARG VAL TYR ILE VAL ARG TYR SER GLU SEQRES 2 B 388 ILE GLY LEU LYS GLY LYS ASN ARG LYS ASP PHE GLU GLU SEQRES 3 B 388 ALA LEU ARG ARG ASN ILE GLU ARG VAL THR GLY MET LYS SEQRES 4 B 388 VAL LYS ARG GLN TRP GLY ARG PHE LEU ILE PRO ILE ASP SEQRES 5 B 388 GLU ASN VAL THR LEU ASP ASP LYS LEU LYS LYS ILE PHE SEQRES 6 B 388 GLY ILE GLN ASN PHE SER LYS GLY PHE LEU VAL SER HIS SEQRES 7 B 388 ASP PHE GLU GLU VAL LYS LYS TYR SER LEU ILE ALA VAL SEQRES 8 B 388 LYS GLU LYS LEU GLU LYS GLY ASN TYR ARG THR PHE LYS SEQRES 9 B 388 VAL GLN ALA LYS LYS ALA TYR LYS GLU TYR LYS LYS GLY SEQRES 10 B 388 VAL TYR GLU ILE ASN SER GLU LEU GLY ALA LEU ILE LEU SEQRES 11 B 388 LYS ASN PHE LYS GLU LEU SER VAL ASP VAL ARG ASN PRO SEQRES 12 B 388 ASP PHE VAL LEU GLY VAL GLU VAL ARG PRO GLU GLY VAL SEQRES 13 B 388 LEU ILE PHE THR ASP ARG VAL GLU CYS TYR GLY GLY LEU SEQRES 14 B 388 PRO VAL GLY THR GLY GLY LYS ALA VAL LEU LEU LEU SER SEQRES 15 B 388 GLY GLY ILE ASP SER PRO VAL ALA GLY TRP TYR ALA LEU SEQRES 16 B 388 LYS ARG GLY VAL LEU ILE GLU SER VAL THR PHE VAL SER SEQRES 17 B 388 PRO PRO PHE THR SER GLU GLY ALA VAL GLU LYS VAL ARG SEQRES 18 B 388 ASP ILE LEU ARG VAL LEU ARG GLU PHE SER GLY GLY HIS SEQRES 19 B 388 PRO LEU ARG LEU HIS ILE VAL ASN LEU THR LYS LEU GLN SEQRES 20 B 388 LEU GLU VAL LYS LYS ARG VAL PRO ASP LYS TYR SER LEU SEQRES 21 B 388 ILE MET TYR ARG ARG SER MET PHE ARG ILE ALA GLU LYS SEQRES 22 B 388 ILE ALA GLU GLU THR GLY ALA VAL ALA PHE TYR THR GLY SEQRES 23 B 388 GLU ASN ILE GLY GLN VAL ALA SER GLN THR LEU GLU ASN SEQRES 24 B 388 LEU TRP SER ILE GLU SER VAL THR THR ARG PRO VAL ILE SEQRES 25 B 388 ARG PRO LEU SER GLY PHE ASP LYS THR GLU ILE VAL GLU SEQRES 26 B 388 LYS ALA LYS GLU ILE GLY THR TYR GLU ILE SER ILE LYS SEQRES 27 B 388 PRO TYR GLN ASP SER CYS VAL PHE PHE ALA PRO LYS ASN SEQRES 28 B 388 PRO ALA THR ARG SER HIS PRO SER ILE LEU GLU LYS LEU SEQRES 29 B 388 GLU GLN GLN VAL PRO ASP LEU PRO VAL LEU GLU GLU GLU SEQRES 30 B 388 ALA PHE THR SER ARG LYS VAL GLU VAL ILE GLU SEQRES 1 M 39 G C C C G G A U A G U G U SEQRES 2 M 39 C C U U G G G A A A C C A SEQRES 3 M 39 A G U C C G G G C A C C A SEQRES 1 X 39 G C C C G G A U A G U G U SEQRES 2 X 39 C C U U G G G A A A C C A SEQRES 3 X 39 A G U C C G G G C A C C A HET ATP A 401 31 HET MG A 402 1 HET ATP B 401 31 HET MG B 402 1 HETNAM ATP ADENOSINE-5'-TRIPHOSPHATE HETNAM MG MAGNESIUM ION FORMUL 5 ATP 2(C10 H16 N5 O13 P3) FORMUL 6 MG 2(MG 2+) HELIX 1 1 GLY A 18 GLY A 37 1 20 HELIX 2 2 LEU A 57 LYS A 63 1 7 HELIX 3 3 ASP A 79 GLY A 98 1 20 HELIX 4 4 GLY A 117 PHE A 133 1 17 HELIX 5 5 ILE A 185 ARG A 197 1 13 HELIX 6 6 GLY A 215 SER A 231 1 17 HELIX 7 7 LEU A 243 VAL A 254 1 12 HELIX 8 8 TYR A 258 GLY A 279 1 22 HELIX 9 9 THR A 296 SER A 305 1 10 HELIX 10 10 ASP A 319 ILE A 330 1 12 HELIX 11 11 THR A 332 LYS A 338 1 7 HELIX 12 12 SER A 359 GLU A 365 1 7 HELIX 13 13 GLN A 366 VAL A 368 5 3 HELIX 14 14 ASP A 370 SER A 381 1 12 HELIX 15 15 ASN B 20 GLY B 37 1 18 HELIX 16 16 LEU B 57 LYS B 63 1 7 HELIX 17 17 ASP B 79 GLY B 98 1 20 HELIX 18 18 GLY B 117 PHE B 133 1 17 HELIX 19 19 ILE B 185 ARG B 197 1 13 HELIX 20 20 SER B 213 SER B 231 1 19 HELIX 21 21 LEU B 243 VAL B 254 1 12 HELIX 22 22 TYR B 258 GLY B 279 1 22 HELIX 23 23 VAL B 292 GLN B 295 5 4 HELIX 24 24 THR B 296 SER B 305 1 10 HELIX 25 25 ASP B 319 ILE B 330 1 12 HELIX 26 26 THR B 332 ILE B 337 1 6 HELIX 27 27 HIS B 357 GLU B 365 1 9 HELIX 28 28 GLN B 366 VAL B 368 5 3 HELIX 29 29 ASP B 370 SER B 381 1 12 SHEET 1 A 7 LYS A 41 GLN A 43 0 SHEET 2 A 7 ARG A 46 PRO A 50 -1 O ARG A 46 N GLN A 43 SHEET 3 A 7 LEU A 4 ARG A 10 -1 N VAL A 9 O PHE A 47 SHEET 4 A 7 ASN A 69 VAL A 76 -1 O SER A 71 N ILE A 8 SHEET 5 A 7 GLY A 155 PHE A 159 -1 O VAL A 156 N VAL A 76 SHEET 6 A 7 PHE A 145 ARG A 152 -1 N GLU A 150 O LEU A 157 SHEET 7 A 7 PHE A 103 LYS A 109 1 N LYS A 108 O VAL A 149 SHEET 1 B 5 LYS A 41 GLN A 43 0 SHEET 2 B 5 ARG A 46 PRO A 50 -1 O ARG A 46 N GLN A 43 SHEET 3 B 5 LEU A 4 ARG A 10 -1 N VAL A 9 O PHE A 47 SHEET 4 B 5 ASN A 69 VAL A 76 -1 O SER A 71 N ILE A 8 SHEET 5 B 5 VAL A 163 GLU A 164 -1 O VAL A 163 N PHE A 70 SHEET 1 C 6 VAL A 311 ILE A 312 0 SHEET 2 C 6 ALA A 282 TYR A 284 1 N PHE A 283 O ILE A 312 SHEET 3 C 6 LYS A 176 LEU A 180 1 N VAL A 178 O ALA A 282 SHEET 4 C 6 LEU A 200 VAL A 207 1 O GLU A 202 N ALA A 177 SHEET 5 C 6 LEU A 236 ASN A 242 1 O HIS A 239 N THR A 205 SHEET 6 C 6 LYS A 383 ILE A 387 -1 O GLU A 385 N LEU A 238 SHEET 1 D 8 LYS B 41 GLN B 43 0 SHEET 2 D 8 ARG B 46 PRO B 50 -1 O ARG B 46 N GLN B 43 SHEET 3 D 8 LEU B 4 ARG B 10 -1 N VAL B 9 O PHE B 47 SHEET 4 D 8 ASN B 69 VAL B 76 -1 O ASN B 69 N ARG B 10 SHEET 5 D 8 GLY B 155 PHE B 159 -1 O ILE B 158 N PHE B 74 SHEET 6 D 8 PHE B 145 ARG B 152 -1 N GLU B 150 O LEU B 157 SHEET 7 D 8 THR B 102 LYS B 109 1 N LYS B 108 O VAL B 149 SHEET 8 D 8 SER B 137 VAL B 138 1 O SER B 137 N PHE B 103 SHEET 1 E 5 LYS B 41 GLN B 43 0 SHEET 2 E 5 ARG B 46 PRO B 50 -1 O ARG B 46 N GLN B 43 SHEET 3 E 5 LEU B 4 ARG B 10 -1 N VAL B 9 O PHE B 47 SHEET 4 E 5 ASN B 69 VAL B 76 -1 O ASN B 69 N ARG B 10 SHEET 5 E 5 VAL B 163 GLU B 164 -1 O VAL B 163 N PHE B 70 SHEET 1 F 6 VAL B 311 ILE B 312 0 SHEET 2 F 6 ALA B 282 TYR B 284 1 N PHE B 283 O ILE B 312 SHEET 3 F 6 LYS B 176 LEU B 180 1 N VAL B 178 O ALA B 282 SHEET 4 F 6 LEU B 200 VAL B 207 1 O VAL B 204 N LEU B 179 SHEET 5 F 6 LEU B 236 ASN B 242 1 O HIS B 239 N THR B 205 SHEET 6 F 6 LYS B 383 ILE B 387 -1 O GLU B 385 N LEU B 238 LINK O3B ATP A 401 MG MG A 402 1555 1555 2.74 LINK O3G ATP A 401 MG MG A 402 1555 1555 2.74 LINK O1G ATP B 401 MG MG B 402 1555 1555 2.94 CISPEP 1 PRO A 209 PRO A 210 0 3.91 CISPEP 2 PRO B 209 PRO B 210 0 0.46 SITE 1 AC1 18 LEU A 180 LEU A 181 SER A 182 GLY A 184 SITE 2 AC1 18 ILE A 185 ASP A 186 SER A 187 VAL A 204 SITE 3 AC1 18 THR A 205 PHE A 206 ARG A 264 MET A 267 SITE 4 AC1 18 THR A 285 GLY A 286 GLU A 287 GLN A 291 SITE 5 AC1 18 GLN A 295 MG A 402 SITE 1 AC2 1 ATP A 401 SITE 1 AC3 14 LEU B 180 LEU B 181 SER B 182 ASP B 186 SITE 2 AC3 14 SER B 187 VAL B 204 PHE B 206 ARG B 264 SITE 3 AC3 14 MET B 267 GLY B 286 GLU B 287 ASN B 288 SITE 4 AC3 14 LYS B 320 MG B 402 SITE 1 AC4 1 ATP B 401 CRYST1 103.170 113.220 133.180 90.00 90.00 90.00 P 21 21 21 8 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 0.009693 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008832 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007509 0.00000 MASTER 470 0 4 29 37 0 11 6 0 0 0 66 END