HEADER LIGASE 24-JAN-13 4IWY TITLE SEMET-SUBSTITUTED RIMK STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOMAL PROTEIN S6 MODIFICATION PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: B0852, JW0836, RIMK; 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: PET28A KEYWDS ATP-GRASP FOLD, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR D.SHI,G.ZHAO,Z.JIN,N.M.ALLEWELL,M.TUCHMAN REVDAT 3 24-JAN-18 4IWY 1 AUTHOR REVDAT 2 09-OCT-13 4IWY 1 JRNL REVDAT 1 08-MAY-13 4IWY 0 JRNL AUTH G.ZHAO,Z.JIN,Y.WANG,N.M.ALLEWELL,M.TUCHMAN,D.SHI JRNL TITL STRUCTURE AND FUNCTION OF ESCHERICHIA COLI RIMK, AN JRNL TITL 2 ATP-GRASP FOLD, L-GLUTAMYL LIGASE ENZYME. JRNL REF PROTEINS V. 81 1847 2013 JRNL REFN ISSN 0887-3585 JRNL PMID 23609986 JRNL DOI 10.1002/PROT.24311 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.56 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 3 NUMBER OF REFLECTIONS : 18059 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1621 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 26.5590 - 6.6057 1.00 2801 141 0.1804 0.2125 REMARK 3 2 6.6057 - 5.2565 1.00 2809 147 0.2183 0.2699 REMARK 3 3 5.2565 - 4.5959 1.00 2787 146 0.1630 0.2093 REMARK 3 4 4.5959 - 4.1775 1.00 2803 153 0.1579 0.2014 REMARK 3 5 4.1775 - 3.8790 1.00 2788 145 0.1948 0.2474 REMARK 3 6 3.8790 - 3.6509 1.00 2785 142 0.2083 0.2655 REMARK 3 7 3.6509 - 3.4685 1.00 2794 149 0.2265 0.3117 REMARK 3 8 3.4685 - 3.3178 1.00 2775 145 0.2526 0.2930 REMARK 3 9 3.3178 - 3.1903 0.97 2730 146 0.2799 0.3375 REMARK 3 10 3.1903 - 3.0804 0.86 2385 129 0.3004 0.3199 REMARK 3 11 3.0804 - 2.9842 0.70 1931 104 0.3043 0.3269 REMARK 3 12 2.9842 - 2.8990 0.50 1413 74 0.3190 0.3459 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.440 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 79.83 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 : 0.011 2349 REMARK 3 ANGLE : 1.589 3186 REMARK 3 CHIRALITY : 0.099 366 REMARK 3 PLANARITY : 0.008 407 REMARK 3 DIHEDRAL : 17.636 886 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN A AND RESID -1:99) REMARK 3 ORIGIN FOR THE GROUP (A): -18.6768 74.0092 73.6544 REMARK 3 T TENSOR REMARK 3 T11: 0.3807 T22: 0.4514 REMARK 3 T33: 0.3815 T12: -0.0144 REMARK 3 T13: -0.0006 T23: -0.0016 REMARK 3 L TENSOR REMARK 3 L11: 3.5408 L22: 3.5171 REMARK 3 L33: 3.4585 L12: -2.4305 REMARK 3 L13: 0.6976 L23: -0.2057 REMARK 3 S TENSOR REMARK 3 S11: -0.0971 S12: -0.2920 S13: 0.0494 REMARK 3 S21: 0.0534 S22: 0.2260 S23: -0.0433 REMARK 3 S31: -0.1801 S32: 0.2034 S33: -0.1263 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 100:115) REMARK 3 ORIGIN FOR THE GROUP (A): -3.5500 55.6888 59.8972 REMARK 3 T TENSOR REMARK 3 T11: 0.6564 T22: 0.6113 REMARK 3 T33: 0.5479 T12: -0.0511 REMARK 3 T13: 0.0335 T23: 0.0149 REMARK 3 L TENSOR REMARK 3 L11: 4.5911 L22: 5.4357 REMARK 3 L33: 4.0750 L12: -1.5220 REMARK 3 L13: 1.2814 L23: -0.8046 REMARK 3 S TENSOR REMARK 3 S11: 0.1177 S12: -0.5821 S13: -0.1639 REMARK 3 S21: -0.4703 S22: -0.0845 S23: -0.2824 REMARK 3 S31: -0.4310 S32: 0.5445 S33: 0.0333 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 116:180) REMARK 3 ORIGIN FOR THE GROUP (A): -14.8888 42.4821 54.7934 REMARK 3 T TENSOR REMARK 3 T11: 0.4544 T22: 0.3492 REMARK 3 T33: 0.5126 T12: 0.0054 REMARK 3 T13: -0.0519 T23: -0.0369 REMARK 3 L TENSOR REMARK 3 L11: 2.5429 L22: 3.9936 REMARK 3 L33: 5.1567 L12: 2.6485 REMARK 3 L13: -0.1830 L23: 0.0712 REMARK 3 S TENSOR REMARK 3 S11: 0.0957 S12: 0.2473 S13: -0.1850 REMARK 3 S21: -0.4378 S22: 0.3026 S23: 0.1364 REMARK 3 S31: 0.0656 S32: 0.1374 S33: -0.3593 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 181:276) REMARK 3 ORIGIN FOR THE GROUP (A): -6.3004 51.2419 75.0353 REMARK 3 T TENSOR REMARK 3 T11: 0.4854 T22: 0.7477 REMARK 3 T33: 0.5790 T12: -0.0233 REMARK 3 T13: -0.1008 T23: 0.0252 REMARK 3 L TENSOR REMARK 3 L11: 0.8133 L22: 2.3361 REMARK 3 L33: 2.9308 L12: -0.8186 REMARK 3 L13: -0.6169 L23: 1.0919 REMARK 3 S TENSOR REMARK 3 S11: 0.0673 S12: -0.1173 S13: -0.2194 REMARK 3 S21: 0.0079 S22: 0.0043 S23: 0.1212 REMARK 3 S31: 0.4483 S32: -0.1715 S33: -0.0960 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 277:292) REMARK 3 ORIGIN FOR THE GROUP (A): -6.1839 71.7582 81.8850 REMARK 3 T TENSOR REMARK 3 T11: 0.5491 T22: 0.6661 REMARK 3 T33: 0.6165 T12: 0.0129 REMARK 3 T13: -0.0828 T23: -0.1375 REMARK 3 L TENSOR REMARK 3 L11: 6.5984 L22: 6.5723 REMARK 3 L33: 5.5082 L12: 1.0898 REMARK 3 L13: -1.6484 L23: -0.7852 REMARK 3 S TENSOR REMARK 3 S11: -0.2265 S12: 0.2183 S13: -0.0310 REMARK 3 S21: 0.2231 S22: 0.5930 S23: -0.8698 REMARK 3 S31: -0.3870 S32: 0.3057 S33: -0.3963 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 4IWY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JAN-13. REMARK 100 THE DEPOSITION ID IS D_1000077313. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97921, 0.97934, 0.97471 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18059 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 200 DATA REDUNDANCY : 15.60 REMARK 200 R MERGE (I) : 0.12600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 53.5 REMARK 200 DATA REDUNDANCY IN SHELL : 7.70 REMARK 200 R MERGE FOR SHELL (I) : 0.80300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 79.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES, AND 1.8 M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K, PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 REMARK 290 7555 Y,X,-Z+1/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+2/3 REMARK 290 10555 -Y,-X,-Z+1/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+2/3 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 57.07933 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 114.15867 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 57.07933 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 114.15867 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 57.07933 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 114.15867 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 57.07933 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 114.15867 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 19430 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 42640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -405.0 KCAL/MOL 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -64.51500 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 111.74326 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 114.15867 REMARK 350 BIOMT1 4 0.500000 0.866025 0.000000 -64.51500 REMARK 350 BIOMT2 4 0.866025 -0.500000 0.000000 111.74326 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 114.15867 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 S SO4 A 408 LIES ON A SPECIAL POSITION. 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 A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 GLU A 293 REMARK 465 TYR A 294 REMARK 465 CYS A 295 REMARK 465 LEU A 296 REMARK 465 LYS A 297 REMARK 465 THR A 298 REMARK 465 GLY A 299 REMARK 465 GLY A 300 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 NH1 ARG A 102 OE2 GLU A 402 2.15 REMARK 500 O GLN A 24 N GLY A 26 2.18 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 A 18 CA - CB - CG ANGL. DEV. = 14.7 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 HIS A 0 86.11 41.99 REMARK 500 ILE A 23 -74.87 -63.82 REMARK 500 ARG A 25 39.55 -3.81 REMARK 500 ASN A 42 -132.10 -71.70 REMARK 500 PRO A 43 87.56 -23.87 REMARK 500 ALA A 44 127.80 -13.74 REMARK 500 ALA A 45 -102.14 74.02 REMARK 500 SER A 46 148.71 65.15 REMARK 500 HIS A 57 105.55 77.51 REMARK 500 ILE A 69 20.61 -142.59 REMARK 500 ASN A 89 108.62 70.07 REMARK 500 ASP A 99 92.16 -68.01 REMARK 500 HIS A 121 -57.46 -137.48 REMARK 500 ASP A 124 -20.84 77.49 REMARK 500 VAL A 133 -31.95 74.05 REMARK 500 VAL A 143 -54.03 -133.10 REMARK 500 GLU A 144 94.40 61.68 REMARK 500 THR A 146 80.67 -156.61 REMARK 500 GLN A 147 -76.41 -153.85 REMARK 500 ILE A 149 20.10 -147.49 REMARK 500 ASN A 171 2.61 -53.63 REMARK 500 HIS A 173 -165.57 58.17 REMARK 500 ILE A 174 138.28 -32.64 REMARK 500 GLU A 182 -98.64 -60.59 REMARK 500 ALA A 183 -126.27 46.82 REMARK 500 GLN A 184 71.37 161.36 REMARK 500 ASP A 209 -148.43 36.36 REMARK 500 PHE A 210 -91.92 -111.97 REMARK 500 ARG A 211 -129.27 48.43 REMARK 500 SER A 212 -17.94 151.91 REMARK 500 ASN A 213 141.08 -35.27 REMARK 500 LEU A 214 -64.57 -12.88 REMARK 500 HIS A 289 -31.82 -130.40 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN A 42 PRO A 43 -139.29 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 ADP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GLU A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 405 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 406 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 407 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 408 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4IWX RELATED DB: PDB REMARK 900 SAME PROTEIN, BUT IT IS NATIVE STRUCTURE. DBREF 4IWY A 2 300 UNP P0C0U4 RIMK_ECOLI 2 300 SEQADV 4IWY MSE A -19 UNP P0C0U4 EXPRESSION TAG SEQADV 4IWY GLY A -18 UNP P0C0U4 EXPRESSION TAG SEQADV 4IWY SER A -17 UNP P0C0U4 EXPRESSION TAG SEQADV 4IWY SER A -16 UNP P0C0U4 EXPRESSION TAG SEQADV 4IWY HIS A -15 UNP P0C0U4 EXPRESSION TAG SEQADV 4IWY HIS A -14 UNP P0C0U4 EXPRESSION TAG SEQADV 4IWY HIS A -13 UNP P0C0U4 EXPRESSION TAG SEQADV 4IWY HIS A -12 UNP P0C0U4 EXPRESSION TAG SEQADV 4IWY HIS A -11 UNP P0C0U4 EXPRESSION TAG SEQADV 4IWY HIS A -10 UNP P0C0U4 EXPRESSION TAG SEQADV 4IWY SER A -9 UNP P0C0U4 EXPRESSION TAG SEQADV 4IWY SER A -8 UNP P0C0U4 EXPRESSION TAG SEQADV 4IWY GLY A -7 UNP P0C0U4 EXPRESSION TAG SEQADV 4IWY LEU A -6 UNP P0C0U4 EXPRESSION TAG SEQADV 4IWY VAL A -5 UNP P0C0U4 EXPRESSION TAG SEQADV 4IWY PRO A -4 UNP P0C0U4 EXPRESSION TAG SEQADV 4IWY ARG A -3 UNP P0C0U4 EXPRESSION TAG SEQADV 4IWY GLY A -2 UNP P0C0U4 EXPRESSION TAG SEQADV 4IWY SER A -1 UNP P0C0U4 EXPRESSION TAG SEQADV 4IWY HIS A 0 UNP P0C0U4 EXPRESSION TAG SEQADV 4IWY MSE A 1 UNP P0C0U4 EXPRESSION TAG SEQRES 1 A 320 MSE GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 320 LEU VAL PRO ARG GLY SER HIS MSE LYS ILE ALA ILE LEU SEQRES 3 A 320 SER ARG ASP GLY THR LEU TYR SER CYS LYS ARG LEU ARG SEQRES 4 A 320 GLU ALA ALA ILE GLN ARG GLY HIS LEU VAL GLU ILE LEU SEQRES 5 A 320 ASP PRO LEU SER CYS TYR MSE ASN ILE ASN PRO ALA ALA SEQRES 6 A 320 SER SER ILE HIS TYR LYS GLY ARG LYS LEU PRO HIS PHE SEQRES 7 A 320 ASP ALA VAL ILE PRO ARG ILE GLY THR ALA ILE THR PHE SEQRES 8 A 320 TYR GLY THR ALA ALA LEU ARG GLN PHE GLU MSE LEU GLY SEQRES 9 A 320 SER TYR PRO LEU ASN GLU SER VAL ALA ILE ALA ARG ALA SEQRES 10 A 320 ARG ASP LYS LEU ARG SER MSE GLN LEU LEU ALA ARG GLN SEQRES 11 A 320 GLY ILE ASP LEU PRO VAL THR GLY ILE ALA HIS SER PRO SEQRES 12 A 320 ASP ASP THR SER ASP LEU ILE ASP MSE VAL GLY GLY ALA SEQRES 13 A 320 PRO LEU VAL VAL LYS LEU VAL GLU GLY THR GLN GLY ILE SEQRES 14 A 320 GLY VAL VAL LEU ALA GLU THR ARG GLN ALA ALA GLU SER SEQRES 15 A 320 VAL ILE ASP ALA PHE ARG GLY LEU ASN ALA HIS ILE LEU SEQRES 16 A 320 VAL GLN GLU TYR ILE LYS GLU ALA GLN GLY CYS ASP ILE SEQRES 17 A 320 ARG CYS LEU VAL VAL GLY ASP GLU VAL VAL ALA ALA ILE SEQRES 18 A 320 GLU ARG ARG ALA LYS GLU GLY ASP PHE ARG SER ASN LEU SEQRES 19 A 320 HIS ARG GLY GLY ALA ALA SER VAL ALA SER ILE THR PRO SEQRES 20 A 320 GLN GLU ARG GLU ILE ALA ILE LYS ALA ALA ARG THR MSE SEQRES 21 A 320 ALA LEU ASP VAL ALA GLY VAL ASP ILE LEU ARG ALA ASN SEQRES 22 A 320 ARG GLY PRO LEU VAL MSE GLU VAL ASN ALA SER PRO GLY SEQRES 23 A 320 LEU GLU GLY ILE GLU LYS THR THR GLY ILE ASP ILE ALA SEQRES 24 A 320 GLY LYS MSE ILE ARG TRP ILE GLU ARG HIS ALA THR THR SEQRES 25 A 320 GLU TYR CYS LEU LYS THR GLY GLY MODRES 4IWY MSE A 1 MET SELENOMETHIONINE MODRES 4IWY MSE A 39 MET SELENOMETHIONINE MODRES 4IWY MSE A 82 MET SELENOMETHIONINE MODRES 4IWY MSE A 104 MET SELENOMETHIONINE MODRES 4IWY MSE A 132 MET SELENOMETHIONINE MODRES 4IWY MSE A 240 MET SELENOMETHIONINE MODRES 4IWY MSE A 259 MET SELENOMETHIONINE MODRES 4IWY MSE A 282 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 39 8 HET MSE A 82 8 HET MSE A 104 8 HET MSE A 132 8 HET MSE A 240 8 HET MSE A 259 8 HET MSE A 282 8 HET ADP A 401 27 HET GLU A 402 10 HET SO4 A 403 5 HET SO4 A 404 5 HET SO4 A 405 5 HET SO4 A 406 5 HET SO4 A 407 5 HET SO4 A 408 5 HETNAM MSE SELENOMETHIONINE HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM GLU GLUTAMIC ACID HETNAM SO4 SULFATE ION FORMUL 1 MSE 8(C5 H11 N O2 SE) FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 GLU C5 H9 N O4 FORMUL 4 SO4 6(O4 S 2-) FORMUL 10 HOH *(H2 O) HELIX 1 1 THR A 11 GLN A 24 1 14 HELIX 2 2 ARG A 25 HIS A 27 5 3 HELIX 3 3 ASP A 33 LEU A 35 5 3 HELIX 4 4 ILE A 69 GLY A 84 1 16 HELIX 5 5 GLU A 90 ASP A 99 1 10 HELIX 6 6 ASP A 99 GLN A 110 1 12 HELIX 7 7 ASP A 125 MSE A 132 1 8 HELIX 8 8 THR A 156 GLY A 169 1 14 HELIX 9 9 LEU A 170 HIS A 173 5 4 HELIX 10 10 THR A 226 ALA A 241 1 16 HELIX 11 11 LEU A 267 GLY A 275 1 9 HELIX 12 12 ASP A 277 ALA A 290 1 14 SHEET 1 A 4 LEU A 28 LEU A 32 0 SHEET 2 A 4 LYS A 2 LEU A 6 1 N ILE A 3 O LEU A 28 SHEET 3 A 4 ALA A 60 PRO A 63 1 O ILE A 62 N ALA A 4 SHEET 4 A 4 TYR A 86 PRO A 87 1 O TYR A 86 N VAL A 61 SHEET 1 B 3 CYS A 37 MSE A 39 0 SHEET 2 B 3 ILE A 48 TYR A 50 -1 O HIS A 49 N TYR A 38 SHEET 3 B 3 ARG A 53 LYS A 54 -1 O ARG A 53 N TYR A 50 SHEET 1 C 4 THR A 117 ALA A 120 0 SHEET 2 C 4 LEU A 175 TYR A 179 -1 O GLN A 177 N GLY A 118 SHEET 3 C 4 LEU A 138 LEU A 142 -1 N VAL A 139 O GLU A 178 SHEET 4 C 4 GLY A 150 ALA A 154 -1 O ALA A 154 N LEU A 138 SHEET 1 D 5 ALA A 219 VAL A 222 0 SHEET 2 D 5 GLU A 196 ARG A 204 -1 N GLU A 202 O SER A 221 SHEET 3 D 5 CYS A 186 VAL A 193 -1 N ARG A 189 O ILE A 201 SHEET 4 D 5 VAL A 244 ALA A 252 -1 O ILE A 249 N ILE A 188 SHEET 5 D 5 GLY A 255 ASN A 262 -1 O LEU A 257 N LEU A 250 LINK C HIS A 0 N MSE A 1 1555 1555 1.33 LINK C MSE A 1 N LYS A 2 1555 1555 1.33 LINK C TYR A 38 N MSE A 39 1555 1555 1.33 LINK C MSE A 39 N ASN A 40 1555 1555 1.33 LINK C GLU A 81 N MSE A 82 1555 1555 1.34 LINK C MSE A 82 N LEU A 83 1555 1555 1.33 LINK C SER A 103 N MSE A 104 1555 1555 1.33 LINK C MSE A 104 N GLN A 105 1555 1555 1.33 LINK C ASP A 131 N MSE A 132 1555 1555 1.33 LINK C MSE A 132 N VAL A 133 1555 1555 1.33 LINK C THR A 239 N MSE A 240 1555 1555 1.33 LINK C MSE A 240 N ALA A 241 1555 1555 1.33 LINK C VAL A 258 N MSE A 259 1555 1555 1.32 LINK C MSE A 259 N GLU A 260 1555 1555 1.33 LINK C LYS A 281 N MSE A 282 1555 1555 1.33 LINK C MSE A 282 N ILE A 283 1555 1555 1.33 SITE 1 AC1 15 LYS A 141 GLU A 178 TYR A 179 ILE A 180 SITE 2 AC1 15 LYS A 181 ASP A 187 ARG A 203 PHE A 210 SITE 3 AC1 15 ARG A 211 SER A 212 ASN A 213 ASP A 248 SITE 4 AC1 15 LEU A 250 MSE A 259 GLU A 260 SITE 1 AC2 7 ARG A 78 VAL A 92 ARG A 96 ARG A 102 SITE 2 AC2 7 GLN A 105 LEU A 106 ARG A 109 SITE 1 AC3 6 ARG A 189 LEU A 214 ASN A 262 PRO A 265 SITE 2 AC3 6 GLY A 266 SO4 A 405 SITE 1 AC4 6 THR A 67 ARG A 98 LYS A 100 ASN A 262 SITE 2 AC4 6 ALA A 263 SER A 264 SITE 1 AC5 4 TYR A 13 LEU A 214 GLY A 269 SO4 A 403 SITE 1 AC6 2 LYS A 51 ARG A 53 SITE 1 AC7 3 SER A 46 SER A 47 LYS A 54 SITE 1 AC8 2 ARG A 284 ARG A 288 CRYST1 129.030 129.030 171.238 90.00 90.00 120.00 P 64 2 2 12 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 0.007750 0.004475 0.000000 0.00000 SCALE2 0.000000 0.008949 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005840 0.00000