HEADER TRANSFERASE/ANTIBIOTIC 28-FEB-16 5IGZ TITLE MACROLIDE 2'-PHOSPHOTRANSFERASE TYPE II - COMPLEX WITH GDP AND TITLE 2 SPIRAMYCIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: MACROLIDE 2'-PHOSPHOTRANSFERASE II; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MACROLIDE 2'-PHOSPHOTRANSFERASE II PROTEIN MPHB,MACROLIDE 2- COMPND 5 PHOSPHOTRANSFERASE,MPH(B); COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 STRAIN: BM2506; SOURCE 5 GENE: MPHB, PO103_99; 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 MACROLIDE PHOSPHOTRANSFERASE, KINASE, TRANSFERASE-ANTIBIOTIC COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.M.BERGHUIS,D.H.FONG REVDAT 6 27-SEP-23 5IGZ 1 LINK REVDAT 5 08-JAN-20 5IGZ 1 REMARK REVDAT 4 13-SEP-17 5IGZ 1 REMARK REVDAT 3 17-MAY-17 5IGZ 1 JRNL REVDAT 2 03-MAY-17 5IGZ 1 JRNL REVDAT 1 26-APR-17 5IGZ 0 JRNL AUTH D.H.FONG,D.L.BURK,J.BLANCHET,A.Y.YAN,A.M.BERGHUIS JRNL TITL STRUCTURAL BASIS FOR KINASE-MEDIATED MACROLIDE ANTIBIOTIC JRNL TITL 2 RESISTANCE. JRNL REF STRUCTURE V. 25 750 2017 JRNL REFN ISSN 1878-4186 JRNL PMID 28416110 JRNL DOI 10.1016/J.STR.2017.03.007 REMARK 2 REMARK 2 RESOLUTION. 1.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.7.1_743 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 41494 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.162 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2076 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 44.9179 - 3.9450 1.00 2809 148 0.1630 0.1862 REMARK 3 2 3.9450 - 3.1315 1.00 2687 142 0.1495 0.1766 REMARK 3 3 3.1315 - 2.7357 1.00 2673 140 0.1479 0.1925 REMARK 3 4 2.7357 - 2.4856 1.00 2624 138 0.1512 0.1703 REMARK 3 5 2.4856 - 2.3075 1.00 2634 139 0.1401 0.1838 REMARK 3 6 2.3075 - 2.1714 1.00 2630 139 0.1436 0.1810 REMARK 3 7 2.1714 - 2.0627 1.00 2594 136 0.1508 0.2080 REMARK 3 8 2.0627 - 1.9729 1.00 2598 137 0.1577 0.2217 REMARK 3 9 1.9729 - 1.8969 1.00 2614 137 0.1662 0.1949 REMARK 3 10 1.8969 - 1.8315 1.00 2610 138 0.1698 0.2175 REMARK 3 11 1.8315 - 1.7742 1.00 2582 136 0.1791 0.2174 REMARK 3 12 1.7742 - 1.7235 1.00 2590 136 0.1949 0.2562 REMARK 3 13 1.7235 - 1.6781 1.00 2580 136 0.2119 0.2459 REMARK 3 14 1.6781 - 1.6372 1.00 2600 137 0.2341 0.2549 REMARK 3 15 1.6372 - 1.5999 1.00 2593 137 0.2596 0.3011 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 0.90 REMARK 3 SHRINKAGE RADIUS : 0.77 REMARK 3 K_SOL : 0.41 REMARK 3 B_SOL : 57.07 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.450 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.27570 REMARK 3 B22 (A**2) : -3.31250 REMARK 3 B33 (A**2) : 11.58830 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 : 0.019 2614 REMARK 3 ANGLE : 1.479 3474 REMARK 3 CHIRALITY : 0.082 374 REMARK 3 PLANARITY : 0.008 443 REMARK 3 DIHEDRAL : 14.492 934 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 1:21) REMARK 3 ORIGIN FOR THE GROUP (A): 12.1143 1.3831 -8.4105 REMARK 3 T TENSOR REMARK 3 T11: 0.1759 T22: 0.2165 REMARK 3 T33: 0.2670 T12: 0.0263 REMARK 3 T13: -0.0570 T23: -0.0122 REMARK 3 L TENSOR REMARK 3 L11: 2.7948 L22: 5.0760 REMARK 3 L33: 3.2640 L12: -0.0784 REMARK 3 L13: -0.8409 L23: 1.3418 REMARK 3 S TENSOR REMARK 3 S11: -0.0225 S12: -0.2147 S13: 0.0557 REMARK 3 S21: 0.2438 S22: 0.1819 S23: -0.4681 REMARK 3 S31: 0.2181 S32: 0.2909 S33: -0.1336 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 22:49) REMARK 3 ORIGIN FOR THE GROUP (A): 7.3109 4.4001 -16.0221 REMARK 3 T TENSOR REMARK 3 T11: 0.2028 T22: 0.2036 REMARK 3 T33: 0.1869 T12: -0.0320 REMARK 3 T13: -0.0002 T23: -0.0276 REMARK 3 L TENSOR REMARK 3 L11: 2.1135 L22: 2.6502 REMARK 3 L33: 1.5667 L12: -0.8929 REMARK 3 L13: -0.2867 L23: -0.0334 REMARK 3 S TENSOR REMARK 3 S11: -0.0919 S12: 0.1513 S13: -0.0962 REMARK 3 S21: -0.0923 S22: 0.1432 S23: -0.3015 REMARK 3 S31: 0.2145 S32: 0.0048 S33: -0.0498 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 50:74) REMARK 3 ORIGIN FOR THE GROUP (A): -9.1161 1.7710 -11.2210 REMARK 3 T TENSOR REMARK 3 T11: 0.1703 T22: 0.1669 REMARK 3 T33: 0.1794 T12: -0.0023 REMARK 3 T13: 0.0241 T23: 0.0309 REMARK 3 L TENSOR REMARK 3 L11: 3.2396 L22: 3.4533 REMARK 3 L33: 3.8084 L12: 1.4584 REMARK 3 L13: 1.8625 L23: 2.1892 REMARK 3 S TENSOR REMARK 3 S11: 0.0604 S12: -0.2832 S13: -0.2226 REMARK 3 S21: 0.2590 S22: -0.1123 S23: 0.2679 REMARK 3 S31: 0.1107 S32: -0.2430 S33: 0.0821 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 75:117) REMARK 3 ORIGIN FOR THE GROUP (A): -1.7052 8.5939 -20.9921 REMARK 3 T TENSOR REMARK 3 T11: 0.1586 T22: 0.1968 REMARK 3 T33: 0.1136 T12: -0.0130 REMARK 3 T13: 0.0209 T23: -0.0082 REMARK 3 L TENSOR REMARK 3 L11: 1.9802 L22: 3.0016 REMARK 3 L33: 1.3620 L12: -0.1992 REMARK 3 L13: 0.5634 L23: -0.2954 REMARK 3 S TENSOR REMARK 3 S11: -0.0061 S12: 0.2038 S13: 0.0680 REMARK 3 S21: -0.2739 S22: -0.0859 S23: -0.0561 REMARK 3 S31: 0.0013 S32: 0.1343 S33: 0.0788 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 118:139) REMARK 3 ORIGIN FOR THE GROUP (A): -15.1584 8.6786 -30.8214 REMARK 3 T TENSOR REMARK 3 T11: 0.2815 T22: 0.2834 REMARK 3 T33: 0.1830 T12: -0.0072 REMARK 3 T13: -0.0750 T23: 0.0062 REMARK 3 L TENSOR REMARK 3 L11: 4.1693 L22: 4.9415 REMARK 3 L33: 3.9436 L12: 1.7704 REMARK 3 L13: -1.3255 L23: -1.6784 REMARK 3 S TENSOR REMARK 3 S11: -0.0315 S12: 0.5353 S13: 0.1212 REMARK 3 S21: -0.6309 S22: 0.0637 S23: 0.2661 REMARK 3 S31: 0.0080 S32: 0.0775 S33: -0.0557 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 140:169) REMARK 3 ORIGIN FOR THE GROUP (A): -25.7016 10.5459 -9.2401 REMARK 3 T TENSOR REMARK 3 T11: 0.1476 T22: 0.2211 REMARK 3 T33: 0.3688 T12: -0.0188 REMARK 3 T13: 0.0444 T23: 0.0124 REMARK 3 L TENSOR REMARK 3 L11: 1.0759 L22: 3.8453 REMARK 3 L33: 1.7701 L12: 0.5347 REMARK 3 L13: 0.2073 L23: 2.0198 REMARK 3 S TENSOR REMARK 3 S11: -0.0205 S12: -0.1814 S13: -0.1482 REMARK 3 S21: 0.1996 S22: -0.1108 S23: 0.6371 REMARK 3 S31: 0.1262 S32: -0.1905 S33: 0.1014 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 170:280) REMARK 3 ORIGIN FOR THE GROUP (A): -20.1646 16.5237 -21.3774 REMARK 3 T TENSOR REMARK 3 T11: 0.1609 T22: 0.1581 REMARK 3 T33: 0.2277 T12: -0.0072 REMARK 3 T13: -0.0654 T23: 0.0066 REMARK 3 L TENSOR REMARK 3 L11: 1.1588 L22: 1.5910 REMARK 3 L33: 1.1362 L12: 0.0182 REMARK 3 L13: 0.1208 L23: 0.0770 REMARK 3 S TENSOR REMARK 3 S11: -0.0575 S12: 0.1820 S13: 0.1095 REMARK 3 S21: -0.2627 S22: -0.0187 S23: 0.4758 REMARK 3 S31: -0.0934 S32: -0.1249 S33: 0.0521 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 281:299) REMARK 3 ORIGIN FOR THE GROUP (A): -10.1050 25.3015 -4.7899 REMARK 3 T TENSOR REMARK 3 T11: 0.2486 T22: 0.1960 REMARK 3 T33: 0.2177 T12: -0.0165 REMARK 3 T13: 0.0179 T23: -0.0483 REMARK 3 L TENSOR REMARK 3 L11: 4.2128 L22: 5.6866 REMARK 3 L33: 2.9447 L12: -1.3421 REMARK 3 L13: -0.0974 L23: -0.7215 REMARK 3 S TENSOR REMARK 3 S11: -0.1352 S12: -0.2904 S13: 0.4196 REMARK 3 S21: 0.5175 S22: 0.1291 S23: 0.1814 REMARK 3 S31: -0.1849 S32: 0.1765 S33: 0.0303 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 5IGZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000218813. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-FEB-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08ID-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : DCM REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41503 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 44.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.5900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.67500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.030 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 5IGV REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CALCIUM ACETATE, 0.1M TRIS, 25 REMARK 280 -40% PEG 4000, PH 7.5, VAPOR DIFFUSION, TEMPERATURE 295K 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 27.62000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.54000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 36.21500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.54000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.62000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 36.21500 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 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 TOTAL BURIED SURFACE AREA: 2600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 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 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 GLN A 300 REMARK 465 GLY A 301 REMARK 465 SER A 302 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET A 1 CG SD CE 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 HZ2 LYS A 93 O HOH A 502 1.25 REMARK 500 O HOH A 525 O HOH A 723 1.90 REMARK 500 O HOH A 719 O HOH A 819 1.94 REMARK 500 O HOH A 501 O HOH A 775 1.95 REMARK 500 O HOH A 763 O HOH A 799 1.96 REMARK 500 OE1 GLU A 153 O HOH A 501 2.02 REMARK 500 O HOH A 505 O HOH A 789 2.02 REMARK 500 NZ LYS A 93 O HOH A 502 2.03 REMARK 500 O HOH A 635 O HOH A 722 2.05 REMARK 500 OE1 GLU A 88 O HOH A 503 2.09 REMARK 500 O HOH A 502 O HOH A 813 2.10 REMARK 500 O HOH A 739 O HOH A 869 2.16 REMARK 500 O HOH A 755 O HOH A 877 2.19 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 O HOH A 535 O HOH A 640 3544 2.04 REMARK 500 O HOH A 537 O HOH A 612 3554 2.10 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 ASN A 118 88.46 -168.20 REMARK 500 ASP A 200 52.28 -149.91 REMARK 500 ASP A 219 86.58 65.69 REMARK 500 THR A 226 -164.92 -164.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 884 DISTANCE = 6.03 ANGSTROMS REMARK 525 HOH A 885 DISTANCE = 6.55 ANGSTROMS 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 ASP A 219 OD1 REMARK 620 2 ASP A 219 OD2 51.3 REMARK 620 3 GDP A 401 O3B 94.5 71.0 REMARK 620 4 HOH A 555 O 79.2 79.1 145.7 REMARK 620 5 HOH A 723 O 132.8 82.9 78.3 81.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 403 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 219 OD2 REMARK 620 2 GDP A 401 O1B 86.7 REMARK 620 3 GDP A 401 O1A 93.0 89.4 REMARK 620 4 HOH A 647 O 176.4 94.5 90.3 REMARK 620 5 HOH A 679 O 89.1 85.6 174.5 87.6 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GDP 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 MG A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SPR A 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5IGU RELATED DB: PDB REMARK 900 RELATED ID: 5IGV RELATED DB: PDB REMARK 900 RELATED ID: 5IGW RELATED DB: PDB REMARK 900 RELATED ID: 5IGY RELATED DB: PDB REMARK 900 RELATED ID: 5IH0 RELATED DB: PDB REMARK 900 RELATED ID: 5IH1 RELATED DB: PDB DBREF 5IGZ A 1 302 UNP O32553 O32553_ECOLX 1 302 SEQRES 1 A 302 MET SER LYS ASP ILE LYS GLN VAL ILE GLU ILE ALA LYS SEQRES 2 A 302 LYS HIS ASN LEU PHE LEU LYS GLU GLU THR ILE GLN PHE SEQRES 3 A 302 ASN GLU SER GLY LEU ASP PHE GLN ALA VAL PHE ALA GLN SEQRES 4 A 302 ASP ASN ASN GLY ILE ASP TRP VAL LEU ARG LEU PRO ARG SEQRES 5 A 302 ARG GLU ASP VAL MET PRO ARG THR LYS VAL GLU LYS GLN SEQRES 6 A 302 ALA LEU ASP LEU VAL ASN LYS TYR ALA ILE SER PHE GLN SEQRES 7 A 302 ALA PRO ASN TRP ILE ILE TYR THR GLU GLU LEU ILE ALA SEQRES 8 A 302 TYR LYS LYS LEU ASP GLY VAL PRO ALA GLY THR ILE ASP SEQRES 9 A 302 HIS ASN ILE GLY ASN TYR ILE TRP GLU ILE ASP ILE ASN SEQRES 10 A 302 ASN VAL PRO GLU LEU PHE HIS LYS SER LEU GLY ARG VAL SEQRES 11 A 302 LEU ALA GLU LEU HIS SER ILE PRO SER ASN LYS ALA ALA SEQRES 12 A 302 ALA LEU ASP LEU VAL VAL HIS THR PRO GLU GLU ALA ARG SEQRES 13 A 302 MET SER MET LYS GLN ARG MET ASP ALA VAL ARG ALA LYS SEQRES 14 A 302 PHE GLY VAL GLY GLU ASN LEU TRP ASN ARG TRP GLN ALA SEQRES 15 A 302 TRP LEU ASN ASP ASP ASP MET TRP PRO LYS LYS THR GLY SEQRES 16 A 302 LEU ILE HIS GLY ASP VAL HIS ALA GLY HIS THR MET ILE SEQRES 17 A 302 ASP LYS ASP ALA ASN VAL THR GLY LEU ILE ASP TRP THR SEQRES 18 A 302 GLU ALA LYS VAL THR ASP VAL SER HIS ASP PHE ILE PHE SEQRES 19 A 302 ASN TYR ARG ALA PHE GLY GLU GLU GLY LEU GLU ALA LEU SEQRES 20 A 302 ILE LEU ALA TYR LYS GLU ILE GLY GLY TYR TYR TRP PRO SEQRES 21 A 302 LYS MET LYS GLU HIS ILE ILE GLU LEU ASN ALA ALA TYR SEQRES 22 A 302 PRO VAL SER ILE ALA GLU PHE ALA LEU VAL SER GLY ILE SEQRES 23 A 302 GLU GLU TYR GLU GLN MET ALA LYS GLU ALA LEU GLU VAL SEQRES 24 A 302 GLN GLY SER HET GDP A 401 40 HET MG A 402 1 HET MG A 403 1 HET SPR A 404 132 HETNAM GDP GUANOSINE-5'-DIPHOSPHATE HETNAM MG MAGNESIUM ION HETNAM SPR SPIRAMYCIN I FORMUL 2 GDP C10 H15 N5 O11 P2 FORMUL 3 MG 2(MG 2+) FORMUL 5 SPR C43 H74 N2 O14 FORMUL 6 HOH *385(H2 O) HELIX 1 AA1 ASP A 4 HIS A 15 1 12 HELIX 2 AA2 LYS A 20 ILE A 24 5 5 HELIX 3 AA3 VAL A 56 PRO A 58 5 3 HELIX 4 AA4 ARG A 59 ALA A 74 1 16 HELIX 5 AA5 PRO A 120 SER A 136 1 17 HELIX 6 AA6 PRO A 138 ALA A 144 1 7 HELIX 7 AA7 THR A 151 GLY A 171 1 21 HELIX 8 AA8 GLY A 173 ASN A 185 1 13 HELIX 9 AA9 ASP A 186 TRP A 190 5 5 HELIX 10 AB1 ASP A 227 ASP A 231 5 5 HELIX 11 AB2 PHE A 232 GLY A 255 1 24 HELIX 12 AB3 LYS A 261 ALA A 272 1 12 HELIX 13 AB4 ALA A 272 GLY A 285 1 14 HELIX 14 AB5 ILE A 286 LEU A 297 1 12 SHEET 1 AA1 5 GLN A 25 ASN A 27 0 SHEET 2 AA1 5 PHE A 33 GLN A 39 -1 O ALA A 35 N ASN A 27 SHEET 3 AA1 5 ASP A 45 PRO A 51 -1 O TRP A 46 N ALA A 38 SHEET 4 AA1 5 ILE A 90 TYR A 92 -1 O ILE A 90 N ARG A 49 SHEET 5 AA1 5 ILE A 84 TYR A 85 -1 N ILE A 84 O ALA A 91 SHEET 1 AA2 3 VAL A 98 PRO A 99 0 SHEET 2 AA2 3 THR A 206 ILE A 208 -1 O ILE A 208 N VAL A 98 SHEET 3 AA2 3 VAL A 214 LEU A 217 -1 O THR A 215 N MET A 207 SHEET 1 AA3 2 GLY A 101 ILE A 103 0 SHEET 2 AA3 2 TYR A 110 TRP A 112 -1 O ILE A 111 N THR A 102 SHEET 1 AA4 2 GLY A 195 ILE A 197 0 SHEET 2 AA4 2 LYS A 224 THR A 226 -1 O LYS A 224 N ILE A 197 LINK OD1 ASP A 219 MG MG A 402 1555 1555 2.31 LINK OD2 ASP A 219 MG MG A 402 1555 1555 2.65 LINK OD2 ASP A 219 MG MG A 403 1555 1555 2.14 LINK O3B GDP A 401 MG MG A 402 1555 1555 2.27 LINK O1B GDP A 401 MG MG A 403 1555 1555 2.04 LINK O1A GDP A 401 MG MG A 403 1555 1555 2.02 LINK MG MG A 402 O HOH A 555 1555 1555 2.31 LINK MG MG A 402 O HOH A 723 1555 1555 2.64 LINK MG MG A 403 O HOH A 647 1555 1555 2.17 LINK MG MG A 403 O HOH A 679 1555 1555 2.17 SITE 1 AC1 26 ASN A 27 SER A 29 GLY A 30 LEU A 31 SITE 2 AC1 26 ASP A 32 PHE A 33 ALA A 35 PHE A 37 SITE 3 AC1 26 ARG A 49 TYR A 92 LYS A 94 LEU A 95 SITE 4 AC1 26 PRO A 99 HIS A 205 MET A 207 ILE A 218 SITE 5 AC1 26 ASP A 219 MG A 402 MG A 403 HOH A 541 SITE 6 AC1 26 HOH A 575 HOH A 579 HOH A 624 HOH A 647 SITE 7 AC1 26 HOH A 679 HOH A 690 SITE 1 AC2 6 ASP A 32 ASP A 219 THR A 221 GDP A 401 SITE 2 AC2 6 HOH A 555 HOH A 723 SITE 1 AC3 5 HIS A 205 ASP A 219 GDP A 401 HOH A 647 SITE 2 AC3 5 HOH A 679 SITE 1 AC4 24 ARG A 59 GLY A 108 TYR A 110 ASP A 200 SITE 2 AC4 24 HIS A 202 GLU A 222 PHE A 234 ARG A 237 SITE 3 AC4 24 TYR A 273 SER A 276 GLU A 279 PHE A 280 SITE 4 AC4 24 GLU A 288 TYR A 289 MET A 292 HOH A 523 SITE 5 AC4 24 HOH A 525 HOH A 557 HOH A 630 HOH A 666 SITE 6 AC4 24 HOH A 668 HOH A 679 HOH A 704 HOH A 723 CRYST1 55.240 72.430 77.080 90.00 90.00 90.00 P 21 21 21 4 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 0.018103 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013806 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012974 0.00000