HEADER TRANSFERASE 11-FEB-23 8CIZ TITLE DNA-POLYMERASE SLIDING CLAMP (DNAN) FROM ESCHERICHIA COLI IN COMPLEX TITLE 2 WITH MYCOPLANECIN A. COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA SLIDING CLAMP; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: BETA CLAMP,SLIDING CLAMP,BETA-CLAMP PROCESSIVITY FACTOR,DNA COMPND 5 POLYMERASE III BETA SLIDING CLAMP SUBUNIT; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: MYCOPLANECIN A; COMPND 9 CHAIN: C, D; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: DNAN, B3701, JW3678; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 MOL_ID: 2; SOURCE 8 SYNTHETIC: YES; SOURCE 9 ORGANISM_SCIENTIFIC: ACTINOPLANES AWAJINENSIS SUBSP. MYCOPLANECINUS; SOURCE 10 ORGANISM_TAXID: 135947 KEYWDS DNAN, SLIDING CLAMP, DNA-POLYMERASE BETA SUBUNIT, ANTIBIOTIC, NATURAL KEYWDS 2 PRODUCT, ANTI-TUBERCULOSIS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.FU,Y.LIU,C.WALT,C.BADER,S.RASHEED,P.LUKAT,M.NEUBER,W.BLANKENFELDT, AUTHOR 2 O.KALININA,R.MUELLER REVDAT 2 07-FEB-24 8CIZ 1 JRNL REVDAT 1 29-NOV-23 8CIZ 0 JRNL AUTH C.FU,Y.LIU,C.WALT,S.RASHEED,C.D.BADER,P.LUKAT,M.NEUBER, JRNL AUTH 2 F.P.J.HAECKL,W.BLANKENFELDT,O.V.KALININA,R.MULLER JRNL TITL ELUCIDATION OF UNUSUAL BIOSYNTHESIS AND DNAN-TARGETING MODE JRNL TITL 2 OF ACTION OF POTENT ANTI-TUBERCULOSIS ANTIBIOTICS JRNL TITL 3 MYCOPLANECINS. JRNL REF NAT COMMUN V. 15 791 2024 JRNL REFN ESSN 2041-1723 JRNL PMID 38278788 JRNL DOI 10.1038/S41467-024-44953-5 REMARK 2 REMARK 2 RESOLUTION. 2.27 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.201-4487 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) : 2.27 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.28 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 39787 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.207 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1961 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 51.2800 - 5.4600 0.98 2735 130 0.1796 0.2308 REMARK 3 2 5.4600 - 4.3400 1.00 2739 139 0.1575 0.1629 REMARK 3 3 4.3400 - 3.7900 1.00 2721 145 0.1778 0.1854 REMARK 3 4 3.7900 - 3.4400 0.99 2704 142 0.2146 0.2528 REMARK 3 5 3.4400 - 3.1900 0.98 2665 130 0.2311 0.2701 REMARK 3 6 3.1900 - 3.0100 0.99 2718 145 0.2580 0.2884 REMARK 3 7 3.0100 - 2.8600 0.99 2699 146 0.2562 0.3037 REMARK 3 8 2.8600 - 2.7300 0.99 2729 140 0.2555 0.3050 REMARK 3 9 2.7300 - 2.6300 0.99 2699 129 0.2627 0.3077 REMARK 3 10 2.6300 - 2.5400 1.00 2725 145 0.2696 0.3138 REMARK 3 11 2.5400 - 2.4600 1.00 2681 153 0.2717 0.3576 REMARK 3 12 2.4600 - 2.3900 0.97 2637 147 0.2700 0.3147 REMARK 3 13 2.3900 - 2.3200 0.99 2669 139 0.2831 0.2797 REMARK 3 14 2.3200 - 2.2700 0.99 2705 131 0.2813 0.3229 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 : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.660 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.003 5948 REMARK 3 ANGLE : 0.586 8079 REMARK 3 CHIRALITY : 0.043 931 REMARK 3 PLANARITY : 0.004 1070 REMARK 3 DIHEDRAL : 7.254 914 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 9 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -1 THROUGH 47 ) REMARK 3 ORIGIN FOR THE GROUP (A): -21.1776 -7.4407 19.7744 REMARK 3 T TENSOR REMARK 3 T11: 0.5623 T22: 0.6561 REMARK 3 T33: 0.5877 T12: -0.0589 REMARK 3 T13: -0.0617 T23: 0.0789 REMARK 3 L TENSOR REMARK 3 L11: 0.6902 L22: 2.2060 REMARK 3 L33: 1.8614 L12: -0.9545 REMARK 3 L13: 0.1356 L23: 0.6762 REMARK 3 S TENSOR REMARK 3 S11: 0.1903 S12: -0.2530 S13: -0.1347 REMARK 3 S21: 0.3561 S22: -0.0470 S23: 0.0846 REMARK 3 S31: 0.1807 S32: 0.1310 S33: -0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 48 THROUGH 101 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.3611 -4.2404 19.8550 REMARK 3 T TENSOR REMARK 3 T11: 0.5187 T22: 0.6246 REMARK 3 T33: 0.4997 T12: -0.1042 REMARK 3 T13: -0.0661 T23: 0.0802 REMARK 3 L TENSOR REMARK 3 L11: 1.0468 L22: 2.3165 REMARK 3 L33: 0.9853 L12: -0.6684 REMARK 3 L13: -0.0351 L23: 0.0965 REMARK 3 S TENSOR REMARK 3 S11: 0.1997 S12: 0.0140 S13: -0.4407 REMARK 3 S21: 0.1685 S22: -0.2275 S23: 0.2993 REMARK 3 S31: -0.0018 S32: 0.1679 S33: 0.0002 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 102 THROUGH 140 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.0397 -12.2265 18.3595 REMARK 3 T TENSOR REMARK 3 T11: 0.6800 T22: 0.5918 REMARK 3 T33: 0.6179 T12: -0.0738 REMARK 3 T13: -0.1370 T23: 0.0256 REMARK 3 L TENSOR REMARK 3 L11: 1.9304 L22: 0.5216 REMARK 3 L33: 0.0648 L12: 0.0521 REMARK 3 L13: -0.0622 L23: -0.1788 REMARK 3 S TENSOR REMARK 3 S11: 0.3419 S12: -0.0472 S13: -0.5439 REMARK 3 S21: -0.1631 S22: -0.1076 S23: -0.0342 REMARK 3 S31: 0.0885 S32: 0.0483 S33: 0.0001 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 141 THROUGH 235 ) REMARK 3 ORIGIN FOR THE GROUP (A): 4.1354 -14.2179 17.9274 REMARK 3 T TENSOR REMARK 3 T11: 0.5322 T22: 0.5192 REMARK 3 T33: 0.6251 T12: -0.0317 REMARK 3 T13: -0.1538 T23: -0.0344 REMARK 3 L TENSOR REMARK 3 L11: 3.9076 L22: 2.2472 REMARK 3 L33: 1.4453 L12: 1.2088 REMARK 3 L13: -0.3202 L23: -0.3068 REMARK 3 S TENSOR REMARK 3 S11: 0.3600 S12: -0.0675 S13: -0.3244 REMARK 3 S21: -0.1416 S22: -0.1485 S23: 0.1522 REMARK 3 S31: 0.0044 S32: -0.1480 S33: 0.0012 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 236 THROUGH 346 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.3236 0.4824 17.1968 REMARK 3 T TENSOR REMARK 3 T11: 0.4601 T22: 0.5002 REMARK 3 T33: 0.4309 T12: -0.0594 REMARK 3 T13: 0.0095 T23: -0.0375 REMARK 3 L TENSOR REMARK 3 L11: 2.5438 L22: 1.3894 REMARK 3 L33: 1.4908 L12: 0.2467 REMARK 3 L13: 0.5309 L23: 0.6527 REMARK 3 S TENSOR REMARK 3 S11: 0.1166 S12: -0.0093 S13: -0.2441 REMARK 3 S21: -0.0585 S22: -0.0542 S23: -0.1581 REMARK 3 S31: -0.0642 S32: 0.1230 S33: 0.0000 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 347 THROUGH 366 ) REMARK 3 ORIGIN FOR THE GROUP (A): 24.5438 -6.3709 18.1908 REMARK 3 T TENSOR REMARK 3 T11: 0.4521 T22: 0.5788 REMARK 3 T33: 0.4721 T12: -0.0857 REMARK 3 T13: -0.1063 T23: -0.0819 REMARK 3 L TENSOR REMARK 3 L11: 1.3693 L22: 1.5705 REMARK 3 L33: 0.9049 L12: -0.6759 REMARK 3 L13: 0.4277 L23: 0.7680 REMARK 3 S TENSOR REMARK 3 S11: 0.5265 S12: -0.4290 S13: -0.2811 REMARK 3 S21: 0.0311 S22: 0.1185 S23: 0.0954 REMARK 3 S31: 0.1690 S32: 0.6839 S33: 0.0002 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID -1 THROUGH 109 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.4443 29.6017 19.9082 REMARK 3 T TENSOR REMARK 3 T11: 0.6156 T22: 0.5573 REMARK 3 T33: 0.5416 T12: -0.1034 REMARK 3 T13: 0.0535 T23: -0.1012 REMARK 3 L TENSOR REMARK 3 L11: 1.7797 L22: 3.1479 REMARK 3 L33: 1.1555 L12: -0.9983 REMARK 3 L13: 0.1692 L23: -0.5748 REMARK 3 S TENSOR REMARK 3 S11: 0.1711 S12: -0.1708 S13: 0.2841 REMARK 3 S21: 0.1240 S22: -0.0821 S23: 0.0202 REMARK 3 S31: -0.1852 S32: -0.1056 S33: 0.0001 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 110 THROUGH 140 ) REMARK 3 ORIGIN FOR THE GROUP (A): 5.8475 41.6760 18.2367 REMARK 3 T TENSOR REMARK 3 T11: 0.7554 T22: 0.5968 REMARK 3 T33: 0.7432 T12: -0.0578 REMARK 3 T13: 0.1964 T23: 0.0261 REMARK 3 L TENSOR REMARK 3 L11: 0.4922 L22: 0.2924 REMARK 3 L33: 0.2693 L12: -0.0912 REMARK 3 L13: 0.1080 L23: 0.2444 REMARK 3 S TENSOR REMARK 3 S11: 0.2286 S12: -0.1358 S13: 0.6508 REMARK 3 S21: -0.1924 S22: -0.0593 S23: -0.1005 REMARK 3 S31: -0.0702 S32: 0.1114 S33: -0.0000 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 141 THROUGH 365 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.4622 31.0642 17.6426 REMARK 3 T TENSOR REMARK 3 T11: 0.5835 T22: 0.5323 REMARK 3 T33: 0.5460 T12: -0.0281 REMARK 3 T13: 0.0714 T23: 0.0434 REMARK 3 L TENSOR REMARK 3 L11: 3.2457 L22: 2.4503 REMARK 3 L33: 0.5366 L12: 1.8160 REMARK 3 L13: 0.0429 L23: 0.2746 REMARK 3 S TENSOR REMARK 3 S11: 0.1984 S12: -0.0814 S13: 0.4602 REMARK 3 S21: 0.0463 S22: -0.0546 S23: 0.2490 REMARK 3 S31: -0.0900 S32: -0.1070 S33: 0.0001 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 8CIZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1292128617. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-FEB-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, DESY REMARK 200 BEAMLINE : P11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.033202 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39802 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.270 REMARK 200 RESOLUTION RANGE LOW (A) : 75.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.11500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.27 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.39 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.66000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL 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 (%): 51.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.53 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M CACL2 0.15 M MGCL2 8.75 % (V/V) REMARK 280 GLYCEROL 17.5 % (W/V) PEG 3350 0.1 M TRIS/HCL PH 9.0 REMARK 280 CRYOPROTECTION: 10 % (V/V) (2R,3R)-2,3-BUTANEDIOL., VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 41.96850 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 75.02500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 41.96850 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 75.02500 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 400 REMARK 400 COMPOUND REMARK 400 ANTIMYCOBACTERIAL REMARK 400 REMARK 400 THE MYCOPLANECIN A IS PEPTIDE-LIKE, A MEMBER OF ANTIMICROBIAL CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: MYCOPLANECIN A REMARK 400 CHAIN: C, D REMARK 400 COMPONENT_1: PEPTIDE LIKE POLYMER REMARK 400 DESCRIPTION: NULL 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 GLY A -2 REMARK 465 LEU A 21 REMARK 465 GLY A 22 REMARK 465 GLY A 23 REMARK 465 ARG A 24 REMARK 465 GLY B -2 REMARK 465 LEU B 21 REMARK 465 GLY B 22 REMARK 465 GLY B 23 REMARK 465 ARG B 24 REMARK 465 GLY B 209 REMARK 465 LEU B 366 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 LEU A 27 CG CD1 CD2 REMARK 470 VAL A 151 CG1 CG2 REMARK 470 ARG A 152 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 153 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASP A 211 CG OD1 OD2 REMARK 470 GLU A 334 CG CD OE1 OE2 REMARK 470 LYS B 235 CG CD CE NZ REMARK 470 ARG B 246 CG CD NE CZ NH1 NH2 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 OE1 GLN A 355 O HOH A 401 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 ALA A 38 126.90 -172.53 REMARK 500 ALA A 38 126.25 -172.53 REMARK 500 ASP A 48 27.15 -140.61 REMARK 500 LEU A 49 -18.11 76.71 REMARK 500 ARG A 152 96.28 -69.11 REMARK 500 SER A 220 -66.84 70.78 REMARK 500 ASP A 229 33.83 -91.20 REMARK 500 THR A 341 -57.14 -120.99 REMARK 500 THR B 26 -126.72 -113.49 REMARK 500 LEU B 49 -22.38 85.51 REMARK 500 SER B 101 114.42 -160.03 REMARK 500 TYR B 153 -39.66 -32.07 REMARK 500 GLU B 287 109.87 -51.78 REMARK 500 THR B 341 -63.03 -126.64 REMARK 500 SER B 354 117.53 -164.47 REMARK 500 REMARK 500 REMARK: NULL DBREF 8CIZ A 1 366 UNP P0A988 DPO3B_ECOLI 1 366 DBREF 8CIZ B 1 366 UNP P0A988 DPO3B_ECOLI 1 366 DBREF 8CIZ C 1 11 PDB 8CIZ 8CIZ 1 11 DBREF 8CIZ D 1 11 PDB 8CIZ 8CIZ 1 11 SEQADV 8CIZ GLY A -2 UNP P0A988 EXPRESSION TAG SEQADV 8CIZ GLY A -1 UNP P0A988 EXPRESSION TAG SEQADV 8CIZ ARG A 0 UNP P0A988 EXPRESSION TAG SEQADV 8CIZ GLY B -2 UNP P0A988 EXPRESSION TAG SEQADV 8CIZ GLY B -1 UNP P0A988 EXPRESSION TAG SEQADV 8CIZ ARG B 0 UNP P0A988 EXPRESSION TAG SEQRES 1 A 369 GLY GLY ARG MET LYS PHE THR VAL GLU ARG GLU HIS LEU SEQRES 2 A 369 LEU LYS PRO LEU GLN GLN VAL SER GLY PRO LEU GLY GLY SEQRES 3 A 369 ARG PRO THR LEU PRO ILE LEU GLY ASN LEU LEU LEU GLN SEQRES 4 A 369 VAL ALA ASP GLY THR LEU SER LEU THR GLY THR ASP LEU SEQRES 5 A 369 GLU MET GLU MET VAL ALA ARG VAL ALA LEU VAL GLN PRO SEQRES 6 A 369 HIS GLU PRO GLY ALA THR THR VAL PRO ALA ARG LYS PHE SEQRES 7 A 369 PHE ASP ILE CYS ARG GLY LEU PRO GLU GLY ALA GLU ILE SEQRES 8 A 369 ALA VAL GLN LEU GLU GLY GLU ARG MET LEU VAL ARG SER SEQRES 9 A 369 GLY ARG SER ARG PHE SER LEU SER THR LEU PRO ALA ALA SEQRES 10 A 369 ASP PHE PRO ASN LEU ASP ASP TRP GLN SER GLU VAL GLU SEQRES 11 A 369 PHE THR LEU PRO GLN ALA THR MET LYS ARG LEU ILE GLU SEQRES 12 A 369 ALA THR GLN PHE SER MET ALA HIS GLN ASP VAL ARG TYR SEQRES 13 A 369 TYR LEU ASN GLY MET LEU PHE GLU THR GLU GLY GLU GLU SEQRES 14 A 369 LEU ARG THR VAL ALA THR ASP GLY HIS ARG LEU ALA VAL SEQRES 15 A 369 CYS SER MET PRO ILE GLY GLN SER LEU PRO SER HIS SER SEQRES 16 A 369 VAL ILE VAL PRO ARG LYS GLY VAL ILE GLU LEU MET ARG SEQRES 17 A 369 MET LEU ASP GLY GLY ASP ASN PRO LEU ARG VAL GLN ILE SEQRES 18 A 369 GLY SER ASN ASN ILE ARG ALA HIS VAL GLY ASP PHE ILE SEQRES 19 A 369 PHE THR SER LYS LEU VAL ASP GLY ARG PHE PRO ASP TYR SEQRES 20 A 369 ARG ARG VAL LEU PRO LYS ASN PRO ASP LYS HIS LEU GLU SEQRES 21 A 369 ALA GLY CYS ASP LEU LEU LYS GLN ALA PHE ALA ARG ALA SEQRES 22 A 369 ALA ILE LEU SER ASN GLU LYS PHE ARG GLY VAL ARG LEU SEQRES 23 A 369 TYR VAL SER GLU ASN GLN LEU LYS ILE THR ALA ASN ASN SEQRES 24 A 369 PRO GLU GLN GLU GLU ALA GLU GLU ILE LEU ASP VAL THR SEQRES 25 A 369 TYR SER GLY ALA GLU MET GLU ILE GLY PHE ASN VAL SER SEQRES 26 A 369 TYR VAL LEU ASP VAL LEU ASN ALA LEU LYS CYS GLU ASN SEQRES 27 A 369 VAL ARG MET MET LEU THR ASP SER VAL SER SER VAL GLN SEQRES 28 A 369 ILE GLU ASP ALA ALA SER GLN SER ALA ALA TYR VAL VAL SEQRES 29 A 369 MET PRO MET ARG LEU SEQRES 1 B 369 GLY GLY ARG MET LYS PHE THR VAL GLU ARG GLU HIS LEU SEQRES 2 B 369 LEU LYS PRO LEU GLN GLN VAL SER GLY PRO LEU GLY GLY SEQRES 3 B 369 ARG PRO THR LEU PRO ILE LEU GLY ASN LEU LEU LEU GLN SEQRES 4 B 369 VAL ALA ASP GLY THR LEU SER LEU THR GLY THR ASP LEU SEQRES 5 B 369 GLU MET GLU MET VAL ALA ARG VAL ALA LEU VAL GLN PRO SEQRES 6 B 369 HIS GLU PRO GLY ALA THR THR VAL PRO ALA ARG LYS PHE SEQRES 7 B 369 PHE ASP ILE CYS ARG GLY LEU PRO GLU GLY ALA GLU ILE SEQRES 8 B 369 ALA VAL GLN LEU GLU GLY GLU ARG MET LEU VAL ARG SER SEQRES 9 B 369 GLY ARG SER ARG PHE SER LEU SER THR LEU PRO ALA ALA SEQRES 10 B 369 ASP PHE PRO ASN LEU ASP ASP TRP GLN SER GLU VAL GLU SEQRES 11 B 369 PHE THR LEU PRO GLN ALA THR MET LYS ARG LEU ILE GLU SEQRES 12 B 369 ALA THR GLN PHE SER MET ALA HIS GLN ASP VAL ARG TYR SEQRES 13 B 369 TYR LEU ASN GLY MET LEU PHE GLU THR GLU GLY GLU GLU SEQRES 14 B 369 LEU ARG THR VAL ALA THR ASP GLY HIS ARG LEU ALA VAL SEQRES 15 B 369 CYS SER MET PRO ILE GLY GLN SER LEU PRO SER HIS SER SEQRES 16 B 369 VAL ILE VAL PRO ARG LYS GLY VAL ILE GLU LEU MET ARG SEQRES 17 B 369 MET LEU ASP GLY GLY ASP ASN PRO LEU ARG VAL GLN ILE SEQRES 18 B 369 GLY SER ASN ASN ILE ARG ALA HIS VAL GLY ASP PHE ILE SEQRES 19 B 369 PHE THR SER LYS LEU VAL ASP GLY ARG PHE PRO ASP TYR SEQRES 20 B 369 ARG ARG VAL LEU PRO LYS ASN PRO ASP LYS HIS LEU GLU SEQRES 21 B 369 ALA GLY CYS ASP LEU LEU LYS GLN ALA PHE ALA ARG ALA SEQRES 22 B 369 ALA ILE LEU SER ASN GLU LYS PHE ARG GLY VAL ARG LEU SEQRES 23 B 369 TYR VAL SER GLU ASN GLN LEU LYS ILE THR ALA ASN ASN SEQRES 24 B 369 PRO GLU GLN GLU GLU ALA GLU GLU ILE LEU ASP VAL THR SEQRES 25 B 369 TYR SER GLY ALA GLU MET GLU ILE GLY PHE ASN VAL SER SEQRES 26 B 369 TYR VAL LEU ASP VAL LEU ASN ALA LEU LYS CYS GLU ASN SEQRES 27 B 369 VAL ARG MET MET LEU THR ASP SER VAL SER SER VAL GLN SEQRES 28 B 369 ILE GLU ASP ALA ALA SER GLN SER ALA ALA TYR VAL VAL SEQRES 29 B 369 MET PRO MET ARG LEU SEQRES 1 C 11 2KT MVA V3C NZC LEU MP8 HLX MVA PRO MLU GLY SEQRES 1 D 11 2KT MVA V3C NZC LEU MP8 HLX MVA PRO MLU GLY HET 2KT C 1 11 HET MVA C 2 19 HET V3C C 3 20 HET NZC C 4 16 HET MP8 C 6 17 HET HLX C 7 22 HET MVA C 8 19 HET MLU C 10 22 HET 2KT D 1 11 HET MVA D 2 19 HET V3C D 3 20 HET NZC D 4 16 HET MP8 D 6 17 HET HLX D 7 22 HET MVA D 8 19 HET MLU D 10 22 HETNAM 2KT 2-KETOBUTYRIC ACID HETNAM MVA N-METHYLVALINE HETNAM V3C TRANS-4-ATHYL-L-PROLINE HETNAM NZC N-METHYLIDENE-L-THREONINE HETNAM MP8 (4R)-4-METHYL-L-PROLINE HETNAM HLX 5-METHYL-L-NORLEUCINE HETNAM MLU N-METHYL-D-LEUCINE HETSYN 2KT 2-OXOBUTANOIC ACID HETSYN V3C (2S,4R)-4-ETHYLPYRROLIDINE-2-CARBOXYLIC ACID; ETHYL-L- HETSYN 2 V3C PROLINE FORMUL 3 2KT 2(C4 H6 O3) FORMUL 3 MVA 4(C6 H13 N O2) FORMUL 3 V3C 2(C7 H13 N O2) FORMUL 3 NZC 2(C5 H11 N O3) FORMUL 3 MP8 2(C6 H11 N O2) FORMUL 3 HLX 2(C7 H15 N O2) FORMUL 3 MLU 2(C7 H15 N O2) FORMUL 5 HOH *70(H2 O) HELIX 1 AA1 ARG A 7 SER A 18 1 12 HELIX 2 AA2 PRO A 28 LEU A 30 5 3 HELIX 3 AA3 ALA A 72 LEU A 82 1 11 HELIX 4 AA4 PRO A 112 PHE A 116 5 5 HELIX 5 AA5 PRO A 131 ALA A 141 1 11 HELIX 6 AA6 THR A 142 MET A 146 5 5 HELIX 7 AA7 ARG A 152 ASN A 156 5 5 HELIX 8 AA8 PRO A 196 LEU A 207 1 12 HELIX 9 AA9 ASP A 243 VAL A 247 5 5 HELIX 10 AB1 CYS A 260 ALA A 271 1 12 HELIX 11 AB2 ILE A 272 SER A 274 5 3 HELIX 12 AB3 VAL A 321 LYS A 332 1 12 HELIX 13 AB4 ARG B 7 SER B 18 1 12 HELIX 14 AB5 PRO B 28 LEU B 30 5 3 HELIX 15 AB6 ALA B 72 LEU B 82 1 11 HELIX 16 AB7 PRO B 112 PHE B 116 5 5 HELIX 17 AB8 GLN B 132 ALA B 141 1 10 HELIX 18 AB9 THR B 142 MET B 146 5 5 HELIX 19 AC1 ARG B 152 GLY B 157 5 6 HELIX 20 AC2 PRO B 196 MET B 206 1 11 HELIX 21 AC3 ASP B 243 VAL B 247 5 5 HELIX 22 AC4 CYS B 260 ILE B 272 1 13 HELIX 23 AC5 VAL B 321 LYS B 332 1 12 SHEET 1 AA1 8 LYS A 2 GLU A 6 0 SHEET 2 AA1 8 GLU A 87 GLU A 93 -1 O VAL A 90 N PHE A 3 SHEET 3 AA1 8 ARG A 96 SER A 101 -1 O ARG A 100 N ALA A 89 SHEET 4 AA1 8 SER A 104 SER A 109 -1 O PHE A 106 N VAL A 99 SHEET 5 AA1 8 GLU B 301 ASP B 307 -1 O GLU B 303 N ARG A 105 SHEET 6 AA1 8 GLN B 289 ASN B 295 -1 N LEU B 290 O LEU B 306 SHEET 7 AA1 8 GLY B 280 SER B 286 -1 N TYR B 284 O LYS B 291 SHEET 8 AA1 8 MET B 315 ASN B 320 -1 O MET B 315 N VAL B 285 SHEET 1 AA2 8 GLY A 66 PRO A 71 0 SHEET 2 AA2 8 ASN A 32 ALA A 38 -1 N LEU A 35 O THR A 68 SHEET 3 AA2 8 THR A 41 THR A 47 -1 O SER A 43 N GLN A 36 SHEET 4 AA2 8 MET A 51 ALA A 58 -1 O VAL A 57 N LEU A 42 SHEET 5 AA2 8 PHE A 230 LYS A 235 -1 O THR A 233 N GLU A 52 SHEET 6 AA2 8 ASN A 222 VAL A 227 -1 N ALA A 225 O PHE A 232 SHEET 7 AA2 8 LEU A 214 ILE A 218 -1 N GLN A 217 O ARG A 224 SHEET 8 AA2 8 VAL A 126 LEU A 130 -1 N PHE A 128 O VAL A 216 SHEET 1 AA3 6 LYS A 254 GLY A 259 0 SHEET 2 AA3 6 ASN A 335 LEU A 340 -1 O MET A 338 N LEU A 256 SHEET 3 AA3 6 VAL A 347 ASP A 351 -1 O GLN A 348 N MET A 339 SHEET 4 AA3 6 SER A 354 VAL A 361 -1 O TYR A 359 N ILE A 349 SHEET 5 AA3 6 ARG A 176 VAL A 195 -1 N LEU A 177 O VAL A 360 SHEET 6 AA3 6 MET A 158 THR A 172 -1 O PHE A 160 N VAL A 193 SHEET 1 AA4 8 MET A 315 ASN A 320 0 SHEET 2 AA4 8 GLY A 280 SER A 286 -1 N LEU A 283 O ILE A 317 SHEET 3 AA4 8 GLN A 289 ASN A 295 -1 O THR A 293 N ARG A 282 SHEET 4 AA4 8 GLU A 301 ASP A 307 -1 O LEU A 306 N LEU A 290 SHEET 5 AA4 8 SER B 104 SER B 109 -1 O SER B 107 N GLU A 301 SHEET 6 AA4 8 ARG B 96 SER B 101 -1 N VAL B 99 O PHE B 106 SHEET 7 AA4 8 GLU B 87 LEU B 92 -1 N GLN B 91 O LEU B 98 SHEET 8 AA4 8 LYS B 2 GLU B 6 -1 N PHE B 3 O VAL B 90 SHEET 1 AA5 8 GLY B 66 PRO B 71 0 SHEET 2 AA5 8 ASN B 32 VAL B 37 -1 N LEU B 35 O THR B 68 SHEET 3 AA5 8 THR B 41 THR B 47 -1 O SER B 43 N GLN B 36 SHEET 4 AA5 8 MET B 51 ALA B 58 -1 O VAL B 57 N LEU B 42 SHEET 5 AA5 8 PHE B 230 LYS B 235 -1 O THR B 233 N GLU B 52 SHEET 6 AA5 8 ASN B 222 VAL B 227 -1 N ALA B 225 O PHE B 232 SHEET 7 AA5 8 PRO B 213 GLY B 219 -1 N GLY B 219 O ASN B 222 SHEET 8 AA5 8 SER B 124 PRO B 131 -1 N PHE B 128 O VAL B 216 SHEET 1 AA6 6 LYS B 254 GLY B 259 0 SHEET 2 AA6 6 ASN B 335 LEU B 340 -1 O MET B 338 N LEU B 256 SHEET 3 AA6 6 VAL B 347 ASP B 351 -1 O GLN B 348 N MET B 339 SHEET 4 AA6 6 SER B 354 VAL B 361 -1 O TYR B 359 N ILE B 349 SHEET 5 AA6 6 ARG B 176 VAL B 195 -1 N VAL B 179 O ALA B 358 SHEET 6 AA6 6 MET B 158 THR B 172 -1 O PHE B 160 N VAL B 193 SSBOND 1 CYS A 260 CYS A 333 1555 1555 2.04 SSBOND 2 CYS B 260 CYS B 333 1555 1555 2.05 LINK C 2KT C 1 N MVA C 2 1555 1555 1.36 LINK C MVA C 2 N V3C C 3 1555 1555 1.34 LINK C V3C C 3 N NZC C 4 1555 1555 1.35 LINK C NZC C 4 N LEU C 5 1555 1555 1.34 LINK OG1 NZC C 4 C GLY C 11 1555 1555 1.34 LINK C LEU C 5 N MP8 C 6 1555 1555 1.34 LINK C MP8 C 6 N HLX C 7 1555 1555 1.34 LINK C HLX C 7 N MVA C 8 1555 1555 1.35 LINK C MVA C 8 N PRO C 9 1555 1555 1.34 LINK C PRO C 9 N MLU C 10 1555 1555 1.35 LINK C MLU C 10 N GLY C 11 1555 1555 1.34 LINK C 2KT D 1 N MVA D 2 1555 1555 1.36 LINK C MVA D 2 N V3C D 3 1555 1555 1.34 LINK C V3C D 3 N NZC D 4 1555 1555 1.35 LINK C NZC D 4 N LEU D 5 1555 1555 1.34 LINK OG1 NZC D 4 C GLY D 11 1555 1555 1.34 LINK C LEU D 5 N MP8 D 6 1555 1555 1.34 LINK C MP8 D 6 N HLX D 7 1555 1555 1.34 LINK C HLX D 7 N MVA D 8 1555 1555 1.35 LINK C MVA D 8 N PRO D 9 1555 1555 1.34 LINK C PRO D 9 N MLU D 10 1555 1555 1.35 LINK C MLU D 10 N GLY D 11 1555 1555 1.34 CISPEP 1 MVA C 8 PRO C 9 0 29.76 CISPEP 2 MVA D 8 PRO D 9 0 -5.62 CRYST1 83.937 150.050 72.381 90.00 103.92 90.00 C 1 2 1 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 0.011914 0.000000 0.002953 0.00000 SCALE2 0.000000 0.006664 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014234 0.00000