HEADER MEMBRANE PROTEIN 03-MAR-21 7NRF TITLE CRYSTAL STRUCTURE OF E.COLI BAMA BETA-BARREL IN COMPLEX WITH TITLE 2 DAROBACTIN (CRYSTAL FORM 2) COMPND MOL_ID: 1; COMPND 2 MOLECULE: OUTER MEMBRANE PROTEIN ASSEMBLY FACTOR BAMA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DAROBACTIN; COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI O157:H7; SOURCE 3 ORGANISM_TAXID: 83334; SOURCE 4 GENE: BAMA, YAET, Z0188, ECS0179; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET15A; SOURCE 8 MOL_ID: 2; SOURCE 9 SYNTHETIC: YES; SOURCE 10 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 11 ORGANISM_TAXID: 32630 KEYWDS BETA-BARREL, OUTER MEMBRANE, PROTEIN INSERTION, PROTEIN FOLDING, KEYWDS 2 PROTEIN MATURATION, ANTIBIOTIC, NATURAL PRODUCT, CYCLIZED PEPTIDE, KEYWDS 3 MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.P.JAKOB,H.KAUR,J.K.MARZINEK,R.GREEN,Y.IMAI,J.BOLLA,C.ROBINSON, AUTHOR 2 P.J.BOND,K.LEWIS,T.MAIER,S.HILLER REVDAT 4 31-JAN-24 7NRF 1 LINK REVDAT 3 19-MAY-21 7NRF 1 JRNL REVDAT 2 28-APR-21 7NRF 1 JRNL REVDAT 1 21-APR-21 7NRF 0 JRNL AUTH H.KAUR,R.P.JAKOB,J.K.MARZINEK,R.GREEN,Y.IMAI,J.R.BOLLA, JRNL AUTH 2 E.AGUSTONI,C.V.ROBINSON,P.J.BOND,K.LEWIS,T.MAIER,S.HILLER JRNL TITL THE ANTIBIOTIC DAROBACTIN MIMICS A BETA-STRAND TO INHIBIT JRNL TITL 2 OUTER MEMBRANE INSERTASE. JRNL REF NATURE V. 593 125 2021 JRNL REFN ESSN 1476-4687 JRNL PMID 33854236 JRNL DOI 10.1038/S41586-021-03455-W REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 27134 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.218 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1371 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 42.8500 - 4.7380 0.99 2637 137 0.2108 0.2400 REMARK 3 2 4.7380 - 3.7614 1.00 2580 145 0.1933 0.1994 REMARK 3 3 3.7614 - 3.2862 0.98 2577 132 0.2013 0.2249 REMARK 3 4 3.2862 - 2.9858 1.00 2590 135 0.2178 0.1941 REMARK 3 5 2.9858 - 2.7718 1.00 2558 149 0.2330 0.2603 REMARK 3 6 2.7718 - 2.6084 1.00 2585 137 0.2315 0.2720 REMARK 3 7 2.6084 - 2.4778 0.98 2515 130 0.2597 0.2663 REMARK 3 8 2.4778 - 2.3700 0.99 2554 145 0.2849 0.3104 REMARK 3 9 2.3700 - 2.2787 1.00 2578 135 0.3024 0.3235 REMARK 3 10 2.2787 - 2.2001 1.00 2589 126 0.3342 0.3197 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.130 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 77.35 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 10 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 424 THROUGH 446 ) REMARK 3 ORIGIN FOR THE GROUP (A): 35.5472 -1.3390 3.8160 REMARK 3 T TENSOR REMARK 3 T11: 0.7620 T22: 0.5573 REMARK 3 T33: 0.6381 T12: 0.0033 REMARK 3 T13: -0.0235 T23: -0.0508 REMARK 3 L TENSOR REMARK 3 L11: 0.0218 L22: 0.0626 REMARK 3 L33: 0.0359 L12: 0.0091 REMARK 3 L13: 0.0415 L23: 0.0150 REMARK 3 S TENSOR REMARK 3 S11: -0.0864 S12: 0.1712 S13: 0.5194 REMARK 3 S21: -0.3026 S22: -0.1102 S23: 0.1995 REMARK 3 S31: -0.7372 S32: 0.3976 S33: -0.0002 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 447 THROUGH 504 ) REMARK 3 ORIGIN FOR THE GROUP (A): 23.6544 -5.0807 -1.0408 REMARK 3 T TENSOR REMARK 3 T11: 0.5040 T22: 0.3492 REMARK 3 T33: 0.4301 T12: -0.0298 REMARK 3 T13: 0.0133 T23: 0.0328 REMARK 3 L TENSOR REMARK 3 L11: 0.9461 L22: 0.2669 REMARK 3 L33: 0.3210 L12: -0.0701 REMARK 3 L13: 0.4364 L23: -0.1912 REMARK 3 S TENSOR REMARK 3 S11: 0.0071 S12: -0.1230 S13: 0.2275 REMARK 3 S21: -0.1811 S22: -0.0736 S23: -0.5178 REMARK 3 S31: -0.0367 S32: 0.3758 S33: -0.0260 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 505 THROUGH 537 ) REMARK 3 ORIGIN FOR THE GROUP (A): 15.7975 -9.1734 1.6805 REMARK 3 T TENSOR REMARK 3 T11: 0.5354 T22: 0.6570 REMARK 3 T33: 0.5690 T12: 0.1623 REMARK 3 T13: -0.1072 T23: -0.0850 REMARK 3 L TENSOR REMARK 3 L11: 0.4089 L22: 0.6650 REMARK 3 L33: 0.4648 L12: 0.3351 REMARK 3 L13: -0.2683 L23: -0.5673 REMARK 3 S TENSOR REMARK 3 S11: -0.1955 S12: -0.0845 S13: 0.4742 REMARK 3 S21: -0.1327 S22: 0.2192 S23: -0.3268 REMARK 3 S31: -0.1675 S32: -0.2439 S33: 0.0039 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 538 THROUGH 563 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.4946 -34.2721 -2.2942 REMARK 3 T TENSOR REMARK 3 T11: 0.7477 T22: 0.5380 REMARK 3 T33: 0.5959 T12: 0.0233 REMARK 3 T13: 0.0005 T23: -0.0976 REMARK 3 L TENSOR REMARK 3 L11: 0.0979 L22: 0.1940 REMARK 3 L33: 0.1954 L12: -0.0284 REMARK 3 L13: 0.0049 L23: 0.0004 REMARK 3 S TENSOR REMARK 3 S11: 0.0649 S12: -0.0092 S13: -0.1242 REMARK 3 S21: -0.1863 S22: 0.0884 S23: -0.2396 REMARK 3 S31: 0.7176 S32: 0.1596 S33: -0.0001 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 564 THROUGH 589 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.8224 -7.9881 10.7471 REMARK 3 T TENSOR REMARK 3 T11: 0.6320 T22: 0.5966 REMARK 3 T33: 0.5287 T12: 0.0713 REMARK 3 T13: -0.0312 T23: -0.0328 REMARK 3 L TENSOR REMARK 3 L11: 0.7466 L22: 0.0967 REMARK 3 L33: 0.7832 L12: -0.0860 REMARK 3 L13: 0.7503 L23: -0.1806 REMARK 3 S TENSOR REMARK 3 S11: -0.0968 S12: -0.1894 S13: 0.0826 REMARK 3 S21: -0.1026 S22: 0.1935 S23: -0.1510 REMARK 3 S31: -0.1631 S32: 0.0719 S33: 0.0002 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 590 THROUGH 620 ) REMARK 3 ORIGIN FOR THE GROUP (A): 14.7547 -14.2672 11.1311 REMARK 3 T TENSOR REMARK 3 T11: 0.5053 T22: 0.7320 REMARK 3 T33: 0.6211 T12: 0.0724 REMARK 3 T13: -0.0232 T23: -0.0979 REMARK 3 L TENSOR REMARK 3 L11: 0.5026 L22: 0.2510 REMARK 3 L33: 0.1128 L12: 0.3467 REMARK 3 L13: -0.0659 L23: -0.0888 REMARK 3 S TENSOR REMARK 3 S11: -0.1578 S12: -0.2227 S13: 0.1882 REMARK 3 S21: 0.1889 S22: -0.2613 S23: 0.3014 REMARK 3 S31: 0.0730 S32: -0.4137 S33: -0.0000 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 621 THROUGH 640 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.0881 -8.5301 26.5870 REMARK 3 T TENSOR REMARK 3 T11: 0.4058 T22: 0.8635 REMARK 3 T33: 0.5025 T12: 0.0589 REMARK 3 T13: 0.0298 T23: -0.1016 REMARK 3 L TENSOR REMARK 3 L11: 0.1726 L22: 0.2627 REMARK 3 L33: 0.2765 L12: 0.2184 REMARK 3 L13: -0.1575 L23: -0.1951 REMARK 3 S TENSOR REMARK 3 S11: -0.0600 S12: -0.6367 S13: -0.0184 REMARK 3 S21: 0.0552 S22: -0.4459 S23: 0.2155 REMARK 3 S31: 0.0552 S32: -0.4126 S33: 0.0003 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 641 THROUGH 766 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.2567 -22.9888 17.1069 REMARK 3 T TENSOR REMARK 3 T11: 0.4806 T22: 0.5558 REMARK 3 T33: 0.5355 T12: -0.0133 REMARK 3 T13: 0.0063 T23: 0.0406 REMARK 3 L TENSOR REMARK 3 L11: 1.4004 L22: 0.3934 REMARK 3 L33: 2.2619 L12: -0.0784 REMARK 3 L13: 0.2257 L23: 0.2914 REMARK 3 S TENSOR REMARK 3 S11: 0.0661 S12: -0.3176 S13: -0.3661 REMARK 3 S21: 0.2022 S22: 0.0910 S23: -0.1928 REMARK 3 S31: 0.3355 S32: -0.2036 S33: -0.0000 REMARK 3 TLS GROUP : 9 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 767 THROUGH 789 ) REMARK 3 ORIGIN FOR THE GROUP (A): 37.4547 -8.3626 23.2148 REMARK 3 T TENSOR REMARK 3 T11: 0.4657 T22: 0.4935 REMARK 3 T33: 0.3938 T12: 0.0293 REMARK 3 T13: 0.0240 T23: -0.0055 REMARK 3 L TENSOR REMARK 3 L11: 0.2293 L22: 0.1804 REMARK 3 L33: 0.7451 L12: 0.0798 REMARK 3 L13: 0.2477 L23: 0.3612 REMARK 3 S TENSOR REMARK 3 S11: -0.0755 S12: -0.1964 S13: -0.4447 REMARK 3 S21: 0.0208 S22: 0.1213 S23: -0.5491 REMARK 3 S31: 0.2698 S32: 0.0256 S33: -0.0001 REMARK 3 TLS GROUP : 10 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 790 THROUGH 810 ) REMARK 3 ORIGIN FOR THE GROUP (A): 36.2354 -17.0028 19.3876 REMARK 3 T TENSOR REMARK 3 T11: 0.5123 T22: 0.4756 REMARK 3 T33: 0.5356 T12: -0.0146 REMARK 3 T13: -0.0152 T23: 0.0301 REMARK 3 L TENSOR REMARK 3 L11: 0.4961 L22: 0.2704 REMARK 3 L33: 0.7378 L12: -0.0592 REMARK 3 L13: 0.1089 L23: 0.4322 REMARK 3 S TENSOR REMARK 3 S11: 0.0009 S12: -0.2645 S13: -0.0060 REMARK 3 S21: -0.1856 S22: 0.0495 S23: -0.4776 REMARK 3 S31: -0.1576 S32: 0.1820 S33: -0.0003 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 7NRF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-APR-21. REMARK 100 THE DEPOSITION ID IS D_1292108228. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-AUG-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000089 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27135 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 42.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.26900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 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: 6QGW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M MAGNESIUM CHLORIDE, 0.03 M TRIS REMARK 280 PH 8.0, 19% W/V POLYETHYLENE GLYCOL 4,000, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-Z+1/2 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 27.17700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.90700 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 42.85103 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 27.17700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 39.90700 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 42.85103 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 HOH A1163 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 REMARK 400 THE DAROBACTIN IS PEPTIDE-LIKE, A MEMBER OF ANTIBIOTIC CLASS. REMARK 400 REMARK 400 GROUP: 1 REMARK 400 NAME: DAROBACTIN REMARK 400 CHAIN: B 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 MET A 400 REMARK 465 GLY A 401 REMARK 465 SER A 402 REMARK 465 SER A 403 REMARK 465 HIS A 404 REMARK 465 HIS A 405 REMARK 465 HIS A 406 REMARK 465 HIS A 407 REMARK 465 HIS A 408 REMARK 465 HIS A 409 REMARK 465 SER A 410 REMARK 465 SER A 411 REMARK 465 GLY A 412 REMARK 465 GLU A 413 REMARK 465 ASN A 414 REMARK 465 LEU A 415 REMARK 465 TYR A 416 REMARK 465 PHE A 417 REMARK 465 GLN A 418 REMARK 465 HIS A 419 REMARK 465 MET A 420 REMARK 465 ARG A 421 REMARK 465 ASN A 422 REMARK 465 THR A 423 REMARK 465 ALA A 679 REMARK 465 SER A 680 REMARK 465 ASN A 681 REMARK 465 TYR A 682 REMARK 465 ASP A 683 REMARK 465 PRO A 684 REMARK 465 ASP A 685 REMARK 465 TYR A 686 REMARK 465 ASP A 687 REMARK 465 TYR A 688 REMARK 465 GLU A 689 REMARK 465 SER A 690 REMARK 465 ALA A 691 REMARK 465 THR A 692 REMARK 465 GLN A 693 REMARK 465 ASP A 694 REMARK 465 GLY A 695 REMARK 465 ALA A 696 REMARK 465 LYS A 697 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 HH TYR A 760 O HOH A 1102 1.59 REMARK 500 O HOH A 1169 O HOH A 1213 2.16 REMARK 500 O ASP A 464 O HOH A 1101 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 ASP A 481 52.28 -102.50 REMARK 500 ASN A 520 -145.47 -161.17 REMARK 500 ASP A 562 75.53 -113.98 REMARK 500 THR A 659 -77.24 -127.72 REMARK 500 SER A 726 154.21 -47.91 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 A1234 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH A1235 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH A1236 DISTANCE = 6.36 ANGSTROMS REMARK 525 HOH A1237 DISTANCE = 7.11 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 ORIGINAL REFINEMENT WAS DONE WITH DAROBACTIN DEFINED AS ONE LIGAND. REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 C8E A 1002 REMARK 610 C8E A 1003 REMARK 610 C8E A 1004 REMARK 610 C8E A 1005 REMARK 610 C8E A 1006 REMARK 610 C8E A 1007 REMARK 610 C8E A 1009 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 A1001 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 497 OD2 REMARK 620 2 ASP A 497 OD2 0.0 REMARK 620 3 HOH A1112 O 84.6 84.6 REMARK 620 4 HOH A1136 O 148.4 148.4 64.1 REMARK 620 N 1 2 3 DBREF 7NRF A 421 810 UNP P0A942 BAMA_ECO57 421 810 DBREF 7NRF B 1 7 PDB 7NRF 7NRF 1 7 SEQADV 7NRF MET A 400 UNP P0A942 INITIATING METHIONINE SEQADV 7NRF GLY A 401 UNP P0A942 EXPRESSION TAG SEQADV 7NRF SER A 402 UNP P0A942 EXPRESSION TAG SEQADV 7NRF SER A 403 UNP P0A942 EXPRESSION TAG SEQADV 7NRF HIS A 404 UNP P0A942 EXPRESSION TAG SEQADV 7NRF HIS A 405 UNP P0A942 EXPRESSION TAG SEQADV 7NRF HIS A 406 UNP P0A942 EXPRESSION TAG SEQADV 7NRF HIS A 407 UNP P0A942 EXPRESSION TAG SEQADV 7NRF HIS A 408 UNP P0A942 EXPRESSION TAG SEQADV 7NRF HIS A 409 UNP P0A942 EXPRESSION TAG SEQADV 7NRF SER A 410 UNP P0A942 EXPRESSION TAG SEQADV 7NRF SER A 411 UNP P0A942 EXPRESSION TAG SEQADV 7NRF GLY A 412 UNP P0A942 EXPRESSION TAG SEQADV 7NRF GLU A 413 UNP P0A942 EXPRESSION TAG SEQADV 7NRF ASN A 414 UNP P0A942 EXPRESSION TAG SEQADV 7NRF LEU A 415 UNP P0A942 EXPRESSION TAG SEQADV 7NRF TYR A 416 UNP P0A942 EXPRESSION TAG SEQADV 7NRF PHE A 417 UNP P0A942 EXPRESSION TAG SEQADV 7NRF GLN A 418 UNP P0A942 EXPRESSION TAG SEQADV 7NRF HIS A 419 UNP P0A942 EXPRESSION TAG SEQADV 7NRF MET A 420 UNP P0A942 EXPRESSION TAG SEQADV 7NRF SER A 690 UNP P0A942 CYS 690 CONFLICT SEQADV 7NRF SER A 700 UNP P0A942 CYS 700 CONFLICT SEQRES 1 A 411 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 411 GLU ASN LEU TYR PHE GLN HIS MET ARG ASN THR GLY SER SEQRES 3 A 411 PHE ASN PHE GLY ILE GLY TYR GLY THR GLU SER GLY VAL SEQRES 4 A 411 SER PHE GLN ALA GLY VAL GLN GLN ASP ASN TRP LEU GLY SEQRES 5 A 411 THR GLY TYR ALA VAL GLY ILE ASN GLY THR LYS ASN ASP SEQRES 6 A 411 TYR GLN THR TYR ALA GLU LEU SER VAL THR ASN PRO TYR SEQRES 7 A 411 PHE THR VAL ASP GLY VAL SER LEU GLY GLY ARG LEU PHE SEQRES 8 A 411 TYR ASN ASP PHE GLN ALA ASP ASP ALA ASP LEU SER ASP SEQRES 9 A 411 TYR THR ASN LYS SER TYR GLY THR ASP VAL THR LEU GLY SEQRES 10 A 411 PHE PRO ILE ASN GLU TYR ASN SER LEU ARG ALA GLY LEU SEQRES 11 A 411 GLY TYR VAL HIS ASN SER LEU SER ASN MET GLN PRO GLN SEQRES 12 A 411 VAL ALA MET TRP ARG TYR LEU TYR SER MET GLY GLU HIS SEQRES 13 A 411 PRO SER THR SER ASP GLN ASP ASN SER PHE LYS THR ASP SEQRES 14 A 411 ASP PHE THR PHE ASN TYR GLY TRP THR TYR ASN LYS LEU SEQRES 15 A 411 ASP ARG GLY TYR PHE PRO THR ASP GLY SER ARG VAL ASN SEQRES 16 A 411 LEU THR GLY LYS VAL THR ILE PRO GLY SER ASP ASN GLU SEQRES 17 A 411 TYR TYR LYS VAL THR LEU ASP THR ALA THR TYR VAL PRO SEQRES 18 A 411 ILE ASP ASP ASP HIS LYS TRP VAL VAL LEU GLY ARG THR SEQRES 19 A 411 ARG TRP GLY TYR GLY ASP GLY LEU GLY GLY LYS GLU MET SEQRES 20 A 411 PRO PHE TYR GLU ASN PHE TYR ALA GLY GLY SER SER THR SEQRES 21 A 411 VAL ARG GLY PHE GLN SER ASN THR ILE GLY PRO LYS ALA SEQRES 22 A 411 VAL TYR PHE PRO HIS GLN ALA SER ASN TYR ASP PRO ASP SEQRES 23 A 411 TYR ASP TYR GLU SER ALA THR GLN ASP GLY ALA LYS ASP SEQRES 24 A 411 LEU SER LYS SER ASP ASP ALA VAL GLY GLY ASN ALA MET SEQRES 25 A 411 ALA VAL ALA SER LEU GLU PHE ILE THR PRO THR PRO PHE SEQRES 26 A 411 ILE SER ASP LYS TYR ALA ASN SER VAL ARG THR SER PHE SEQRES 27 A 411 PHE TRP ASP MET GLY THR VAL TRP ASP THR ASN TRP ASP SEQRES 28 A 411 SER SER GLN TYR SER GLY TYR PRO ASP TYR SER ASP PRO SEQRES 29 A 411 SER ASN ILE ARG MET SER ALA GLY ILE ALA LEU GLN TRP SEQRES 30 A 411 MET SER PRO LEU GLY PRO LEU VAL PHE SER TYR ALA GLN SEQRES 31 A 411 PRO PHE LYS LYS TYR ASP GLY ASP LYS ALA GLU GLN PHE SEQRES 32 A 411 GLN PHE ASN ILE GLY LYS THR TRP SEQRES 1 B 7 TRP ASN UX8 SER LYS SER PHE HET UX8 B 3 23 HET MG A1001 1 HET C8E A1002 40 HET C8E A1003 36 HET C8E A1004 36 HET C8E A1005 39 HET C8E A1006 33 HET C8E A1007 26 HET C8E A1008 55 HET C8E A1009 36 HETNAM UX8 (2~{S},3~{R})-2-AZANYL-3-(1~{H}-INDOL-3-YL)-3-OXIDANYL- HETNAM 2 UX8 PROPANOIC ACID HETNAM MG MAGNESIUM ION HETNAM C8E (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE FORMUL 2 UX8 C11 H12 N2 O3 FORMUL 3 MG MG 2+ FORMUL 4 C8E 8(C16 H34 O5) FORMUL 12 HOH *137(H2 O) HELIX 1 AA1 ASP A 497 ASP A 500 5 4 HELIX 2 AA2 GLN A 542 MET A 552 1 11 HELIX 3 AA3 PRO A 647 ASN A 651 5 5 HELIX 4 AA4 SER A 726 ALA A 730 5 5 SHEET 1 AA118 ASN B 2 SER B 6 0 SHEET 2 AA118 SER A 425 GLY A 433 -1 N PHE A 428 O UX8 B 3 SHEET 3 AA118 PHE A 802 ILE A 806 -1 O ILE A 806 N TYR A 432 SHEET 4 AA118 GLY A 781 LYS A 792 -1 N SER A 786 O GLN A 803 SHEET 5 AA118 ARG A 767 SER A 778 -1 N LEU A 774 O PHE A 785 SHEET 6 AA118 VAL A 733 TRP A 745 -1 N PHE A 738 O GLY A 771 SHEET 7 AA118 ALA A 710 THR A 720 -1 N PHE A 718 O PHE A 737 SHEET 8 AA118 VAL A 628 GLY A 640 -1 N ARG A 634 O VAL A 713 SHEET 9 AA118 TYR A 608 PRO A 620 -1 N VAL A 619 O VAL A 629 SHEET 10 AA118 GLY A 590 THR A 600 -1 N GLY A 590 O TYR A 618 SHEET 11 AA118 SER A 564 ASN A 579 -1 N TRP A 576 O LEU A 595 SHEET 12 AA118 ASN A 523 SER A 537 -1 N LEU A 536 O PHE A 565 SHEET 13 AA118 THR A 505 PRO A 518 -1 N LEU A 515 O ALA A 527 SHEET 14 AA118 SER A 484 GLN A 495 -1 N GLY A 486 O THR A 514 SHEET 15 AA118 GLN A 466 ASN A 475 -1 N THR A 467 O ASP A 493 SHEET 16 AA118 ALA A 455 LYS A 462 -1 N ALA A 455 O THR A 474 SHEET 17 AA118 GLY A 437 GLN A 446 -1 N VAL A 444 O ILE A 458 SHEET 18 AA118 SER A 425 GLY A 433 -1 N GLY A 429 O GLN A 441 SHEET 1 AA2 2 GLY A 662 PHE A 663 0 SHEET 2 AA2 2 ALA A 799 GLU A 800 -1 O GLU A 800 N GLY A 662 SHEET 1 AA3 2 LYS A 671 TYR A 674 0 SHEET 2 AA3 2 SER A 700 ALA A 705 -1 O ASP A 704 N ALA A 672 LINK CZ2 TRP B 1 O9 UX8 B 3 1555 1555 1.37 LINK C ASN B 2 N UX8 B 3 1555 1555 1.43 LINK C UX8 B 3 N SER B 4 1555 1555 1.42 LINK CH2 UX8 B 3 CB LYS B 5 1555 1555 1.41 LINK OD2 ASP A 497 MG MG A1001 1555 1555 2.17 LINK OD2 ASP A 497 MG MG A1001 1555 2655 2.42 LINK MG MG A1001 O HOH A1112 1555 1555 2.65 LINK MG MG A1001 O HOH A1136 1555 2655 2.26 CRYST1 79.610 79.814 89.346 90.00 106.42 90.00 I 1 2 1 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 0.012561 0.000000 0.003703 0.00000 SCALE2 0.000000 0.012529 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011669 0.00000