HEADER LIGASE 08-MAR-23 8CRL TITLE CRYSTAL STRUCTURE OF LPLA1 IN COMPLEX WITH THE INHIBITOR C3 (LISTERIA TITLE 2 MONOCYTOGENES) COMPND MOL_ID: 1; COMPND 2 MOLECULE: LIPOATE--PROTEIN LIGASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 6.3.1.20; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LISTERIA MONOCYTOGENES; SOURCE 3 ORGANISM_TAXID: 1639; SOURCE 4 GENE: AF817_03905, AF817_17765, APD94_04200, APD94_16795, SOURCE 5 D4271_05835, D4271_17085, D4C60_07100, D4C60_17245, D4D89_06525, SOURCE 6 D4D89_17125, D4U23_01750, D4U23_16900, E0I39_06590, E0I39_16500, SOURCE 7 E1V33_06915, E1W43_02450, E1W43_16025, FJU19_06430, FJU19_16220, SOURCE 8 FORC68_0962, G3R95_001339, G3R95_003435, GON91_05790, GT011_03885, SOURCE 9 GT011_16715, GXB45_04655, GXB45_16710, GYP27_11270, GYP27_15895, SOURCE 10 GYU24_04270, GYU24_17075; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 12 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS LIPOATE, SALVAGE, ANTI-INFECTIVES, DRUG DEVELOPMENT, INHIBITOR, KEYWDS 2 LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR J.-N.DIENEMANN,S.-Y.CHEN,M.HITZENBERGER,M.L.SIEVERT,S.M.HACKER, AUTHOR 2 S.T.PRIGGE,M.ZACHARIAS,M.GROLL,S.A.SIEBER REVDAT 3 20-SEP-23 8CRL 1 REMARK REVDAT 2 02-AUG-23 8CRL 1 JRNL REVDAT 1 07-JUN-23 8CRL 0 JRNL AUTH J.N.DIENEMANN,S.Y.CHEN,M.HITZENBERGER,M.L.SIEVERT, JRNL AUTH 2 S.M.HACKER,S.T.PRIGGE,M.ZACHARIAS,M.GROLL,S.A.SIEBER JRNL TITL A CHEMICAL PROTEOMIC STRATEGY REVEALS INHIBITORS OF LIPOATE JRNL TITL 2 SALVAGE IN BACTERIA AND PARASITES. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 62 04533 2023 JRNL REFN ESSN 1521-3773 JRNL PMID 37249408 JRNL DOI 10.1002/ANIE.202304533 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 3 NUMBER OF REFLECTIONS : 22646 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.235 REMARK 3 FREE R VALUE : 0.273 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1192 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.67 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1704 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.63 REMARK 3 BIN R VALUE (WORKING SET) : 0.3700 REMARK 3 BIN FREE R VALUE SET COUNT : 90 REMARK 3 BIN FREE R VALUE : 0.3940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4604 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 37 REMARK 3 SOLVENT ATOMS : 21 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.50000 REMARK 3 B22 (A**2) : -2.72000 REMARK 3 B33 (A**2) : -0.19000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -9.11000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.332 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.313 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 36.348 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.934 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4724 ; 0.005 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 4496 ; 0.002 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6381 ; 1.291 ; 1.647 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10336 ; 1.232 ; 1.598 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 560 ; 5.862 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 270 ;33.186 ;23.852 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 840 ;18.570 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 23 ;15.323 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 603 ; 0.059 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5337 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1098 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2255 ; 1.563 ; 5.527 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2254 ; 1.561 ; 5.527 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2810 ; 2.230 ; 8.280 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2811 ; 2.230 ; 8.280 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2469 ; 1.426 ; 5.721 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2470 ; 1.426 ; 5.722 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3572 ; 2.069 ; 8.511 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A -1 A 331 REMARK 3 ORIGIN FOR THE GROUP (A): 18.9186 -16.2118 2.1246 REMARK 3 T TENSOR REMARK 3 T11: 0.0151 T22: 0.0624 REMARK 3 T33: 0.0659 T12: -0.0000 REMARK 3 T13: 0.0288 T23: 0.0044 REMARK 3 L TENSOR REMARK 3 L11: 0.1099 L22: 0.4860 REMARK 3 L33: 0.3484 L12: 0.0345 REMARK 3 L13: 0.0882 L23: 0.2349 REMARK 3 S TENSOR REMARK 3 S11: 0.0186 S12: -0.0097 S13: 0.0095 REMARK 3 S21: 0.0007 S22: -0.0255 S23: 0.0208 REMARK 3 S31: -0.0017 S32: -0.0307 S33: 0.0069 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 1 B 331 REMARK 3 ORIGIN FOR THE GROUP (A): 1.1271 -19.0329 39.2949 REMARK 3 T TENSOR REMARK 3 T11: 0.0257 T22: 0.0428 REMARK 3 T33: 0.0441 T12: -0.0054 REMARK 3 T13: 0.0184 T23: 0.0054 REMARK 3 L TENSOR REMARK 3 L11: 0.0969 L22: 0.3764 REMARK 3 L33: 0.5807 L12: -0.1842 REMARK 3 L13: 0.1505 L23: -0.3594 REMARK 3 S TENSOR REMARK 3 S11: 0.0088 S12: 0.0065 S13: 0.0137 REMARK 3 S21: -0.0184 S22: -0.0176 S23: -0.0024 REMARK 3 S31: 0.0658 S32: 0.0610 S33: 0.0088 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 8CRL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-MAR-23. REMARK 100 THE DEPOSITION ID IS D_1292129092. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 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) : 1.0 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23850 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.4 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.67300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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: 8CRI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS, 0.2 M CACL2, 25% PEG 4000, REMARK 280 PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 37.13500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 -3 REMARK 465 SER A -2 REMARK 465 PRO A 165 REMARK 465 ARG A 166 REMARK 465 LYS A 167 REMARK 465 ASP A 168 REMARK 465 LYS A 169 REMARK 465 ILE A 170 REMARK 465 GLU A 171 REMARK 465 SER A 172 REMARK 465 LYS A 173 REMARK 465 GLY A 174 REMARK 465 ILE A 175 REMARK 465 LYS A 176 REMARK 465 SER A 177 REMARK 465 VAL A 178 REMARK 465 ARG A 179 REMARK 465 SER A 180 REMARK 465 GLY B -3 REMARK 465 SER B -2 REMARK 465 HIS B -1 REMARK 465 MET B 0 REMARK 465 ASP B 91 REMARK 465 ASP B 92 REMARK 465 GLY B 93 REMARK 465 GLU B 94 REMARK 465 SER B 95 REMARK 465 PHE B 96 REMARK 465 HIS B 97 REMARK 465 ASN B 98 REMARK 465 PHE B 99 REMARK 465 ALA B 100 REMARK 465 LYS B 101 REMARK 465 PHE B 102 REMARK 465 THR B 103 REMARK 465 GLN B 104 REMARK 465 PRO B 105 REMARK 465 ILE B 106 REMARK 465 VAL B 107 REMARK 465 GLU B 108 REMARK 465 ALA B 109 REMARK 465 LEU B 110 REMARK 465 LYS B 111 REMARK 465 ARG B 112 REMARK 465 LEU B 113 REMARK 465 GLY B 114 REMARK 465 VAL B 115 REMARK 465 ASN B 116 REMARK 465 ALA B 117 REMARK 465 GLU B 118 REMARK 465 LEU B 119 REMARK 465 LYS B 120 REMARK 465 GLY B 121 REMARK 465 ARG B 122 REMARK 465 ASN B 123 REMARK 465 ASP B 124 REMARK 465 LEU B 125 REMARK 465 LEU B 126 REMARK 465 ILE B 127 REMARK 465 ASP B 128 REMARK 465 GLY B 129 REMARK 465 PHE B 130 REMARK 465 LYS B 131 REMARK 465 VAL B 132 REMARK 465 SER B 133 REMARK 465 GLY B 134 REMARK 465 ASN B 135 REMARK 465 ALA B 136 REMARK 465 GLN B 137 REMARK 465 PHE B 138 REMARK 465 ALA B 139 REMARK 465 THR B 140 REMARK 465 LYS B 141 REMARK 465 GLY B 142 REMARK 465 LYS B 143 REMARK 465 MET B 144 REMARK 465 LYS B 164 REMARK 465 PRO B 165 REMARK 465 ARG B 166 REMARK 465 LYS B 167 REMARK 465 ASP B 168 REMARK 465 LYS B 169 REMARK 465 ILE B 170 REMARK 465 GLU B 171 REMARK 465 SER B 172 REMARK 465 LYS B 173 REMARK 465 GLY B 174 REMARK 465 ILE B 175 REMARK 465 LYS B 176 REMARK 465 SER B 177 REMARK 465 VAL B 178 REMARK 465 ARG B 179 REMARK 465 SER B 180 REMARK 465 ARG B 181 REMARK 465 VAL B 182 REMARK 465 ALA B 183 REMARK 465 ASN B 184 REMARK 465 ILE B 185 REMARK 465 SER B 186 REMARK 465 ASP B 187 REMARK 465 PHE B 188 REMARK 465 MET B 189 REMARK 465 ASP B 190 REMARK 465 GLN B 191 REMARK 465 GLU B 192 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 GLU A 80 -9.89 -58.24 REMARK 500 SER A 95 -51.70 -141.18 REMARK 500 HIS A 97 -7.19 91.54 REMARK 500 ARG A 122 -7.61 68.92 REMARK 500 ASP A 153 43.38 -145.02 REMARK 500 ARG A 235 -50.40 -129.89 REMARK 500 TYR A 243 -83.33 -103.79 REMARK 500 ASN A 320 77.62 -62.96 REMARK 500 PRO B 40 119.51 -39.93 REMARK 500 MET B 151 58.87 -93.25 REMARK 500 ASP B 153 33.96 -141.61 REMARK 500 VAL B 212 -2.40 78.05 REMARK 500 ARG B 235 -75.11 -125.09 REMARK 500 TYR B 243 -82.39 -106.79 REMARK 500 LYS B 255 137.20 -172.14 REMARK 500 ASN B 320 50.52 32.54 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 403 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 TYR A 331 O REMARK 620 2 TYR A 331 OXT 47.7 REMARK 620 3 TYR B 331 OXT 98.8 115.6 REMARK 620 N 1 2 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8CRI RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF LPLA1 IN COMPLEX WITH LIPOIC ACID (LISTERIA REMARK 900 MONOCYTOGENES) REMARK 900 RELATED ID: 8CRJ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF LPLA1 IN COMPLEX WITH LIPOYL-AMP (LISTERIA REMARK 900 MONOCYTOGENES) DBREF1 8CRL A 1 331 UNP A0A1D2IX29_LISMN DBREF2 8CRL A A0A1D2IX29 1 331 DBREF1 8CRL B 1 331 UNP A0A1D2IX29_LISMN DBREF2 8CRL B A0A1D2IX29 1 331 SEQADV 8CRL GLY A -3 UNP A0A1D2IX2 EXPRESSION TAG SEQADV 8CRL SER A -2 UNP A0A1D2IX2 EXPRESSION TAG SEQADV 8CRL HIS A -1 UNP A0A1D2IX2 EXPRESSION TAG SEQADV 8CRL MET A 0 UNP A0A1D2IX2 EXPRESSION TAG SEQADV 8CRL GLY B -3 UNP A0A1D2IX2 EXPRESSION TAG SEQADV 8CRL SER B -2 UNP A0A1D2IX2 EXPRESSION TAG SEQADV 8CRL HIS B -1 UNP A0A1D2IX2 EXPRESSION TAG SEQADV 8CRL MET B 0 UNP A0A1D2IX2 EXPRESSION TAG SEQRES 1 A 335 GLY SER HIS MET MET TYR PHE ILE ASP ASN ASN ASN GLU SEQRES 2 A 335 LYS ASP PRO ARG ILE ASN LEU ALA VAL GLU GLU PHE ILE SEQRES 3 A 335 LEU THR GLU LEU ASN LEU ASP GLU PRO VAL LEU LEU PHE SEQRES 4 A 335 TYR ILE ASN LYS PRO SER ILE ILE ILE GLY ARG ASN GLN SEQRES 5 A 335 ASN THR VAL GLU GLU ILE ASP THR GLU TYR VAL GLU LYS SEQRES 6 A 335 ASN ASP VAL ILE VAL VAL ARG ARG LEU SER GLY GLY GLY SEQRES 7 A 335 ALA VAL TYR HIS ASP GLU GLY ASN LEU ASN PHE SER PHE SEQRES 8 A 335 ILE THR GLU ASP ASP GLY GLU SER PHE HIS ASN PHE ALA SEQRES 9 A 335 LYS PHE THR GLN PRO ILE VAL GLU ALA LEU LYS ARG LEU SEQRES 10 A 335 GLY VAL ASN ALA GLU LEU LYS GLY ARG ASN ASP LEU LEU SEQRES 11 A 335 ILE ASP GLY PHE LYS VAL SER GLY ASN ALA GLN PHE ALA SEQRES 12 A 335 THR LYS GLY LYS MET PHE SER HIS GLY THR LEU MET TYR SEQRES 13 A 335 ASP LEU ASN LEU ASP ASN VAL ALA ALA SER LEU LYS PRO SEQRES 14 A 335 ARG LYS ASP LYS ILE GLU SER LYS GLY ILE LYS SER VAL SEQRES 15 A 335 ARG SER ARG VAL ALA ASN ILE SER ASP PHE MET ASP GLN SEQRES 16 A 335 GLU MET THR THR GLU GLU PHE ARG ASP LEU LEU LEU LEU SEQRES 17 A 335 TYR ILE PHE GLY VAL GLU LYS VAL GLU ASP VAL LYS GLU SEQRES 18 A 335 TYR LYS LEU THR ALA ALA ASP TRP GLU LYS ILE HIS GLU SEQRES 19 A 335 ILE SER ALA LYS ARG TYR GLY ASN TRP ASP TRP ASN TYR SEQRES 20 A 335 GLY LYS SER PRO LYS PHE ASP LEU THR ARG THR LYS ARG SEQRES 21 A 335 PHE PRO VAL GLY ALA VAL ASP VAL ARG LEU ASN VAL GLN SEQRES 22 A 335 LYS GLY VAL ILE THR ASP ILE LYS ILE PHE GLY ASP PHE SEQRES 23 A 335 PHE GLY VAL LYS ASN VAL ALA ASP ILE GLU GLU LYS LEU SEQRES 24 A 335 VAL ASN THR THR TYR LYS ARG GLU VAL LEU ALA GLU ALA SEQRES 25 A 335 LEU VAL ASP ILE ASP VAL LYS GLU TYR PHE GLY ASN ILE SEQRES 26 A 335 THR LYS ASP GLU PHE LEU ASP LEU LEU TYR SEQRES 1 B 335 GLY SER HIS MET MET TYR PHE ILE ASP ASN ASN ASN GLU SEQRES 2 B 335 LYS ASP PRO ARG ILE ASN LEU ALA VAL GLU GLU PHE ILE SEQRES 3 B 335 LEU THR GLU LEU ASN LEU ASP GLU PRO VAL LEU LEU PHE SEQRES 4 B 335 TYR ILE ASN LYS PRO SER ILE ILE ILE GLY ARG ASN GLN SEQRES 5 B 335 ASN THR VAL GLU GLU ILE ASP THR GLU TYR VAL GLU LYS SEQRES 6 B 335 ASN ASP VAL ILE VAL VAL ARG ARG LEU SER GLY GLY GLY SEQRES 7 B 335 ALA VAL TYR HIS ASP GLU GLY ASN LEU ASN PHE SER PHE SEQRES 8 B 335 ILE THR GLU ASP ASP GLY GLU SER PHE HIS ASN PHE ALA SEQRES 9 B 335 LYS PHE THR GLN PRO ILE VAL GLU ALA LEU LYS ARG LEU SEQRES 10 B 335 GLY VAL ASN ALA GLU LEU LYS GLY ARG ASN ASP LEU LEU SEQRES 11 B 335 ILE ASP GLY PHE LYS VAL SER GLY ASN ALA GLN PHE ALA SEQRES 12 B 335 THR LYS GLY LYS MET PHE SER HIS GLY THR LEU MET TYR SEQRES 13 B 335 ASP LEU ASN LEU ASP ASN VAL ALA ALA SER LEU LYS PRO SEQRES 14 B 335 ARG LYS ASP LYS ILE GLU SER LYS GLY ILE LYS SER VAL SEQRES 15 B 335 ARG SER ARG VAL ALA ASN ILE SER ASP PHE MET ASP GLN SEQRES 16 B 335 GLU MET THR THR GLU GLU PHE ARG ASP LEU LEU LEU LEU SEQRES 17 B 335 TYR ILE PHE GLY VAL GLU LYS VAL GLU ASP VAL LYS GLU SEQRES 18 B 335 TYR LYS LEU THR ALA ALA ASP TRP GLU LYS ILE HIS GLU SEQRES 19 B 335 ILE SER ALA LYS ARG TYR GLY ASN TRP ASP TRP ASN TYR SEQRES 20 B 335 GLY LYS SER PRO LYS PHE ASP LEU THR ARG THR LYS ARG SEQRES 21 B 335 PHE PRO VAL GLY ALA VAL ASP VAL ARG LEU ASN VAL GLN SEQRES 22 B 335 LYS GLY VAL ILE THR ASP ILE LYS ILE PHE GLY ASP PHE SEQRES 23 B 335 PHE GLY VAL LYS ASN VAL ALA ASP ILE GLU GLU LYS LEU SEQRES 24 B 335 VAL ASN THR THR TYR LYS ARG GLU VAL LEU ALA GLU ALA SEQRES 25 B 335 LEU VAL ASP ILE ASP VAL LYS GLU TYR PHE GLY ASN ILE SEQRES 26 B 335 THR LYS ASP GLU PHE LEU ASP LEU LEU TYR HET VK9 A 401 29 HET CA A 402 1 HET CA A 403 1 HET NA A 404 1 HET NA A 405 1 HET EDO A 406 4 HETNAM VK9 ~{N}-[3-[2-(6-AMINOPURIN-9-YL)ETHANOYLAMINO]PROPYL]-5- HETNAM 2 VK9 [(3~{R})-1,2-DITHIOLAN-3-YL]PENTANAMIDE HETNAM CA CALCIUM ION HETNAM NA SODIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 VK9 C18 H27 N7 O2 S2 FORMUL 4 CA 2(CA 2+) FORMUL 6 NA 2(NA 1+) FORMUL 8 EDO C2 H6 O2 FORMUL 9 HOH *21(H2 O) HELIX 1 AA1 ASP A 11 LEU A 26 1 16 HELIX 2 AA2 ASN A 49 ILE A 54 5 6 HELIX 3 AA3 ASP A 55 ASP A 63 1 9 HELIX 4 AA4 THR A 103 LEU A 113 1 11 HELIX 5 AA5 ASN A 155 LEU A 163 1 9 HELIX 6 AA6 ASN A 184 MET A 189 5 6 HELIX 7 AA7 THR A 194 GLY A 208 1 15 HELIX 8 AA8 LYS A 211 VAL A 215 5 5 HELIX 9 AA9 THR A 221 ARG A 235 1 15 HELIX 10 AB1 ASN A 238 TYR A 243 1 6 HELIX 11 AB2 VAL A 288 VAL A 296 1 9 HELIX 12 AB3 LYS A 301 LEU A 309 1 9 HELIX 13 AB4 VAL A 314 GLY A 319 1 6 HELIX 14 AB5 THR A 322 ASP A 328 1 7 HELIX 15 AB6 ASP B 11 ASN B 27 1 17 HELIX 16 AB7 ASN B 49 GLU B 53 5 5 HELIX 17 AB8 ASP B 55 ASN B 62 1 8 HELIX 18 AB9 LEU B 156 LEU B 163 1 8 HELIX 19 AC1 THR B 194 GLY B 208 1 15 HELIX 20 AC2 THR B 221 ARG B 235 1 15 HELIX 21 AC3 ASN B 238 TYR B 243 1 6 HELIX 22 AC4 VAL B 288 VAL B 296 1 9 HELIX 23 AC5 LYS B 301 LEU B 309 1 9 HELIX 24 AC6 ASP B 313 TYR B 317 5 5 HELIX 25 AC7 THR B 322 TYR B 331 1 10 SHEET 1 AA1 5 TYR A 2 ILE A 4 0 SHEET 2 AA1 5 VAL A 32 TYR A 36 1 O LEU A 33 N TYR A 2 SHEET 3 AA1 5 ASN A 82 GLU A 90 -1 O ASN A 84 N TYR A 36 SHEET 4 AA1 5 LYS A 143 MET A 151 -1 O MET A 144 N THR A 89 SHEET 5 AA1 5 ASN A 135 THR A 140 -1 N PHE A 138 O PHE A 145 SHEET 1 AA2 3 ILE A 65 ARG A 68 0 SHEET 2 AA2 3 SER A 41 ILE A 44 1 N ILE A 44 O VAL A 67 SHEET 3 AA2 3 VAL A 76 HIS A 78 -1 O HIS A 78 N SER A 41 SHEET 1 AA3 3 GLU A 118 LYS A 120 0 SHEET 2 AA3 3 ASP A 124 ILE A 127 -1 O LEU A 126 N GLU A 118 SHEET 3 AA3 3 PHE A 130 SER A 133 -1 O VAL A 132 N LEU A 125 SHEET 1 AA4 3 LEU A 251 PHE A 257 0 SHEET 2 AA4 3 GLY A 260 GLN A 269 -1 O VAL A 264 N ARG A 253 SHEET 3 AA4 3 VAL A 272 GLY A 280 -1 O PHE A 279 N ASP A 263 SHEET 1 AA5 4 TYR B 2 PHE B 3 0 SHEET 2 AA5 4 VAL B 32 TYR B 36 1 O LEU B 33 N TYR B 2 SHEET 3 AA5 4 LEU B 83 ILE B 88 -1 O ASN B 84 N TYR B 36 SHEET 4 AA5 4 SER B 146 LEU B 150 -1 O SER B 146 N PHE B 87 SHEET 1 AA6 3 ILE B 65 ARG B 68 0 SHEET 2 AA6 3 SER B 41 ILE B 44 1 N ILE B 42 O VAL B 67 SHEET 3 AA6 3 VAL B 76 HIS B 78 -1 O HIS B 78 N SER B 41 SHEET 1 AA7 3 LEU B 251 PHE B 257 0 SHEET 2 AA7 3 GLY B 260 GLN B 269 -1 O VAL B 264 N ARG B 253 SHEET 3 AA7 3 VAL B 272 GLY B 280 -1 O PHE B 279 N ASP B 263 LINK OD2 ASP A 5 CA CA A 402 1555 1555 2.60 LINK OD1 ASP A 153 NA NA A 405 1555 1555 2.79 LINK OD1 ASP A 240 NA NA A 404 1555 2645 3.02 LINK O TYR A 331 CA CA A 403 1555 1555 2.65 LINK OXT TYR A 331 CA CA A 403 1555 1555 2.63 LINK CA CA A 403 OXT TYR B 331 2555 1555 2.72 CRYST1 59.320 74.270 92.730 90.00 98.06 90.00 P 1 21 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 0.016858 0.000000 0.002387 0.00000 SCALE2 0.000000 0.013464 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010892 0.00000