HEADER ANTIMICROBIAL PROTEIN 08-NOV-22 8BK3 TITLE CRYSTAL STRUCTURE OF THE TRANSPEPTIDASE LDTMT2 FROM MYCOBACTERIUM TITLE 2 TUBERCULOSIS IN COMPLEX WITH DIEPOXIDE KETONE 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: L,D-TRANSPEPTIDASE 2; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: LDT 2,LDT(MT2); COMPND 5 EC: 2.3.2.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: LDTB, MT2594, V735_02606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS L, D-TRANSPEPTIDASE, LDTMT2, INHIBITOR, COVALENT, ANTIMICROBIAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.DE MUNNIK,C.J.SCHOFIELD REVDAT 1 22-NOV-23 8BK3 0 JRNL AUTH M.DE MUNNIK,J.LITHGOW,L.BREWITZ,K.E.CHRISTENSEN,R.H.BATES, JRNL AUTH 2 B.RODRIGUEZ-MIQUEL,C.J.SCHOFIELD JRNL TITL ALPHA BETA , ALPHA ' BETA '-DIEPOXYKETONES ARE JRNL TITL 2 MECHANISM-BASED INHIBITORS OF NUCLEOPHILIC CYSTEINE ENZYMES. JRNL REF CHEM.COMMUN.(CAMB.) V. 59 12859 2023 JRNL REFN ESSN 1364-548X JRNL PMID 37815791 JRNL DOI 10.1039/D3CC02932H REMARK 2 REMARK 2 RESOLUTION. 2.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 2.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 75.46 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 46328 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.920 REMARK 3 FREE R VALUE TEST SET COUNT : 2279 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 75.4600 - 5.4200 1.00 2850 150 0.1913 0.2110 REMARK 3 2 5.4100 - 4.3000 1.00 2796 154 0.1442 0.1942 REMARK 3 3 4.3000 - 3.7600 1.00 2792 156 0.1550 0.1896 REMARK 3 4 3.7500 - 3.4100 1.00 2755 161 0.1876 0.2000 REMARK 3 5 3.4100 - 3.1700 1.00 2787 148 0.1845 0.2174 REMARK 3 6 3.1700 - 2.9800 1.00 2803 136 0.2133 0.2511 REMARK 3 7 2.9800 - 2.8300 1.00 2788 133 0.2214 0.2703 REMARK 3 8 2.8300 - 2.7100 1.00 2783 139 0.2343 0.2927 REMARK 3 9 2.7100 - 2.6000 1.00 2773 143 0.2474 0.2848 REMARK 3 10 2.6000 - 2.5100 1.00 2761 124 0.2698 0.3615 REMARK 3 11 2.5100 - 2.4400 0.99 2752 138 0.2697 0.3045 REMARK 3 12 2.4400 - 2.3700 1.00 2776 147 0.2759 0.3033 REMARK 3 13 2.3700 - 2.3000 1.00 2772 136 0.2907 0.3490 REMARK 3 14 2.3000 - 2.2500 0.94 2610 141 0.4099 0.4892 REMARK 3 15 2.2500 - 2.2000 0.91 2500 149 0.4605 0.5024 REMARK 3 16 2.2000 - 2.1500 0.99 2751 124 0.2993 0.3237 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 29.010 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 : 0.005 5524 REMARK 3 ANGLE : 0.594 7575 REMARK 3 CHIRALITY : 0.050 842 REMARK 3 PLANARITY : 0.004 1006 REMARK 3 DIHEDRAL : 14.312 1907 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 57 THROUGH 248 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.5140-103.1577 17.2449 REMARK 3 T TENSOR REMARK 3 T11: 0.2204 T22: 0.2586 REMARK 3 T33: 0.2222 T12: 0.0510 REMARK 3 T13: -0.0214 T23: 0.0068 REMARK 3 L TENSOR REMARK 3 L11: 0.6043 L22: 0.8570 REMARK 3 L33: 4.6526 L12: 0.0209 REMARK 3 L13: -0.7606 L23: 1.2467 REMARK 3 S TENSOR REMARK 3 S11: 0.0728 S12: 0.1795 S13: -0.0448 REMARK 3 S21: -0.1844 S22: 0.1074 S23: -0.0339 REMARK 3 S31: -0.1326 S32: 0.1376 S33: -0.1739 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 249 THROUGH 407 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.3090 -92.1398 54.5374 REMARK 3 T TENSOR REMARK 3 T11: 0.2318 T22: 0.2310 REMARK 3 T33: 0.1569 T12: -0.0089 REMARK 3 T13: 0.0465 T23: 0.0022 REMARK 3 L TENSOR REMARK 3 L11: 2.6761 L22: 1.3498 REMARK 3 L33: 2.2506 L12: 0.0218 REMARK 3 L13: 1.1301 L23: -0.0601 REMARK 3 S TENSOR REMARK 3 S11: 0.0671 S12: -0.2804 S13: 0.0467 REMARK 3 S21: 0.1245 S22: -0.1028 S23: -0.0961 REMARK 3 S31: -0.0796 S32: 0.0392 S33: 0.0360 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 57 THROUGH 157 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.7435 -80.3157 -32.2604 REMARK 3 T TENSOR REMARK 3 T11: 0.1725 T22: 0.1743 REMARK 3 T33: 0.2108 T12: 0.0097 REMARK 3 T13: 0.0325 T23: -0.0274 REMARK 3 L TENSOR REMARK 3 L11: 0.6076 L22: 3.2445 REMARK 3 L33: 3.9767 L12: 0.2229 REMARK 3 L13: 0.7251 L23: -1.7938 REMARK 3 S TENSOR REMARK 3 S11: -0.0402 S12: -0.0491 S13: 0.1141 REMARK 3 S21: -0.2097 S22: 0.0463 S23: 0.0535 REMARK 3 S31: 0.0221 S32: -0.2141 S33: -0.0037 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 158 THROUGH 289 ) REMARK 3 ORIGIN FOR THE GROUP (A): -10.7207 -91.9170 3.8027 REMARK 3 T TENSOR REMARK 3 T11: 0.2615 T22: 0.3324 REMARK 3 T33: 0.2340 T12: 0.1147 REMARK 3 T13: -0.0204 T23: -0.0253 REMARK 3 L TENSOR REMARK 3 L11: 0.5124 L22: 0.2605 REMARK 3 L33: 4.2345 L12: 0.3972 REMARK 3 L13: 0.3627 L23: 0.1360 REMARK 3 S TENSOR REMARK 3 S11: 0.0856 S12: 0.0924 S13: -0.0391 REMARK 3 S21: 0.0727 S22: 0.0766 S23: -0.0838 REMARK 3 S31: 0.0852 S32: 0.2696 S33: -0.1512 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 290 THROUGH 308 ) REMARK 3 ORIGIN FOR THE GROUP (A): -24.3728 -94.8798 13.4155 REMARK 3 T TENSOR REMARK 3 T11: 0.3700 T22: 0.5923 REMARK 3 T33: 0.2156 T12: 0.0020 REMARK 3 T13: -0.0717 T23: -0.0219 REMARK 3 L TENSOR REMARK 3 L11: 4.2141 L22: 0.4877 REMARK 3 L33: 0.5247 L12: -0.7375 REMARK 3 L13: -1.2401 L23: 0.0568 REMARK 3 S TENSOR REMARK 3 S11: 0.1128 S12: 0.5519 S13: -0.1269 REMARK 3 S21: -0.1471 S22: -0.1321 S23: 0.1186 REMARK 3 S31: 0.1441 S32: -0.7782 S33: 0.0201 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 309 THROUGH 341 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.4459 -98.8884 18.1495 REMARK 3 T TENSOR REMARK 3 T11: 0.3684 T22: 0.3204 REMARK 3 T33: 0.3169 T12: 0.0081 REMARK 3 T13: -0.0529 T23: -0.0627 REMARK 3 L TENSOR REMARK 3 L11: 3.9070 L22: 0.1713 REMARK 3 L33: 2.4717 L12: 0.2193 REMARK 3 L13: -0.2928 L23: -0.5809 REMARK 3 S TENSOR REMARK 3 S11: 0.1214 S12: 0.2075 S13: -0.4685 REMARK 3 S21: -0.1918 S22: -0.0594 S23: 0.1575 REMARK 3 S31: 0.3325 S32: -0.4357 S33: -0.0476 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 342 THROUGH 368 ) REMARK 3 ORIGIN FOR THE GROUP (A): -20.9725 -93.5620 26.2466 REMARK 3 T TENSOR REMARK 3 T11: 0.3404 T22: 0.4040 REMARK 3 T33: 0.1830 T12: 0.0005 REMARK 3 T13: -0.0191 T23: -0.0188 REMARK 3 L TENSOR REMARK 3 L11: 2.7414 L22: 5.3871 REMARK 3 L33: 0.9645 L12: 1.7253 REMARK 3 L13: 0.0008 L23: 2.0320 REMARK 3 S TENSOR REMARK 3 S11: 0.1461 S12: -0.2731 S13: -0.0648 REMARK 3 S21: 0.4167 S22: -0.2829 S23: 0.0907 REMARK 3 S31: 0.1468 S32: -0.3778 S33: 0.1347 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 369 THROUGH 407 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.4939 -99.5174 8.7602 REMARK 3 T TENSOR REMARK 3 T11: 0.4254 T22: 0.4372 REMARK 3 T33: 0.2638 T12: 0.1740 REMARK 3 T13: -0.0832 T23: -0.0858 REMARK 3 L TENSOR REMARK 3 L11: 0.8986 L22: 0.9268 REMARK 3 L33: 5.6903 L12: 0.4607 REMARK 3 L13: -0.5281 L23: 0.9546 REMARK 3 S TENSOR REMARK 3 S11: 0.2082 S12: 0.3337 S13: -0.2483 REMARK 3 S21: -0.0308 S22: -0.0703 S23: -0.0808 REMARK 3 S31: 0.5727 S32: 0.4618 S33: -0.1064 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 8BK3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 16-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1292126183. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-MAY-22 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 : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46881 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.150 REMARK 200 RESOLUTION RANGE LOW (A) : 75.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.16700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.19 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 1.35100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: 6RRM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.21 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM NITRATE, 20% PEG 3350, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 47.52850 REMARK 290 SMTRY3 2 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: 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 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 54 REMARK 465 SER A 55 REMARK 465 ALA A 408 REMARK 465 GLN B 54 REMARK 465 SER B 55 REMARK 465 ASP B 56 REMARK 465 ALA B 408 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 57 CG CD1 CD2 REMARK 470 LEU A 58 CD1 CD2 REMARK 470 LYS A 61 CD CE NZ REMARK 470 ARG A 99 NE CZ NH1 NH2 REMARK 470 ARG A 104 NE CZ NH1 NH2 REMARK 470 LEU A 131 CD2 REMARK 470 LEU A 133 CD1 REMARK 470 LYS A 186 CE NZ REMARK 470 LYS A 189 CD CE NZ REMARK 470 LYS A 299 CE NZ REMARK 470 ASN A 313 CG OD1 ND2 REMARK 470 VAL A 342 CG1 REMARK 470 LYS A 407 CE NZ REMARK 470 LEU B 57 CG CD1 CD2 REMARK 470 VAL B 59 CG1 CG2 REMARK 470 LYS B 61 CD CE NZ REMARK 470 ARG B 99 CD NE CZ NH1 NH2 REMARK 470 LEU B 133 CG CD1 CD2 REMARK 470 LYS B 186 NZ REMARK 470 LYS B 189 CG CD CE NZ REMARK 470 LYS B 217 CE NZ REMARK 470 LYS B 299 CE NZ REMARK 470 LYS B 407 CE NZ 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 97 -138.79 -85.26 REMARK 500 TRP A 324 67.65 40.00 REMARK 500 HIS A 347 -57.10 -137.42 REMARK 500 ASN A 405 45.70 -145.14 REMARK 500 ASN B 227 66.70 -100.10 REMARK 500 MET B 303 109.49 -59.00 REMARK 500 HIS B 347 -56.59 -137.87 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 987 DISTANCE = 6.18 ANGSTROMS REMARK 525 HOH B 954 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH B 955 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH B 956 DISTANCE = 6.05 ANGSTROMS DBREF 8BK3 A 56 408 UNP O53223 LDT2_MYCTO 56 408 DBREF 8BK3 B 56 408 UNP O53223 LDT2_MYCTO 56 408 SEQADV 8BK3 GLN A 54 UNP O53223 EXPRESSION TAG SEQADV 8BK3 SER A 55 UNP O53223 EXPRESSION TAG SEQADV 8BK3 GLN B 54 UNP O53223 EXPRESSION TAG SEQADV 8BK3 SER B 55 UNP O53223 EXPRESSION TAG SEQRES 1 A 355 GLN SER ASP LEU LEU VAL PRO LYS LEU THR ALA SER VAL SEQRES 2 A 355 THR ASP GLY ALA VAL GLY VAL THR VAL ASP ALA PRO VAL SEQRES 3 A 355 SER VAL THR ALA ALA ASP GLY VAL LEU ALA ALA VAL THR SEQRES 4 A 355 MET VAL ASN ASP ASN GLY ARG PRO VAL ALA GLY ARG LEU SEQRES 5 A 355 SER PRO ASP GLY LEU ARG TRP SER THR THR GLU GLN LEU SEQRES 6 A 355 GLY TYR ASN ARG ARG TYR THR LEU ASN ALA THR ALA LEU SEQRES 7 A 355 GLY LEU GLY GLY ALA ALA THR ARG GLN LEU THR PHE GLN SEQRES 8 A 355 THR SER SER PRO ALA HIS LEU THR MET PRO TYR VAL MET SEQRES 9 A 355 PRO GLY ASP GLY GLU VAL VAL GLY VAL GLY GLU PRO VAL SEQRES 10 A 355 ALA ILE ARG PHE ASP GLU ASN ILE ALA ASP ARG GLY ALA SEQRES 11 A 355 ALA GLU LYS ALA ILE LYS ILE THR THR ASN PRO PRO VAL SEQRES 12 A 355 GLU GLY ALA PHE TYR TRP LEU ASN ASN ARG GLU VAL ARG SEQRES 13 A 355 TRP ARG PRO GLU HIS PHE TRP LYS PRO GLY THR ALA VAL SEQRES 14 A 355 ASP VAL ALA VAL ASN THR TYR GLY VAL ASP LEU GLY GLU SEQRES 15 A 355 GLY MET PHE GLY GLU ASP ASN VAL GLN THR HIS PHE THR SEQRES 16 A 355 ILE GLY ASP GLU VAL ILE ALA THR ALA ASP ASP ASN THR SEQRES 17 A 355 LYS ILE LEU THR VAL ARG VAL ASN GLY GLU VAL VAL LYS SEQRES 18 A 355 SER MET PRO THR SER MET GLY LYS ASP SER THR PRO THR SEQRES 19 A 355 ALA ASN GLY ILE TYR ILE VAL GLY SER ARG TYR LYS HIS SEQRES 20 A 355 ILE ILE MET ASP SER SER THR TYR GLY VAL PRO VAL ASN SEQRES 21 A 355 SER PRO ASN GLY TYR ARG THR ASP VAL ASP TRP ALA THR SEQRES 22 A 355 GLN ILE SER TYR SER GLY VAL PHE VAL HIS SER ALA PRO SEQRES 23 A 355 TRP SER VAL GLY ALA GLN GLY HIS THR ASN THR SER HIS SEQRES 24 A 355 GLY CYS LEU ASN VAL SER PRO SER ASN ALA GLN TRP PHE SEQRES 25 A 355 TYR ASP HIS VAL LYS ARG GLY ASP ILE VAL GLU VAL VAL SEQRES 26 A 355 ASN THR VAL GLY GLY THR LEU PRO GLY ILE ASP GLY LEU SEQRES 27 A 355 GLY ASP TRP ASN ILE PRO TRP ASP GLN TRP ARG ALA GLY SEQRES 28 A 355 ASN ALA LYS ALA SEQRES 1 B 355 GLN SER ASP LEU LEU VAL PRO LYS LEU THR ALA SER VAL SEQRES 2 B 355 THR ASP GLY ALA VAL GLY VAL THR VAL ASP ALA PRO VAL SEQRES 3 B 355 SER VAL THR ALA ALA ASP GLY VAL LEU ALA ALA VAL THR SEQRES 4 B 355 MET VAL ASN ASP ASN GLY ARG PRO VAL ALA GLY ARG LEU SEQRES 5 B 355 SER PRO ASP GLY LEU ARG TRP SER THR THR GLU GLN LEU SEQRES 6 B 355 GLY TYR ASN ARG ARG TYR THR LEU ASN ALA THR ALA LEU SEQRES 7 B 355 GLY LEU GLY GLY ALA ALA THR ARG GLN LEU THR PHE GLN SEQRES 8 B 355 THR SER SER PRO ALA HIS LEU THR MET PRO TYR VAL MET SEQRES 9 B 355 PRO GLY ASP GLY GLU VAL VAL GLY VAL GLY GLU PRO VAL SEQRES 10 B 355 ALA ILE ARG PHE ASP GLU ASN ILE ALA ASP ARG GLY ALA SEQRES 11 B 355 ALA GLU LYS ALA ILE LYS ILE THR THR ASN PRO PRO VAL SEQRES 12 B 355 GLU GLY ALA PHE TYR TRP LEU ASN ASN ARG GLU VAL ARG SEQRES 13 B 355 TRP ARG PRO GLU HIS PHE TRP LYS PRO GLY THR ALA VAL SEQRES 14 B 355 ASP VAL ALA VAL ASN THR TYR GLY VAL ASP LEU GLY GLU SEQRES 15 B 355 GLY MET PHE GLY GLU ASP ASN VAL GLN THR HIS PHE THR SEQRES 16 B 355 ILE GLY ASP GLU VAL ILE ALA THR ALA ASP ASP ASN THR SEQRES 17 B 355 LYS ILE LEU THR VAL ARG VAL ASN GLY GLU VAL VAL LYS SEQRES 18 B 355 SER MET PRO THR SER MET GLY LYS ASP SER THR PRO THR SEQRES 19 B 355 ALA ASN GLY ILE TYR ILE VAL GLY SER ARG TYR LYS HIS SEQRES 20 B 355 ILE ILE MET ASP SER SER THR TYR GLY VAL PRO VAL ASN SEQRES 21 B 355 SER PRO ASN GLY TYR ARG THR ASP VAL ASP TRP ALA THR SEQRES 22 B 355 GLN ILE SER TYR SER GLY VAL PHE VAL HIS SER ALA PRO SEQRES 23 B 355 TRP SER VAL GLY ALA GLN GLY HIS THR ASN THR SER HIS SEQRES 24 B 355 GLY CYS LEU ASN VAL SER PRO SER ASN ALA GLN TRP PHE SEQRES 25 B 355 TYR ASP HIS VAL LYS ARG GLY ASP ILE VAL GLU VAL VAL SEQRES 26 B 355 ASN THR VAL GLY GLY THR LEU PRO GLY ILE ASP GLY LEU SEQRES 27 B 355 GLY ASP TRP ASN ILE PRO TRP ASP GLN TRP ARG ALA GLY SEQRES 28 B 355 ASN ALA LYS ALA HET QXU A 501 12 HET NO3 A 502 4 HET NO3 A 503 4 HET NO3 A 504 4 HET GOL A 505 6 HET EDO A 506 4 HET NO3 B 501 4 HET DMS B 502 4 HET DMS B 503 4 HETNAM QXU 1-[(2~{S},3~{R})-3-PHENYLOXIRAN-2-YL]ETHANONE HETNAM NO3 NITRATE ION HETNAM GOL GLYCEROL HETNAM EDO 1,2-ETHANEDIOL HETNAM DMS DIMETHYL SULFOXIDE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 QXU C10 H10 O2 FORMUL 4 NO3 4(N O3 1-) FORMUL 7 GOL C3 H8 O3 FORMUL 8 EDO C2 H6 O2 FORMUL 10 DMS 2(C2 H6 O S) FORMUL 12 HOH *743(H2 O) HELIX 1 AA1 ASP A 180 ALA A 187 1 8 HELIX 2 AA2 SER A 306 GLY A 309 5 4 HELIX 3 AA3 PRO A 339 VAL A 342 5 4 HELIX 4 AA4 SER A 358 VAL A 369 1 12 HELIX 5 AA5 GLY A 392 ILE A 396 5 5 HELIX 6 AA6 PRO A 397 GLY A 404 1 8 HELIX 7 AA7 ASP B 180 ALA B 187 1 8 HELIX 8 AA8 SER B 306 GLY B 309 5 4 HELIX 9 AA9 PRO B 339 VAL B 342 5 4 HELIX 10 AB1 SER B 358 VAL B 369 1 12 HELIX 11 AB2 GLY B 392 ILE B 396 5 5 HELIX 12 AB3 PRO B 397 GLY B 404 1 8 SHEET 1 AA1 4 LYS A 61 ALA A 64 0 SHEET 2 AA1 4 SER A 80 ALA A 84 -1 O THR A 82 N THR A 63 SHEET 3 AA1 4 ARG A 111 THR A 114 -1 O TRP A 112 N VAL A 81 SHEET 4 AA1 4 GLY A 103 LEU A 105 -1 N ARG A 104 O SER A 113 SHEET 1 AA2 3 VAL A 87 VAL A 94 0 SHEET 2 AA2 3 ARG A 123 GLY A 132 -1 O THR A 125 N VAL A 94 SHEET 3 AA2 3 GLY A 135 GLN A 144 -1 O LEU A 141 N LEU A 126 SHEET 1 AA3 2 HIS A 150 THR A 152 0 SHEET 2 AA3 2 MET A 237 GLY A 239 1 O PHE A 238 N HIS A 150 SHEET 1 AA4 4 PRO A 154 MET A 157 0 SHEET 2 AA4 4 VAL A 170 PHE A 174 -1 O ARG A 173 N TYR A 155 SHEET 3 AA4 4 GLU A 207 PRO A 212 -1 O TRP A 210 N VAL A 170 SHEET 4 AA4 4 GLY A 198 TRP A 202 -1 N TYR A 201 O ARG A 209 SHEET 1 AA5 4 VAL A 163 VAL A 164 0 SHEET 2 AA5 4 VAL A 243 ILE A 249 1 O THR A 248 N VAL A 164 SHEET 3 AA5 4 ALA A 221 VAL A 226 -1 N VAL A 224 O THR A 245 SHEET 4 AA5 4 ILE A 188 ASN A 193 -1 N ASN A 193 O ALA A 221 SHEET 1 AA6 5 GLU A 271 PRO A 277 0 SHEET 2 AA6 5 ILE A 263 VAL A 268 -1 N LEU A 264 O MET A 276 SHEET 3 AA6 5 VAL A 253 ASP A 258 -1 N THR A 256 O THR A 265 SHEET 4 AA6 5 ILE A 374 VAL A 378 1 O ILE A 374 N ALA A 255 SHEET 5 AA6 5 GLY A 290 ILE A 293 -1 N TYR A 292 O VAL A 375 SHEET 1 AA7 4 ARG A 297 ASP A 304 0 SHEET 2 AA7 4 ARG A 319 GLN A 327 -1 O THR A 320 N MET A 303 SHEET 3 AA7 4 PHE A 334 SER A 337 -1 O VAL A 335 N THR A 326 SHEET 4 AA7 4 LEU A 355 VAL A 357 1 O LEU A 355 N PHE A 334 SHEET 1 AA8 4 LYS B 61 ALA B 64 0 SHEET 2 AA8 4 SER B 80 ALA B 84 -1 O THR B 82 N THR B 63 SHEET 3 AA8 4 ARG B 111 THR B 114 -1 O TRP B 112 N VAL B 81 SHEET 4 AA8 4 GLY B 103 LEU B 105 -1 N ARG B 104 O SER B 113 SHEET 1 AA9 3 VAL B 87 VAL B 94 0 SHEET 2 AA9 3 ARG B 123 GLY B 132 -1 O THR B 125 N VAL B 94 SHEET 3 AA9 3 GLY B 135 GLN B 144 -1 O ALA B 137 N ALA B 130 SHEET 1 AB1 2 HIS B 150 THR B 152 0 SHEET 2 AB1 2 MET B 237 GLY B 239 1 O PHE B 238 N HIS B 150 SHEET 1 AB2 4 PRO B 154 MET B 157 0 SHEET 2 AB2 4 VAL B 170 PHE B 174 -1 O ARG B 173 N TYR B 155 SHEET 3 AB2 4 GLU B 207 PRO B 212 -1 O TRP B 210 N VAL B 170 SHEET 4 AB2 4 GLY B 198 TRP B 202 -1 N TYR B 201 O ARG B 209 SHEET 1 AB3 4 VAL B 163 VAL B 164 0 SHEET 2 AB3 4 VAL B 243 ILE B 249 1 O THR B 248 N VAL B 164 SHEET 3 AB3 4 ALA B 221 VAL B 226 -1 N VAL B 226 O VAL B 243 SHEET 4 AB3 4 ILE B 188 ASN B 193 -1 N ASN B 193 O ALA B 221 SHEET 1 AB4 5 GLU B 271 PRO B 277 0 SHEET 2 AB4 5 ILE B 263 VAL B 268 -1 N LEU B 264 O MET B 276 SHEET 3 AB4 5 VAL B 253 ASP B 258 -1 N THR B 256 O THR B 265 SHEET 4 AB4 5 ILE B 374 VAL B 378 1 O GLU B 376 N ALA B 257 SHEET 5 AB4 5 GLY B 290 ILE B 293 -1 N TYR B 292 O VAL B 375 SHEET 1 AB5 4 ARG B 297 ASP B 304 0 SHEET 2 AB5 4 ARG B 319 GLN B 327 -1 O ALA B 325 N TYR B 298 SHEET 3 AB5 4 PHE B 334 SER B 337 -1 O VAL B 335 N THR B 326 SHEET 4 AB5 4 LEU B 355 VAL B 357 1 O LEU B 355 N PHE B 334 LINK SG CYS A 354 C12 QXU A 501 1555 1555 1.82 CISPEP 1 MET A 157 PRO A 158 0 0.31 CISPEP 2 ASN A 193 PRO A 194 0 -0.60 CISPEP 3 MET B 157 PRO B 158 0 0.04 CISPEP 4 MET B 157 PRO B 158 0 -0.03 CISPEP 5 ASN B 193 PRO B 194 0 0.38 CRYST1 60.933 95.057 75.535 90.00 92.60 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 0.016411 0.000000 0.000745 0.00000 SCALE2 0.000000 0.010520 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013253 0.00000