HEADER ANTIMICROBIAL PROTEIN 20-MAY-19 6RRM TITLE CRYSTAL STRUCTURE OF LDTMT2 FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO TITLE 2 EBSELEN 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 CDC1551; SOURCE 3 ORGANISM_TAXID: 83331; SOURCE 4 VARIANT: CDC 1551 / OSHKOSH; SOURCE 5 GENE: LDTB, MT2594, V735_02606; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA LACTMASE, ANTIBIOTIC RESISTANCE, TUBERCULOSIS, ANTIMICROBIAL KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.BREM,C.LOHANS,C.SCHOFIELD REVDAT 5 07-FEB-24 6RRM 1 REMARK REVDAT 4 12-APR-23 6RRM 1 COMPND HETNAM HETSYN REVDAT 3 04-SEP-19 6RRM 1 JRNL REVDAT 2 21-AUG-19 6RRM 1 REMARK REVDAT 1 14-AUG-19 6RRM 0 JRNL AUTH M.DE MUNNIK,C.T.LOHANS,P.A.LANG,G.W.LANGLEY,T.R.MALLA, JRNL AUTH 2 A.TUMBER,C.J.SCHOFIELD,J.BREM JRNL TITL TARGETING THE MYCOBACTERIUM TUBERCULOSIS TRANSPEPTIDASE JRNL TITL 2 LDTMT2WITH CYSTEINE-REACTIVE INHIBITORS INCLUDING EBSELEN. JRNL REF CHEM.COMMUN.(CAMB.) V. 55 10214 2019 JRNL REFN ESSN 1364-548X JRNL PMID 31380528 JRNL DOI 10.1039/C9CC04145A REMARK 2 REMARK 2 RESOLUTION. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.75 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 103680 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.200 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 5088 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 48.7742 - 5.0940 1.00 3394 150 0.1869 0.1742 REMARK 3 2 5.0940 - 4.0439 1.00 3310 177 0.1503 0.1570 REMARK 3 3 4.0439 - 3.5329 0.99 3294 187 0.1754 0.1845 REMARK 3 4 3.5329 - 3.2100 1.00 3304 164 0.1914 0.2013 REMARK 3 5 3.2100 - 2.9799 1.00 3308 163 0.1973 0.2376 REMARK 3 6 2.9799 - 2.8042 1.00 3244 179 0.2087 0.2401 REMARK 3 7 2.8042 - 2.6638 1.00 3279 183 0.2081 0.2578 REMARK 3 8 2.6638 - 2.5479 1.00 3285 169 0.1975 0.2213 REMARK 3 9 2.5479 - 2.4498 1.00 3288 163 0.1896 0.2337 REMARK 3 10 2.4498 - 2.3653 1.00 3298 180 0.1959 0.2352 REMARK 3 11 2.3653 - 2.2913 1.00 3269 173 0.1890 0.2506 REMARK 3 12 2.2913 - 2.2258 1.00 3277 163 0.1997 0.2182 REMARK 3 13 2.2258 - 2.1672 1.00 3303 169 0.1964 0.2413 REMARK 3 14 2.1672 - 2.1143 1.00 3240 195 0.2036 0.2463 REMARK 3 15 2.1143 - 2.0663 1.00 3298 179 0.2121 0.2692 REMARK 3 16 2.0663 - 2.0223 1.00 3290 188 0.2203 0.2589 REMARK 3 17 2.0223 - 1.9818 1.00 3234 161 0.2175 0.2412 REMARK 3 18 1.9818 - 1.9444 1.00 3322 167 0.2150 0.2557 REMARK 3 19 1.9444 - 1.9097 1.00 3269 157 0.2363 0.2942 REMARK 3 20 1.9097 - 1.8773 1.00 3289 158 0.2378 0.2933 REMARK 3 21 1.8773 - 1.8471 1.00 3269 169 0.2486 0.3186 REMARK 3 22 1.8471 - 1.8186 1.00 3308 163 0.2630 0.3108 REMARK 3 23 1.8186 - 1.7919 1.00 3268 174 0.2756 0.3327 REMARK 3 24 1.7919 - 1.7666 1.00 3304 177 0.2857 0.3217 REMARK 3 25 1.7666 - 1.7428 1.00 3255 158 0.3014 0.3254 REMARK 3 26 1.7428 - 1.7201 1.00 3268 156 0.3251 0.3535 REMARK 3 27 1.7201 - 1.6986 1.00 3313 163 0.3509 0.4160 REMARK 3 28 1.6986 - 1.6782 1.00 3286 175 0.3600 0.3560 REMARK 3 29 1.6782 - 1.6587 1.00 3281 159 0.3816 0.3937 REMARK 3 30 1.6587 - 1.6400 1.00 3245 169 0.3972 0.4214 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) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.790 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 37.50 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 : 0.006 5552 REMARK 3 ANGLE : 0.810 7622 REMARK 3 CHIRALITY : 0.057 843 REMARK 3 PLANARITY : 0.005 1010 REMARK 3 DIHEDRAL : 12.962 3177 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 249 THROUGH 407 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.4339 -91.4348 54.5638 REMARK 3 T TENSOR REMARK 3 T11: 0.2272 T22: 0.2054 REMARK 3 T33: 0.2298 T12: -0.0383 REMARK 3 T13: 0.0098 T23: 0.0074 REMARK 3 L TENSOR REMARK 3 L11: 2.3982 L22: 1.4333 REMARK 3 L33: 2.5908 L12: -0.6496 REMARK 3 L13: 1.1294 L23: -0.2857 REMARK 3 S TENSOR REMARK 3 S11: 0.0405 S12: -0.2192 S13: 0.2429 REMARK 3 S21: 0.0574 S22: -0.1116 S23: -0.1919 REMARK 3 S31: -0.2166 S32: 0.0960 S33: 0.0506 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 57 THROUGH 289 ) REMARK 3 ORIGIN FOR THE GROUP (A): -11.2902 -87.3982 -11.5905 REMARK 3 T TENSOR REMARK 3 T11: 0.2165 T22: 0.3447 REMARK 3 T33: 0.2804 T12: 0.0402 REMARK 3 T13: 0.0021 T23: -0.0226 REMARK 3 L TENSOR REMARK 3 L11: 0.0210 L22: 0.6688 REMARK 3 L33: 3.0236 L12: 0.0292 REMARK 3 L13: -0.2429 L23: -0.8906 REMARK 3 S TENSOR REMARK 3 S11: 0.0176 S12: -0.0899 S13: 0.0466 REMARK 3 S21: 0.0902 S22: 0.0632 S23: -0.0494 REMARK 3 S31: -0.0399 S32: 0.1798 S33: -0.0882 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 290 THROUGH 318 ) REMARK 3 ORIGIN FOR THE GROUP (A): -27.8092 -99.8239 14.9677 REMARK 3 T TENSOR REMARK 3 T11: 0.4658 T22: 0.4022 REMARK 3 T33: 0.2958 T12: 0.1210 REMARK 3 T13: -0.1592 T23: -0.0074 REMARK 3 L TENSOR REMARK 3 L11: 6.9434 L22: 1.7453 REMARK 3 L33: 4.2924 L12: -0.4584 REMARK 3 L13: -0.6535 L23: 0.9250 REMARK 3 S TENSOR REMARK 3 S11: 0.4915 S12: 0.2078 S13: -0.7876 REMARK 3 S21: 0.1090 S22: -0.0729 S23: 0.3994 REMARK 3 S31: 0.5852 S32: -0.3267 S33: -0.0120 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'B' AND (RESID 319 THROUGH 407 ) REMARK 3 ORIGIN FOR THE GROUP (A): -17.6931 -97.1301 16.8762 REMARK 3 T TENSOR REMARK 3 T11: 0.3733 T22: 0.2937 REMARK 3 T33: 0.2606 T12: 0.0783 REMARK 3 T13: -0.0599 T23: -0.0238 REMARK 3 L TENSOR REMARK 3 L11: 1.5274 L22: 0.9704 REMARK 3 L33: 3.2239 L12: -0.2358 REMARK 3 L13: -0.4060 L23: 0.3410 REMARK 3 S TENSOR REMARK 3 S11: 0.2126 S12: 0.0495 S13: -0.2514 REMARK 3 S21: 0.0602 S22: -0.1035 S23: -0.0086 REMARK 3 S31: 0.3405 S32: 0.0962 S33: -0.1438 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 57 THROUGH 248 ) REMARK 3 ORIGIN FOR THE GROUP (A): 10.3521-102.7432 17.2768 REMARK 3 T TENSOR REMARK 3 T11: 0.2599 T22: 0.3662 REMARK 3 T33: 0.2535 T12: 0.0894 REMARK 3 T13: -0.0038 T23: 0.0310 REMARK 3 L TENSOR REMARK 3 L11: 0.0068 L22: 0.2494 REMARK 3 L33: 4.2889 L12: 0.1626 REMARK 3 L13: -0.3701 L23: 1.3637 REMARK 3 S TENSOR REMARK 3 S11: 0.0267 S12: 0.1547 S13: 0.0036 REMARK 3 S21: -0.0732 S22: 0.0947 S23: -0.0465 REMARK 3 S31: -0.0126 S32: 0.4353 S33: -0.1139 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 6RRM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1292102484. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-AUG-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.3 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) : 0.97625 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.1 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 103762 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 58.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.68 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 1.56300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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 2.7.16 REMARK 200 STARTING MODEL: 5DUJ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.15 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM NITRATE PH 6.3, 20% PEG REMARK 280 3350, 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 46.78500 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 SER A 54 REMARK 465 MET A 55 REMARK 465 ASP A 56 REMARK 465 ALA A 408 REMARK 465 SER B 54 REMARK 465 MET 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 LYS A 61 CE NZ REMARK 470 ARG A 99 CZ NH1 NH2 REMARK 470 ARG A 104 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 123 CZ NH1 NH2 REMARK 470 LEU A 133 CD1 REMARK 470 LYS A 189 CE NZ REMARK 470 LYS A 299 CG CD CE NZ REMARK 470 LYS A 407 CE NZ REMARK 470 LEU B 57 CG CD1 CD2 REMARK 470 LEU B 58 CG CD1 CD2 REMARK 470 LYS B 61 CE NZ REMARK 470 ARG B 99 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 104 CD NE CZ NH1 NH2 REMARK 470 ARG B 123 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 CD CE NZ REMARK 470 SER B 306 OG REMARK 470 THR B 307 OG1 CG2 REMARK 470 VAL B 310 CG1 CG2 REMARK 470 ASN B 313 CG OD1 ND2 REMARK 470 ASN B 316 CG OD1 ND2 REMARK 470 VAL B 322 CG1 CG2 REMARK 470 ARG B 402 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 O HOH B 740 O HOH B 853 1.86 REMARK 500 O HOH A 654 O HOH A 755 1.98 REMARK 500 O HOH B 798 O HOH B 813 2.00 REMARK 500 O HOH B 735 O HOH B 760 2.09 REMARK 500 O HOH B 661 O HOH B 805 2.12 REMARK 500 OE2 GLU A 213 O HOH A 601 2.13 REMARK 500 O HOH A 610 O HOH A 806 2.15 REMARK 500 O PRO A 311 OG SER A 314 2.18 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 180 78.49 -119.33 REMARK 500 ASN A 227 64.58 -102.44 REMARK 500 MET A 280 -165.74 -104.13 REMARK 500 HIS A 347 -60.12 -131.01 REMARK 500 ASN A 405 37.21 -146.86 REMARK 500 ASN B 204 -167.54 -162.82 REMARK 500 ASN B 227 62.37 -101.60 REMARK 500 MET B 280 -159.60 -100.18 REMARK 500 TYR B 308 -155.50 -105.44 REMARK 500 HIS B 347 -56.84 -130.40 REMARK 500 ASN B 405 36.68 -144.45 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NH4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NH4 A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9JT A 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NH4 B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 504 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide 9JT B 503 and CYS B REMARK 800 354 DBREF 6RRM A 56 408 UNP O53223 LDT2_MYCTO 56 408 DBREF 6RRM B 56 408 UNP O53223 LDT2_MYCTO 56 408 SEQADV 6RRM SER A 54 UNP O53223 EXPRESSION TAG SEQADV 6RRM MET A 55 UNP O53223 EXPRESSION TAG SEQADV 6RRM SER B 54 UNP O53223 EXPRESSION TAG SEQADV 6RRM MET B 55 UNP O53223 EXPRESSION TAG SEQRES 1 A 355 SER MET 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 SER MET 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 NH4 A 501 1 HET GOL A 502 6 HET NH4 A 503 1 HET 9JT A 504 32 HET EDO B 501 4 HET NH4 B 502 1 HET 9JT B 503 16 HET EDO B 504 4 HETNAM NH4 AMMONIUM ION HETNAM GOL GLYCEROL HETNAM 9JT N-PHENYL-2-SELANYLBENZAMIDE HETNAM EDO 1,2-ETHANEDIOL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL HETSYN 9JT ~{N}-PHENYL-2-SELANYL-BENZAMIDE; EBSELEN, BOUND FORM HETSYN EDO ETHYLENE GLYCOL FORMUL 3 NH4 3(H4 N 1+) FORMUL 4 GOL C3 H8 O3 FORMUL 6 9JT 2(C13 H11 N O SE) FORMUL 7 EDO 2(C2 H6 O2) FORMUL 11 HOH *532(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 TYR B 308 5 3 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 LEU A 131 N VAL A 87 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 226 O VAL A 243 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 GLU A 376 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 ALA B 84 N LYS B 61 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 ASN B 127 N THR B 92 SHEET 3 AA9 3 GLY B 135 GLN B 144 -1 O LEU B 141 N LEU B 126 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 ILE B 374 N ALA B 255 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 THR B 320 N MET B 303 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 ACYS A 354 SE1 A9JT A 504 1555 1555 2.24 LINK SG BCYS A 354 SE1 B9JT A 504 1555 1555 2.23 LINK SG CYS B 354 SE1 9JT B 503 1555 1555 2.25 CISPEP 1 MET A 157 PRO A 158 0 -0.54 CISPEP 2 ASN A 193 PRO A 194 0 0.33 CISPEP 3 MET B 157 PRO B 158 0 -3.41 CISPEP 4 ASN B 193 PRO B 194 0 -2.05 SITE 1 AC1 1 ALA A 171 SITE 1 AC2 3 HIS A 214 PHE A 215 ILE A 291 SITE 1 AC3 1 ILE A 190 SITE 1 AC4 12 MET A 303 ASN A 316 GLY A 317 TYR A 318 SITE 2 AC4 12 SER A 331 GLY A 332 PHE A 334 HIS A 336 SITE 3 AC4 12 HIS A 352 GLY A 353 CYS A 354 HOH A 670 SITE 1 AC5 6 HOH A 779 ASN B 95 VAL B 101 GLN B 117 SITE 2 AC5 6 ARG B 122 TYR B 124 SITE 1 AC6 1 ALA B 171 SITE 1 AC7 2 LYS A 299 TRP A 324 SITE 1 AC8 15 SER B 279 MET B 280 MET B 303 TYR B 318 SITE 2 AC8 15 SER B 331 GLY B 332 PHE B 334 HIS B 336 SITE 3 AC8 15 SER B 351 HIS B 352 GLY B 353 LEU B 355 SITE 4 AC8 15 ASN B 356 HOH B 615 HOH B 710 CRYST1 61.220 93.570 75.490 90.00 93.01 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 0.016335 0.000000 0.000859 0.00000 SCALE2 0.000000 0.010687 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013265 0.00000