HEADER LYASE 02-APR-16 5J5D TITLE CRYSTAL STRUCTURE OF DIHYDRODIPICOLINATE SYNTHASE FROM MYCOBACTERIUM TITLE 2 TUBERCULOSIS IN COMPLEX WITH ALPHA-KETOPIMELIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: 4-HYDROXY-TETRAHYDRODIPICOLINATE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DIHYDRODIPICOLINATE SYNTHASE; COMPND 5 EC: 4.3.3.7; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS H37RV; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: DAPA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DAP PATHWAY, L-LYSINE, ALPHA-KETOPIMELIC ACID, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR V.NAVRATNA,B.GOPAL REVDAT 3 08-NOV-23 5J5D 1 LINK REVDAT 2 20-DEC-17 5J5D 1 JRNL REMARK REVDAT 1 17-AUG-16 5J5D 0 JRNL AUTH P.SHRIVASTAVA,V.NAVRATNA,Y.SILLA,R.P.DEWANGAN,A.PRAMANIK, JRNL AUTH 2 S.CHAUDHARY,G.RAYASAM,A.KUMAR,B.GOPAL,S.RAMACHANDRAN JRNL TITL INHIBITION OF MYCOBACTERIUM TUBERCULOSIS DIHYDRODIPICOLINATE JRNL TITL 2 SYNTHASE BY ALPHA-KETOPIMELIC ACID AND ITS OTHER STRUCTURAL JRNL TITL 3 ANALOGUES JRNL REF SCI REP V. 6 30827 2016 JRNL REFN ESSN 2045-2322 JRNL PMID 27501775 JRNL DOI 10.1038/SREP30827 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10_2142: ???) 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.78 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 12276 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.830 REMARK 3 FREE R VALUE TEST SET COUNT : 593 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 48.7906 - 3.8094 0.99 3108 153 0.1569 0.1942 REMARK 3 2 3.8094 - 3.0237 0.99 2915 149 0.1926 0.2641 REMARK 3 3 3.0237 - 2.6415 0.98 2866 143 0.2481 0.3111 REMARK 3 4 2.6415 - 2.4000 0.97 2794 148 0.2515 0.3022 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) : 0.350 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.680 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.53 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 : 0.004 2178 REMARK 3 ANGLE : 0.681 2966 REMARK 3 CHIRALITY : 0.043 359 REMARK 3 PLANARITY : 0.004 389 REMARK 3 DIHEDRAL : 14.072 1307 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 4:11) REMARK 3 ORIGIN FOR THE GROUP (A): 112.6165 98.0621 104.6818 REMARK 3 T TENSOR REMARK 3 T11: 0.6491 T22: 0.5289 REMARK 3 T33: 0.7712 T12: -0.0481 REMARK 3 T13: 0.3385 T23: 0.1125 REMARK 3 L TENSOR REMARK 3 L11: 0.3577 L22: 1.8223 REMARK 3 L33: 0.2279 L12: -0.7098 REMARK 3 L13: -0.2827 L23: 0.5985 REMARK 3 S TENSOR REMARK 3 S11: -0.0368 S12: 0.3181 S13: 0.2777 REMARK 3 S21: -0.2902 S22: 0.0865 S23: -1.0530 REMARK 3 S31: -0.1351 S32: 0.7126 S33: -0.0351 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: (CHAIN A AND RESID 12:76) REMARK 3 ORIGIN FOR THE GROUP (A): 91.0943 102.9552 97.9298 REMARK 3 T TENSOR REMARK 3 T11: 0.8015 T22: 0.6150 REMARK 3 T33: 0.3410 T12: -0.1452 REMARK 3 T13: 0.0680 T23: 0.2846 REMARK 3 L TENSOR REMARK 3 L11: 1.9091 L22: 1.8233 REMARK 3 L33: 1.4167 L12: 0.4431 REMARK 3 L13: -0.3088 L23: -0.4730 REMARK 3 S TENSOR REMARK 3 S11: -0.0566 S12: 0.8993 S13: 0.5298 REMARK 3 S21: -0.8964 S22: -0.0501 S23: -0.0758 REMARK 3 S31: -0.5916 S32: 0.1277 S33: -0.0007 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: (CHAIN A AND RESID 77:88) REMARK 3 ORIGIN FOR THE GROUP (A): 100.7168 102.3175 97.8196 REMARK 3 T TENSOR REMARK 3 T11: 0.7279 T22: 0.7859 REMARK 3 T33: 0.3825 T12: -0.3464 REMARK 3 T13: 0.2893 T23: 0.2915 REMARK 3 L TENSOR REMARK 3 L11: 2.8693 L22: 0.3470 REMARK 3 L33: 0.6632 L12: 0.0275 REMARK 3 L13: -0.0810 L23: 0.4770 REMARK 3 S TENSOR REMARK 3 S11: -0.0198 S12: 0.7757 S13: 0.4831 REMARK 3 S21: -0.7315 S22: -0.0426 S23: -0.4692 REMARK 3 S31: -0.3972 S32: 0.2642 S33: 0.0592 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: (CHAIN A AND RESID 89:129) REMARK 3 ORIGIN FOR THE GROUP (A): 95.6474 84.3598 101.6798 REMARK 3 T TENSOR REMARK 3 T11: 0.4976 T22: 0.4686 REMARK 3 T33: 0.2895 T12: -0.0814 REMARK 3 T13: 0.1898 T23: -0.0395 REMARK 3 L TENSOR REMARK 3 L11: 2.3232 L22: 1.0830 REMARK 3 L33: 1.3820 L12: 0.3394 REMARK 3 L13: -0.5370 L23: 0.0288 REMARK 3 S TENSOR REMARK 3 S11: -0.1754 S12: 0.7533 S13: -0.2812 REMARK 3 S21: -0.7924 S22: 0.1727 S23: -0.4100 REMARK 3 S31: -0.1240 S32: 0.3640 S33: 0.1061 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: (CHAIN A AND RESID 130:138) REMARK 3 ORIGIN FOR THE GROUP (A): 105.1230 84.9446 98.3130 REMARK 3 T TENSOR REMARK 3 T11: 0.5895 T22: 0.8306 REMARK 3 T33: 0.5940 T12: -0.0985 REMARK 3 T13: 0.3632 T23: -0.0417 REMARK 3 L TENSOR REMARK 3 L11: 1.1616 L22: 1.8157 REMARK 3 L33: 0.6091 L12: -1.3527 REMARK 3 L13: 0.4415 L23: -0.1799 REMARK 3 S TENSOR REMARK 3 S11: -0.0801 S12: 0.9309 S13: 0.1420 REMARK 3 S21: -0.8804 S22: -0.1717 S23: -0.7396 REMARK 3 S31: -0.1687 S32: 0.6385 S33: 0.1856 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: (CHAIN A AND RESID 139:223) REMARK 3 ORIGIN FOR THE GROUP (A): 100.5989 94.1935 114.4891 REMARK 3 T TENSOR REMARK 3 T11: 0.2844 T22: 0.3339 REMARK 3 T33: 0.3460 T12: -0.1304 REMARK 3 T13: 0.0651 T23: 0.1162 REMARK 3 L TENSOR REMARK 3 L11: 1.7236 L22: 1.1344 REMARK 3 L33: 1.0055 L12: 0.4070 REMARK 3 L13: 0.1331 L23: -0.2958 REMARK 3 S TENSOR REMARK 3 S11: -0.0337 S12: 0.4350 S13: 0.1867 REMARK 3 S21: -0.3971 S22: -0.1040 S23: -0.5125 REMARK 3 S31: -0.1863 S32: 0.5174 S33: 0.1145 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: (CHAIN A AND RESID 224:239) REMARK 3 ORIGIN FOR THE GROUP (A): 103.6994 112.2485 121.3377 REMARK 3 T TENSOR REMARK 3 T11: 0.5570 T22: 0.3457 REMARK 3 T33: 0.6905 T12: -0.2585 REMARK 3 T13: -0.0595 T23: 0.0619 REMARK 3 L TENSOR REMARK 3 L11: 1.8033 L22: 0.6708 REMARK 3 L33: 3.4660 L12: 0.1713 REMARK 3 L13: -1.9148 L23: 0.7916 REMARK 3 S TENSOR REMARK 3 S11: 0.0377 S12: 0.2265 S13: 0.5251 REMARK 3 S21: -0.0532 S22: -0.0257 S23: -0.4877 REMARK 3 S31: -0.5754 S32: 0.4349 S33: -0.0752 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: (CHAIN A AND RESID 240:300) REMARK 3 ORIGIN FOR THE GROUP (A): 81.6092 108.4162 111.5069 REMARK 3 T TENSOR REMARK 3 T11: 0.5392 T22: 0.3126 REMARK 3 T33: 0.4264 T12: 0.0253 REMARK 3 T13: -0.1113 T23: 0.1367 REMARK 3 L TENSOR REMARK 3 L11: 1.4260 L22: 1.0483 REMARK 3 L33: 1.3206 L12: 0.2768 REMARK 3 L13: -0.1970 L23: 0.2625 REMARK 3 S TENSOR REMARK 3 S11: -0.0457 S12: 0.4620 S13: 0.7304 REMARK 3 S21: -0.4142 S22: -0.1095 S23: 0.0550 REMARK 3 S31: -0.6759 S32: -0.1751 S33: 0.1115 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 5J5D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-APR-16. REMARK 100 THE DEPOSITION ID IS D_1000205647. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12296 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 55.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : 0.10600 REMARK 200 FOR THE DATA SET : 13.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.42000 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 2.5.1 REMARK 200 STARTING MODEL: 1XXX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.34M TRI-SODIUM CITRATE, 0.1M TRIS REMARK 280 -HCL, PH 7.5, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 2 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 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 42.39000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 42.39000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 41.96000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 42.39000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 42.39000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 41.96000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 42.39000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 42.39000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 41.96000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 42.39000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 42.39000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 41.96000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37330 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -136.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 169.56000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 169.56000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 251.76000 REMARK 350 BIOMT1 4 0.000000 -1.000000 0.000000 169.56000 REMARK 350 BIOMT2 4 -1.000000 0.000000 0.000000 169.56000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 251.76000 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 A 541 LIES ON A SPECIAL POSITION. 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 1 REMARK 465 THR A 2 REMARK 465 THR A 3 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 GLU A 75 CG CD OE1 OE2 REMARK 470 LYS A 239 CE NZ REMARK 470 ARG A 300 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 OE2 GLU A 68 O HOH A 501 2.15 REMARK 500 O HOH A 547 O HOH A 550 2.16 REMARK 500 O ILE A 167 O HOH A 502 2.19 REMARK 500 O HOH A 575 O HOH A 587 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ALA A 18 90.09 -65.80 REMARK 500 TYR A 117 -55.20 67.24 REMARK 500 ALA A 150 -0.46 77.47 REMARK 500 ALA A 218 42.46 -149.80 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 NA A 401 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 154 OE2 REMARK 620 2 HOH A 566 O 121.0 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 6GT A 403 DBREF 5J5D A 1 300 UNP P9WP25 DAPA_MYCTU 1 300 SEQRES 1 A 300 MET THR THR VAL GLY PHE ASP VAL ALA ALA ARG LEU GLY SEQRES 2 A 300 THR LEU LEU THR ALA MET VAL THR PRO PHE SER GLY ASP SEQRES 3 A 300 GLY SER LEU ASP THR ALA THR ALA ALA ARG LEU ALA ASN SEQRES 4 A 300 HIS LEU VAL ASP GLN GLY CYS ASP GLY LEU VAL VAL SER SEQRES 5 A 300 GLY THR THR GLY GLU SER PRO THR THR THR ASP GLY GLU SEQRES 6 A 300 LYS ILE GLU LEU LEU ARG ALA VAL LEU GLU ALA VAL GLY SEQRES 7 A 300 ASP ARG ALA ARG VAL ILE ALA GLY ALA GLY THR TYR ASP SEQRES 8 A 300 THR ALA HIS SER ILE ARG LEU ALA LYS ALA CYS ALA ALA SEQRES 9 A 300 GLU GLY ALA HIS GLY LEU LEU VAL VAL THR PRO TYR TYR SEQRES 10 A 300 SER LYS PRO PRO GLN ARG GLY LEU GLN ALA HIS PHE THR SEQRES 11 A 300 ALA VAL ALA ASP ALA THR GLU LEU PRO MET LEU LEU TYR SEQRES 12 A 300 ASP ILE PRO GLY ARG SER ALA VAL PRO ILE GLU PRO ASP SEQRES 13 A 300 THR ILE ARG ALA LEU ALA SER HIS PRO ASN ILE VAL GLY SEQRES 14 A 300 VAL LYS ASP ALA LYS ALA ASP LEU HIS SER GLY ALA GLN SEQRES 15 A 300 ILE MET ALA ASP THR GLY LEU ALA TYR TYR SER GLY ASP SEQRES 16 A 300 ASP ALA LEU ASN LEU PRO TRP LEU ALA MET GLY ALA THR SEQRES 17 A 300 GLY PHE ILE SER VAL ILE ALA HIS LEU ALA ALA GLY GLN SEQRES 18 A 300 LEU ARG GLU LEU LEU SER ALA PHE GLY SER GLY ASP ILE SEQRES 19 A 300 ALA THR ALA ARG LYS ILE ASN ILE ALA VAL ALA PRO LEU SEQRES 20 A 300 CYS ASN ALA MET SER ARG LEU GLY GLY VAL THR LEU SER SEQRES 21 A 300 LYS ALA GLY LEU ARG LEU GLN GLY ILE ASP VAL GLY ASP SEQRES 22 A 300 PRO ARG LEU PRO GLN VAL ALA ALA THR PRO GLU GLN ILE SEQRES 23 A 300 ASP ALA LEU ALA ALA ASP MET ARG ALA ALA SER VAL LEU SEQRES 24 A 300 ARG HET NA A 401 1 HET NA A 402 1 HET 6GT A 403 11 HETNAM NA SODIUM ION HETNAM 6GT 2-OXOHEPTANEDIOIC ACID HETSYN 6GT 2-KETOPIMELIC ACID FORMUL 2 NA 2(NA 1+) FORMUL 4 6GT C7 H10 O5 FORMUL 5 HOH *97(H2 O) HELIX 1 AA1 ASP A 7 LEU A 12 1 6 HELIX 2 AA2 ASP A 30 GLN A 44 1 15 HELIX 3 AA3 GLU A 57 THR A 61 5 5 HELIX 4 AA4 THR A 62 GLY A 78 1 17 HELIX 5 AA5 ASP A 91 GLU A 105 1 15 HELIX 6 AA6 PRO A 121 ALA A 135 1 15 HELIX 7 AA7 ILE A 145 ALA A 150 1 6 HELIX 8 AA8 GLU A 154 SER A 163 1 10 HELIX 9 AA9 ASP A 176 GLY A 188 1 13 HELIX 10 AB1 ASP A 195 ALA A 197 5 3 HELIX 11 AB2 LEU A 198 GLY A 206 1 9 HELIX 12 AB3 ILE A 214 SER A 231 1 18 HELIX 13 AB4 ASP A 233 VAL A 244 1 12 HELIX 14 AB5 VAL A 244 GLY A 255 1 12 HELIX 15 AB6 GLY A 255 GLN A 267 1 13 HELIX 16 AB7 THR A 282 ALA A 296 1 15 SHEET 1 AA1 9 LEU A 15 ALA A 18 0 SHEET 2 AA1 9 GLY A 48 VAL A 51 1 O VAL A 50 N THR A 17 SHEET 3 AA1 9 ARG A 82 GLY A 86 1 O ILE A 84 N LEU A 49 SHEET 4 AA1 9 GLY A 109 VAL A 113 1 O GLY A 109 N ALA A 85 SHEET 5 AA1 9 MET A 140 ASP A 144 1 O LEU A 141 N LEU A 110 SHEET 6 AA1 9 ILE A 167 ASP A 172 1 O LYS A 171 N LEU A 142 SHEET 7 AA1 9 ALA A 190 SER A 193 1 O TYR A 192 N VAL A 170 SHEET 8 AA1 9 GLY A 209 SER A 212 1 O GLY A 209 N SER A 193 SHEET 9 AA1 9 LEU A 15 ALA A 18 1 N LEU A 16 O PHE A 210 LINK NZ LYS A 171 CAL 6GT A 403 1555 1555 1.99 LINK OE2 GLU A 154 NA NA A 401 1555 1555 2.81 LINK OD2 ASP A 156 NA NA A 402 1555 1555 3.02 LINK NA NA A 401 O HOH A 566 1555 1555 3.17 CISPEP 1 VAL A 4 GLY A 5 0 5.18 CISPEP 2 LEU A 276 PRO A 277 0 8.59 SITE 1 AC1 4 PRO A 152 GLU A 154 PRO A 155 LYS A 174 SITE 1 AC2 2 GLU A 154 ASP A 156 SITE 1 AC3 11 ALA A 18 THR A 54 THR A 55 TYR A 143 SITE 2 AC3 11 ILE A 145 ARG A 148 LYS A 171 GLY A 194 SITE 3 AC3 11 VAL A 213 HOH A 530 HOH A 578 CRYST1 84.780 84.780 83.920 90.00 90.00 90.00 P 42 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.011795 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011795 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011916 0.00000