HEADER TRANSFERASE/TRANSFERASE INHIBITOR 20-SEP-16 5TE2 TITLE CRYSTAL STRUCTURE OF 7,8-DIAMINOPELARGONIC ACID SYNTHASE (BIOA) FROM TITLE 2 MYCOBACTERIUM TUBERCULOSIS, COMPLEXED WITH A MECHANISM-BASED TITLE 3 INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE; COMPND 3 CHAIN: B, A; COMPND 4 SYNONYM: 7,8-DIAMINO-PELARGONIC ACID AMINOTRANSFERASE,DAPA COMPND 5 AMINOTRANSFERASE,8-DIAMINONONANOATE SYNTHASE,DANS,DIAMINOPELARGONIC COMPND 6 ACID SYNTHASE; COMPND 7 EC: 2.6.1.62; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM BOVIS (STRAIN ATCC BAA-935 / SOURCE 3 AF2122/97); SOURCE 4 ORGANISM_TAXID: 233413; SOURCE 5 STRAIN: ATCC BAA-935 / AF2122/97; SOURCE 6 GENE: BIOA, MB1595; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INHIBITOR COMPLEX, TRANSAMINASE, PLP, TRANSFERASE, TRANSFERASE- KEYWDS 2 INHIBITOR COMPLEX, MECHANISM-BASED INHIBITOR, TRANSFERASE- KEYWDS 3 TRANSFERASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR K.M.MAIZE,C.EIDEN,C.C.ALDRICH,B.C.FINZEL REVDAT 5 04-OCT-23 5TE2 1 REMARK REVDAT 4 11-DEC-19 5TE2 1 REMARK REVDAT 3 20-SEP-17 5TE2 1 REMARK REVDAT 2 14-JUN-17 5TE2 1 JRNL REVDAT 1 31-MAY-17 5TE2 0 JRNL AUTH C.G.EIDEN,K.M.MAIZE,B.C.FINZEL,J.D.LIPSCOMB,C.C.ALDRICH JRNL TITL RATIONAL OPTIMIZATION OF MECHANISM-BASED INHIBITORS THROUGH JRNL TITL 2 DETERMINATION OF THE MICROSCOPIC RATE CONSTANTS OF JRNL TITL 3 INACTIVATION. JRNL REF J. AM. CHEM. SOC. V. 139 7132 2017 JRNL REFN ESSN 1520-5126 JRNL PMID 28510452 JRNL DOI 10.1021/JACS.7B00962 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.61 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 79762 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.780 REMARK 3 FREE R VALUE TEST SET COUNT : 3809 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 41.6194 - 5.3962 1.00 3060 141 0.1646 0.1758 REMARK 3 2 5.3962 - 4.2845 1.00 2914 149 0.1353 0.1370 REMARK 3 3 4.2845 - 3.7433 1.00 2840 175 0.1350 0.1493 REMARK 3 4 3.7433 - 3.4013 1.00 2866 136 0.1625 0.1754 REMARK 3 5 3.4013 - 3.1576 1.00 2834 124 0.1723 0.1833 REMARK 3 6 3.1576 - 2.9715 1.00 2855 138 0.1733 0.2216 REMARK 3 7 2.9715 - 2.8227 1.00 2818 133 0.1805 0.2187 REMARK 3 8 2.8227 - 2.6998 1.00 2818 146 0.1784 0.2003 REMARK 3 9 2.6998 - 2.5959 1.00 2815 141 0.1770 0.1884 REMARK 3 10 2.5959 - 2.5063 1.00 2817 132 0.1800 0.2333 REMARK 3 11 2.5063 - 2.4280 1.00 2807 136 0.1684 0.2031 REMARK 3 12 2.4280 - 2.3586 1.00 2791 153 0.1748 0.2018 REMARK 3 13 2.3586 - 2.2965 1.00 2796 143 0.1648 0.2032 REMARK 3 14 2.2965 - 2.2405 1.00 2770 145 0.1748 0.2372 REMARK 3 15 2.2405 - 2.1895 1.00 2804 151 0.1740 0.2240 REMARK 3 16 2.1895 - 2.1430 1.00 2753 151 0.1744 0.1972 REMARK 3 17 2.1430 - 2.1001 1.00 2806 134 0.1766 0.2161 REMARK 3 18 2.1001 - 2.0605 1.00 2847 111 0.1787 0.2074 REMARK 3 19 2.0605 - 2.0237 1.00 2742 129 0.1785 0.2229 REMARK 3 20 2.0237 - 1.9894 1.00 2799 161 0.1761 0.2033 REMARK 3 21 1.9894 - 1.9573 1.00 2736 144 0.1764 0.2022 REMARK 3 22 1.9573 - 1.9272 1.00 2824 143 0.1811 0.2074 REMARK 3 23 1.9272 - 1.8988 1.00 2709 141 0.1918 0.2504 REMARK 3 24 1.8988 - 1.8721 1.00 2821 155 0.1928 0.2487 REMARK 3 25 1.8721 - 1.8468 1.00 2746 143 0.1951 0.2289 REMARK 3 26 1.8468 - 1.8228 1.00 2822 129 0.2052 0.2554 REMARK 3 27 1.8228 - 1.8000 1.00 2743 125 0.2041 0.2678 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.000 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.06 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 6632 REMARK 3 ANGLE : 0.862 9074 REMARK 3 CHIRALITY : 0.054 1040 REMARK 3 PLANARITY : 0.006 1165 REMARK 3 DIHEDRAL : 15.329 3863 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5TE2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-SEP-16. REMARK 100 THE DEPOSITION ID IS D_1000224043. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-APR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 17-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 79860 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 101.978 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 6.500 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.37300 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 2.5.6 REMARK 200 STARTING MODEL: 4W1X REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM HEPES, 7% PEG 8000, PH 7.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 31.34800 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 101.97800 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.18200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 101.97800 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.34800 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.18200 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26110 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -74.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 B -19 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 MET B 1 REMARK 465 ALA B 2 REMARK 465 ALA B 3 REMARK 465 ALA B 4 REMARK 465 THR B 5 REMARK 465 GLY B 6 REMARK 465 SER B 435 REMARK 465 LEU B 436 REMARK 465 PRO B 437 REMARK 465 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 ALA A 3 REMARK 465 ALA A 4 REMARK 465 THR A 5 REMARK 465 GLY A 6 REMARK 465 GLY A 7 REMARK 465 LEU A 436 REMARK 465 PRO A 437 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 ARG B 360 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 403 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 30 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 31 CG CD OE1 OE2 REMARK 470 VAL A 33 CG1 CG2 REMARK 470 ARG A 85 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 180 CG OD1 OD2 REMARK 470 ARG A 403 CG CD 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 OE1 GLN B 137 O HOH B 601 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 665 O HOH A 775 3554 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 168 CB CYS A 168 SG 0.122 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 MET B 87 109.62 -164.55 REMARK 500 VAL B 222 -47.75 70.55 REMARK 500 LYS B 283 -96.05 44.72 REMARK 500 ARG B 403 -125.62 50.38 REMARK 500 MET A 87 112.52 -163.34 REMARK 500 HIS A 89 145.35 -170.56 REMARK 500 HIS A 158 15.99 -141.36 REMARK 500 HIS A 171 -73.90 -107.77 REMARK 500 VAL A 222 -49.74 73.27 REMARK 500 LYS A 283 -96.84 46.53 REMARK 500 ALA A 373 50.29 -91.08 REMARK 500 ARG A 403 -129.94 48.99 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 841 DISTANCE = 5.98 ANGSTROMS REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 7B9 B 501 REMARK 610 7B9 A 501 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 7B9 B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEG B 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 7B9 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGE A 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3TFU RELATED DB: PDB REMARK 900 3TFU CONTAINS THE SAME PROTEIN WITH A DIFFERENT MECHANISM-BASED REMARK 900 INHIBITOR REMARK 900 RELATED ID: 3TFT RELATED DB: PDB REMARK 900 3TFT CONTAINS THE SAME PROTEIN THE PRE-REACTION STATE REMARK 900 RELATED ID: 4CXQ RELATED DB: PDB REMARK 900 4CXQ CONTAINS THE SAME PROTEIN BOUND TO KAPA, THE NATURAL SUBSTRATE. DBREF 5TE2 B 1 437 UNP P0A4X7 BIOA_MYCBO 1 437 DBREF 5TE2 A 1 437 UNP P0A4X7 BIOA_MYCBO 1 437 SEQADV 5TE2 MET B -19 UNP P0A4X7 INITIATING METHIONINE SEQADV 5TE2 GLY B -18 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 SER B -17 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 SER B -16 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 HIS B -15 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 HIS B -14 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 HIS B -13 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 HIS B -12 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 HIS B -11 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 HIS B -10 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 SER B -9 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 SER B -8 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 GLY B -7 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 LEU B -6 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 VAL B -5 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 PRO B -4 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 ARG B -3 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 GLY B -2 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 SER B -1 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 HIS B 0 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 MET A -19 UNP P0A4X7 INITIATING METHIONINE SEQADV 5TE2 GLY A -18 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 SER A -17 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 SER A -16 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 HIS A -15 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 HIS A -14 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 HIS A -13 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 HIS A -12 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 HIS A -11 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 HIS A -10 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 SER A -9 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 SER A -8 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 GLY A -7 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 LEU A -6 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 VAL A -5 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 PRO A -4 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 ARG A -3 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 GLY A -2 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 SER A -1 UNP P0A4X7 EXPRESSION TAG SEQADV 5TE2 HIS A 0 UNP P0A4X7 EXPRESSION TAG SEQRES 1 B 457 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 457 LEU VAL PRO ARG GLY SER HIS MET ALA ALA ALA THR GLY SEQRES 3 B 457 GLY LEU THR PRO GLU GLN ILE ILE ALA VAL ASP GLY ALA SEQRES 4 B 457 HIS LEU TRP HIS PRO TYR SER SER ILE GLY ARG GLU ALA SEQRES 5 B 457 VAL SER PRO VAL VAL ALA VAL ALA ALA HIS GLY ALA TRP SEQRES 6 B 457 LEU THR LEU ILE ARG ASP GLY GLN PRO ILE GLU VAL LEU SEQRES 7 B 457 ASP ALA MET SER SER TRP TRP THR ALA ILE HIS GLY HIS SEQRES 8 B 457 GLY HIS PRO ALA LEU ASP GLN ALA LEU THR THR GLN LEU SEQRES 9 B 457 ARG VAL MET ASN HIS VAL MET PHE GLY GLY LEU THR HIS SEQRES 10 B 457 GLU PRO ALA ALA ARG LEU ALA LYS LEU LEU VAL ASP ILE SEQRES 11 B 457 THR PRO ALA GLY LEU ASP THR VAL PHE PHE SER ASP SER SEQRES 12 B 457 GLY SER VAL SER VAL GLU VAL ALA ALA LYS MET ALA LEU SEQRES 13 B 457 GLN TYR TRP ARG GLY ARG GLY LEU PRO GLY LYS ARG ARG SEQRES 14 B 457 LEU MET THR TRP ARG GLY GLY TYR HIS GLY ASP THR PHE SEQRES 15 B 457 LEU ALA MET SER ILE CYS ASP PRO HIS GLY GLY MET HIS SEQRES 16 B 457 SER LEU TRP THR ASP VAL LEU ALA ALA GLN VAL PHE ALA SEQRES 17 B 457 PRO GLN VAL PRO ARG ASP TYR ASP PRO ALA TYR SER ALA SEQRES 18 B 457 ALA PHE GLU ALA GLN LEU ALA GLN HIS ALA GLY GLU LEU SEQRES 19 B 457 ALA ALA VAL VAL VAL GLU PRO VAL VAL GLN GLY ALA GLY SEQRES 20 B 457 GLY MET ARG PHE HIS ASP PRO ARG TYR LEU HIS ASP LEU SEQRES 21 B 457 ARG ASP ILE CYS ARG ARG TYR GLU VAL LEU LEU ILE PHE SEQRES 22 B 457 ASP GLU ILE ALA THR GLY PHE GLY ARG THR GLY ALA LEU SEQRES 23 B 457 PHE ALA ALA ASP HIS ALA GLY VAL SER PRO ASP ILE MET SEQRES 24 B 457 CYS VAL GLY LYS ALA LEU THR GLY GLY TYR LEU SER LEU SEQRES 25 B 457 ALA ALA THR LEU CYS THR ALA ASP VAL ALA HIS THR ILE SEQRES 26 B 457 SER ALA GLY ALA ALA GLY ALA LEU MET HIS GLY PRO THR SEQRES 27 B 457 PHE MET ALA ASN PRO LEU ALA CYS ALA VAL SER VAL ALA SEQRES 28 B 457 SER VAL GLU LEU LEU LEU GLY GLN ASP TRP ARG THR ARG SEQRES 29 B 457 ILE THR GLU LEU ALA ALA GLY LEU THR ALA GLY LEU ASP SEQRES 30 B 457 THR ALA ARG ALA LEU PRO ALA VAL THR ASP VAL ARG VAL SEQRES 31 B 457 CYS GLY ALA ILE GLY VAL ILE GLU CYS ASP ARG PRO VAL SEQRES 32 B 457 ASP LEU ALA VAL ALA THR PRO ALA ALA LEU ASP ARG GLY SEQRES 33 B 457 VAL TRP LEU ARG PRO PHE ARG ASN LEU VAL TYR ALA MET SEQRES 34 B 457 PRO PRO TYR ILE CYS THR PRO ALA GLU ILE THR GLN ILE SEQRES 35 B 457 THR SER ALA MET VAL GLU VAL ALA ARG LEU VAL GLY SER SEQRES 36 B 457 LEU PRO SEQRES 1 A 457 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 457 LEU VAL PRO ARG GLY SER HIS MET ALA ALA ALA THR GLY SEQRES 3 A 457 GLY LEU THR PRO GLU GLN ILE ILE ALA VAL ASP GLY ALA SEQRES 4 A 457 HIS LEU TRP HIS PRO TYR SER SER ILE GLY ARG GLU ALA SEQRES 5 A 457 VAL SER PRO VAL VAL ALA VAL ALA ALA HIS GLY ALA TRP SEQRES 6 A 457 LEU THR LEU ILE ARG ASP GLY GLN PRO ILE GLU VAL LEU SEQRES 7 A 457 ASP ALA MET SER SER TRP TRP THR ALA ILE HIS GLY HIS SEQRES 8 A 457 GLY HIS PRO ALA LEU ASP GLN ALA LEU THR THR GLN LEU SEQRES 9 A 457 ARG VAL MET ASN HIS VAL MET PHE GLY GLY LEU THR HIS SEQRES 10 A 457 GLU PRO ALA ALA ARG LEU ALA LYS LEU LEU VAL ASP ILE SEQRES 11 A 457 THR PRO ALA GLY LEU ASP THR VAL PHE PHE SER ASP SER SEQRES 12 A 457 GLY SER VAL SER VAL GLU VAL ALA ALA LYS MET ALA LEU SEQRES 13 A 457 GLN TYR TRP ARG GLY ARG GLY LEU PRO GLY LYS ARG ARG SEQRES 14 A 457 LEU MET THR TRP ARG GLY GLY TYR HIS GLY ASP THR PHE SEQRES 15 A 457 LEU ALA MET SER ILE CYS ASP PRO HIS GLY GLY MET HIS SEQRES 16 A 457 SER LEU TRP THR ASP VAL LEU ALA ALA GLN VAL PHE ALA SEQRES 17 A 457 PRO GLN VAL PRO ARG ASP TYR ASP PRO ALA TYR SER ALA SEQRES 18 A 457 ALA PHE GLU ALA GLN LEU ALA GLN HIS ALA GLY GLU LEU SEQRES 19 A 457 ALA ALA VAL VAL VAL GLU PRO VAL VAL GLN GLY ALA GLY SEQRES 20 A 457 GLY MET ARG PHE HIS ASP PRO ARG TYR LEU HIS ASP LEU SEQRES 21 A 457 ARG ASP ILE CYS ARG ARG TYR GLU VAL LEU LEU ILE PHE SEQRES 22 A 457 ASP GLU ILE ALA THR GLY PHE GLY ARG THR GLY ALA LEU SEQRES 23 A 457 PHE ALA ALA ASP HIS ALA GLY VAL SER PRO ASP ILE MET SEQRES 24 A 457 CYS VAL GLY LYS ALA LEU THR GLY GLY TYR LEU SER LEU SEQRES 25 A 457 ALA ALA THR LEU CYS THR ALA ASP VAL ALA HIS THR ILE SEQRES 26 A 457 SER ALA GLY ALA ALA GLY ALA LEU MET HIS GLY PRO THR SEQRES 27 A 457 PHE MET ALA ASN PRO LEU ALA CYS ALA VAL SER VAL ALA SEQRES 28 A 457 SER VAL GLU LEU LEU LEU GLY GLN ASP TRP ARG THR ARG SEQRES 29 A 457 ILE THR GLU LEU ALA ALA GLY LEU THR ALA GLY LEU ASP SEQRES 30 A 457 THR ALA ARG ALA LEU PRO ALA VAL THR ASP VAL ARG VAL SEQRES 31 A 457 CYS GLY ALA ILE GLY VAL ILE GLU CYS ASP ARG PRO VAL SEQRES 32 A 457 ASP LEU ALA VAL ALA THR PRO ALA ALA LEU ASP ARG GLY SEQRES 33 A 457 VAL TRP LEU ARG PRO PHE ARG ASN LEU VAL TYR ALA MET SEQRES 34 A 457 PRO PRO TYR ILE CYS THR PRO ALA GLU ILE THR GLN ILE SEQRES 35 A 457 THR SER ALA MET VAL GLU VAL ALA ARG LEU VAL GLY SER SEQRES 36 A 457 LEU PRO HET 7B9 B 501 24 HET PEG B 502 7 HET EDO B 503 4 HET 7B9 A 501 24 HET PGE A 502 10 HETNAM 7B9 [5-HYDROXY-4-({[6-(3-HYDROXYPROPYL)-4-OXO-1,4- HETNAM 2 7B9 DIHYDROPYRIDIN-3-YL]AMINO}METHYL)-6-METHYLPYRIDIN-3- HETNAM 3 7B9 YL]METHYL DIHYDROGEN PHOSPHATE HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM EDO 1,2-ETHANEDIOL HETNAM PGE TRIETHYLENE GLYCOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 7B9 2(C16 H22 N3 O7 P) FORMUL 4 PEG C4 H10 O3 FORMUL 5 EDO C2 H6 O2 FORMUL 7 PGE C6 H14 O4 FORMUL 8 HOH *447(H2 O) HELIX 1 AA1 THR B 9 LEU B 21 1 13 HELIX 2 AA2 MET B 61 THR B 66 1 6 HELIX 3 AA3 HIS B 73 ARG B 85 1 13 HELIX 4 AA4 HIS B 97 THR B 111 1 15 HELIX 5 AA5 SER B 123 ARG B 142 1 20 HELIX 6 AA6 THR B 161 ILE B 167 1 7 HELIX 7 AA7 MET B 174 THR B 179 5 6 HELIX 8 AA8 ASP B 196 ALA B 211 1 16 HELIX 9 AA9 PRO B 234 GLU B 248 1 15 HELIX 10 AB1 PHE B 267 ALA B 272 5 6 HELIX 11 AB2 GLY B 282 GLY B 287 5 6 HELIX 12 AB3 ALA B 299 GLY B 308 1 10 HELIX 13 AB4 ASN B 322 GLY B 338 1 17 HELIX 14 AB5 ASP B 340 ASP B 357 1 18 HELIX 15 AB6 THR B 358 LEU B 362 5 5 HELIX 16 AB7 ASP B 384 ARG B 395 1 12 HELIX 17 AB8 THR B 415 GLY B 434 1 20 HELIX 18 AB9 THR A 9 LEU A 21 1 13 HELIX 19 AC1 MET A 61 THR A 66 1 6 HELIX 20 AC2 HIS A 73 MET A 87 1 15 HELIX 21 AC3 HIS A 97 THR A 111 1 15 HELIX 22 AC4 SER A 123 ARG A 142 1 20 HELIX 23 AC5 THR A 161 SER A 166 1 6 HELIX 24 AC6 HIS A 175 LEU A 182 5 8 HELIX 25 AC7 ASP A 196 ALA A 211 1 16 HELIX 26 AC8 PRO A 234 GLU A 248 1 15 HELIX 27 AC9 PHE A 267 ALA A 272 5 6 HELIX 28 AD1 GLY A 282 GLY A 287 5 6 HELIX 29 AD2 ALA A 299 GLY A 308 1 10 HELIX 30 AD3 ASN A 322 GLY A 338 1 17 HELIX 31 AD4 ASP A 340 ASP A 357 1 18 HELIX 32 AD5 THR A 358 LEU A 362 5 5 HELIX 33 AD6 ASP A 384 ARG A 395 1 12 HELIX 34 AD7 THR A 415 GLY A 434 1 20 SHEET 1 AA1 5 VAL B 397 TRP B 398 0 SHEET 2 AA1 5 GLN B 53 ASP B 59 1 N LEU B 58 O TRP B 398 SHEET 3 AA1 5 TRP B 45 ARG B 50 -1 N LEU B 46 O VAL B 57 SHEET 4 AA1 5 VAL B 36 HIS B 42 -1 N ALA B 40 O THR B 47 SHEET 5 AA1 5 LEU A 95 THR A 96 1 O THR A 96 N ALA B 38 SHEET 1 AA2 5 LEU B 95 THR B 96 0 SHEET 2 AA2 5 VAL A 36 HIS A 42 1 O ALA A 38 N THR B 96 SHEET 3 AA2 5 TRP A 45 ARG A 50 -1 O THR A 47 N ALA A 40 SHEET 4 AA2 5 GLN A 53 ASP A 59 -1 O VAL A 57 N LEU A 46 SHEET 5 AA2 5 VAL A 397 TRP A 398 1 O TRP A 398 N LEU A 58 SHEET 1 AA3 7 LEU B 115 SER B 121 0 SHEET 2 AA3 7 ALA B 293 THR B 298 -1 O THR B 295 N PHE B 119 SHEET 3 AA3 7 ILE B 278 VAL B 281 -1 N MET B 279 O LEU B 296 SHEET 4 AA3 7 LEU B 250 ASP B 254 1 N PHE B 253 O CYS B 280 SHEET 5 AA3 7 LEU B 214 VAL B 219 1 N VAL B 217 O ILE B 252 SHEET 6 AA3 7 ARG B 149 TRP B 153 1 N ARG B 149 O ALA B 215 SHEET 7 AA3 7 VAL B 186 ALA B 188 1 O ALA B 188 N THR B 152 SHEET 1 AA4 2 VAL B 223 GLN B 224 0 SHEET 2 AA4 2 ARG B 230 PHE B 231 -1 O ARG B 230 N GLN B 224 SHEET 1 AA5 3 VAL B 365 VAL B 370 0 SHEET 2 AA5 3 GLY B 375 CYS B 379 -1 O GLU B 378 N THR B 366 SHEET 3 AA5 3 LEU B 405 ALA B 408 -1 O VAL B 406 N ILE B 377 SHEET 1 AA6 7 LEU A 115 SER A 121 0 SHEET 2 AA6 7 ALA A 293 THR A 298 -1 O THR A 295 N PHE A 119 SHEET 3 AA6 7 ILE A 278 VAL A 281 -1 N MET A 279 O LEU A 296 SHEET 4 AA6 7 LEU A 250 ASP A 254 1 N PHE A 253 O ILE A 278 SHEET 5 AA6 7 LEU A 214 VAL A 219 1 N VAL A 217 O ILE A 252 SHEET 6 AA6 7 ARG A 149 TRP A 153 1 N ARG A 149 O ALA A 215 SHEET 7 AA6 7 VAL A 186 ALA A 188 1 O ALA A 188 N THR A 152 SHEET 1 AA7 2 VAL A 223 GLN A 224 0 SHEET 2 AA7 2 ARG A 230 PHE A 231 -1 O ARG A 230 N GLN A 224 SHEET 1 AA8 3 VAL A 365 VAL A 370 0 SHEET 2 AA8 3 GLY A 375 CYS A 379 -1 O GLU A 378 N THR A 366 SHEET 3 AA8 3 LEU A 405 ALA A 408 -1 O VAL A 406 N ILE A 377 SITE 1 AC1 19 GLY A 316 PRO A 317 THR A 318 HOH A 613 SITE 2 AC1 19 TRP B 64 GLY B 124 SER B 125 TYR B 157 SITE 3 AC1 19 HIS B 158 GLY B 159 GLU B 220 ASP B 254 SITE 4 AC1 19 ILE B 256 LYS B 283 HOH B 654 HOH B 662 SITE 5 AC1 19 HOH B 682 HOH B 684 HOH B 745 SITE 1 AC2 5 ARG B 193 VAL B 222 HIS B 232 ASP B 233 SITE 2 AC2 5 HOH B 602 SITE 1 AC3 18 TYR A 25 TRP A 64 GLY A 124 SER A 125 SITE 2 AC3 18 TYR A 157 HIS A 158 GLY A 159 GLU A 220 SITE 3 AC3 18 ASP A 254 ILE A 256 LYS A 283 HOH A 607 SITE 4 AC3 18 HOH A 662 HOH A 672 GLY B 316 PRO B 317 SITE 5 AC3 18 THR B 318 HOH B 603 SITE 1 AC4 8 ARG A 193 PHE A 231 HIS A 232 ASP A 233 SITE 2 AC4 8 PRO A 234 HIS A 271 HOH A 646 HOH A 666 CRYST1 62.696 66.364 203.956 90.00 90.00 90.00 P 21 21 21 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 0.015950 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015068 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004903 0.00000