HEADER HYDROLASE 02-JUL-21 7F8P TITLE CRYSTAL STRUCTURE OF THE MYCOBACTERIUM TUBERCULOSIS L,D- TITLE 2 TRANSPEPTIDASE-2 (LDTMT2) WITH NEW CARBAPENEM DRUG T203 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 (STRAIN ATCC 25618 / SOURCE 3 H37RV); SOURCE 4 ORGANISM_TAXID: 83332; SOURCE 5 GENE: LDTB, LPPS, RV2518C, RVBD_2518C, P425_02624; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS L, D-TRANSPEPTIDASE, CYSTEINE PROTEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR P.KUMAR,G.LAMICHHANE REVDAT 3 29-NOV-23 7F8P 1 REMARK REVDAT 2 25-MAY-22 7F8P 1 JRNL REVDAT 1 11-MAY-22 7F8P 0 JRNL AUTH N.AHMAD,S.DUGAD,V.CHAUHAN,S.AHMED,K.SHARMA,S.KACHHAP, JRNL AUTH 2 R.ZAIDI,W.R.BISHAI,G.LAMICHHANE,P.KUMAR JRNL TITL ALLOSTERIC COOPERATION IN BETA-LACTAM BINDING TO A JRNL TITL 2 NON-CLASSICAL TRANSPEPTIDASE. JRNL REF ELIFE V. 11 2022 JRNL REFN ESSN 2050-084X JRNL PMID 35475970 JRNL DOI 10.7554/ELIFE.73055 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 80.3 REMARK 3 NUMBER OF REFLECTIONS : 147316 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.220 REMARK 3 FREE R VALUE TEST SET COUNT : 3275 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 30.3500 - 4.8400 0.98 7629 177 0.1793 0.1783 REMARK 3 2 4.8400 - 3.8400 0.99 7718 165 0.1416 0.1703 REMARK 3 3 3.8400 - 3.3600 0.98 7639 173 0.1490 0.1710 REMARK 3 4 3.3600 - 3.0500 0.98 7649 185 0.1560 0.1717 REMARK 3 5 3.0500 - 2.8300 0.98 7742 175 0.1650 0.1837 REMARK 3 6 2.8300 - 2.6700 0.98 7650 174 0.1717 0.1847 REMARK 3 7 2.6700 - 2.5300 0.98 7629 177 0.1744 0.1970 REMARK 3 8 2.5300 - 2.4200 0.98 7594 167 0.1708 0.1756 REMARK 3 9 2.4200 - 2.3300 0.98 7647 176 0.1692 0.2279 REMARK 3 10 2.3300 - 2.2500 0.97 7464 177 0.1672 0.1809 REMARK 3 11 2.2500 - 2.1800 0.94 7385 171 0.1657 0.1809 REMARK 3 12 2.1800 - 2.1200 0.90 6983 170 0.1613 0.2034 REMARK 3 13 2.1200 - 2.0600 0.85 6727 150 0.1568 0.2109 REMARK 3 14 2.0600 - 2.0100 0.80 6191 129 0.1632 0.1805 REMARK 3 15 2.0100 - 1.9600 0.73 5672 145 0.1643 0.1973 REMARK 3 16 1.9600 - 1.9200 0.67 5232 113 0.1680 0.1909 REMARK 3 17 1.9200 - 1.8800 0.62 4853 114 0.1721 0.1928 REMARK 3 18 1.8800 - 1.8500 0.58 4524 88 0.1817 0.1856 REMARK 3 19 1.8500 - 1.8200 0.55 4309 108 0.1923 0.2378 REMARK 3 20 1.8200 - 1.7800 0.53 4104 82 0.2053 0.2540 REMARK 3 21 1.7800 - 1.7600 0.52 4054 85 0.2132 0.2548 REMARK 3 22 1.7600 - 1.7300 0.51 3946 92 0.2164 0.2428 REMARK 3 23 1.7300 - 1.7000 0.47 3700 82 0.2411 0.2585 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) : 0.146 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.598 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.97 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.58 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 5484 REMARK 3 ANGLE : 0.969 7514 REMARK 3 CHIRALITY : 0.060 845 REMARK 3 PLANARITY : 0.005 982 REMARK 3 DIHEDRAL : 20.680 774 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 7F8P COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1300023080. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-APR-16 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 : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2095305 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 30.350 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 5.000 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : 0.06200 REMARK 200 FOR THE DATA SET : 23.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.73800 REMARK 200 R SYM FOR SHELL (I) : 0.84500 REMARK 200 FOR SHELL : 3.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 5DU7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% 5000 MME, 200MM AMMONIUM SULFATE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 47.13900 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -1.0 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 39 REMARK 465 HIS A 40 REMARK 465 MET A 41 REMARK 465 ALA A 42 REMARK 465 PRO A 43 REMARK 465 ILE A 44 REMARK 465 LYS A 45 REMARK 465 VAL A 46 REMARK 465 ILE A 47 REMARK 465 ALA A 48 REMARK 465 ASP A 49 REMARK 465 LYS A 50 REMARK 465 GLY A 51 REMARK 465 THR A 52 REMARK 465 PRO A 53 REMARK 465 PHE A 54 REMARK 465 ALA A 55 REMARK 465 ASP A 56 REMARK 465 ALA A 408 REMARK 465 GLY B 39 REMARK 465 HIS B 40 REMARK 465 MET B 41 REMARK 465 ALA B 42 REMARK 465 PRO B 43 REMARK 465 ILE B 44 REMARK 465 LYS B 45 REMARK 465 VAL B 46 REMARK 465 ILE B 47 REMARK 465 ALA B 48 REMARK 465 ASP B 49 REMARK 465 LYS B 50 REMARK 465 GLY B 51 REMARK 465 THR B 52 REMARK 465 PRO B 53 REMARK 465 PHE B 54 REMARK 465 ALA B 55 REMARK 465 ASP B 56 REMARK 465 LEU B 57 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 ARG A 104 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 217 CG CD CE NZ REMARK 470 GLN B 144 CG CD OE1 NE2 REMARK 470 LYS B 407 CG CD CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 THR B 67 CA CB OG1 CG2 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 O15 59I A 601 O HOH A 701 1.85 REMARK 500 O HOH A 704 O HOH A 1057 2.02 REMARK 500 O HOH B 711 O HOH B 924 2.08 REMARK 500 O HOH B 911 O HOH B 986 2.09 REMARK 500 O HOH B 862 O HOH B 934 2.12 REMARK 500 OE2 GLU B 240 O HOH B 601 2.12 REMARK 500 O HOH B 869 O HOH B 943 2.13 REMARK 500 O HOH B 764 O HOH B 1000 2.13 REMARK 500 O HOH B 961 O HOH B 975 2.14 REMARK 500 O HOH B 617 O HOH B 731 2.14 REMARK 500 NH2 ARG B 139 O HOH B 602 2.15 REMARK 500 O HOH B 913 O HOH B 931 2.15 REMARK 500 O HOH B 854 O HOH B 966 2.16 REMARK 500 O HOH A 1019 O HOH A 1047 2.16 REMARK 500 O HOH A 813 O HOH A 1024 2.16 REMARK 500 OE1 GLU B 252 O HOH B 603 2.16 REMARK 500 O HOH A 768 O HOH A 1068 2.17 REMARK 500 O HOH B 911 O HOH B 990 2.17 REMARK 500 O HOH A 1053 O HOH A 1098 2.17 REMARK 500 O HOH B 824 O HOH B 931 2.18 REMARK 500 O HOH A 738 O HOH A 979 2.18 REMARK 500 O HOH A 892 O HOH A 978 2.18 REMARK 500 O HOH A 1017 O HOH B 809 2.18 REMARK 500 O HOH B 758 O HOH B 978 2.18 REMARK 500 O HOH B 798 O HOH B 934 2.18 REMARK 500 O HOH B 797 O HOH B 925 2.18 REMARK 500 O HOH B 856 O HOH B 872 2.18 REMARK 500 O HOH A 702 O HOH A 1029 2.18 REMARK 500 OE1 GLN A 244 O HOH A 702 2.19 REMARK 500 O HOH A 1041 O HOH A 1080 2.19 REMARK 500 O HOH A 916 O HOH A 986 2.19 REMARK 500 O HOH B 922 O HOH B 968 2.19 REMARK 500 O HOH A 802 O HOH A 989 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 A 1050 O HOH B 966 2548 2.14 REMARK 500 O HOH A 949 O HOH B 938 2548 2.14 REMARK 500 O HOH A 979 O HOH B 864 2548 2.14 REMARK 500 O HOH B 909 O HOH B 916 1556 2.16 REMARK 500 O HOH A 918 O HOH B 876 1654 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 ASN A 204 -169.43 -161.90 REMARK 500 ASN A 227 64.57 -101.21 REMARK 500 HIS A 347 -55.61 -133.57 REMARK 500 ASN A 405 38.26 -149.78 REMARK 500 ASN B 204 -169.16 -160.68 REMARK 500 MET B 280 -165.36 -101.10 REMARK 500 HIS B 347 -53.04 -132.72 REMARK 500 ASN B 405 41.90 -152.63 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 A1129 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH B1025 DISTANCE = 6.05 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 59I A 601 REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 59I A 601 REMARK 615 56X A 605 DBREF 7F8P A 42 408 UNP I6Y9J2 LDT2_MYCTU 42 408 DBREF 7F8P B 42 408 UNP I6Y9J2 LDT2_MYCTU 42 408 SEQADV 7F8P GLY A 39 UNP I6Y9J2 EXPRESSION TAG SEQADV 7F8P HIS A 40 UNP I6Y9J2 EXPRESSION TAG SEQADV 7F8P MET A 41 UNP I6Y9J2 EXPRESSION TAG SEQADV 7F8P GLY B 39 UNP I6Y9J2 EXPRESSION TAG SEQADV 7F8P HIS B 40 UNP I6Y9J2 EXPRESSION TAG SEQADV 7F8P MET B 41 UNP I6Y9J2 EXPRESSION TAG SEQRES 1 A 370 GLY HIS MET ALA PRO ILE LYS VAL ILE ALA ASP LYS GLY SEQRES 2 A 370 THR PRO PHE ALA ASP LEU LEU VAL PRO LYS LEU THR ALA SEQRES 3 A 370 SER VAL THR ASP GLY ALA VAL GLY VAL THR VAL ASP ALA SEQRES 4 A 370 PRO VAL SER VAL THR ALA ALA ASP GLY VAL LEU ALA ALA SEQRES 5 A 370 VAL THR MET VAL ASN ASP ASN GLY ARG PRO VAL ALA GLY SEQRES 6 A 370 ARG LEU SER PRO ASP GLY LEU ARG TRP SER THR THR GLU SEQRES 7 A 370 GLN LEU GLY TYR ASN ARG ARG TYR THR LEU ASN ALA THR SEQRES 8 A 370 ALA LEU GLY LEU GLY GLY ALA ALA THR ARG GLN LEU THR SEQRES 9 A 370 PHE GLN THR SER SER PRO ALA HIS LEU THR MET PRO TYR SEQRES 10 A 370 VAL MET PRO GLY ASP GLY GLU VAL VAL GLY VAL GLY GLU SEQRES 11 A 370 PRO VAL ALA ILE ARG PHE ASP GLU ASN ILE ALA ASP ARG SEQRES 12 A 370 GLY ALA ALA GLU LYS ALA ILE LYS ILE THR THR ASN PRO SEQRES 13 A 370 PRO VAL GLU GLY ALA PHE TYR TRP LEU ASN ASN ARG GLU SEQRES 14 A 370 VAL ARG TRP ARG PRO GLU HIS PHE TRP LYS PRO GLY THR SEQRES 15 A 370 ALA VAL ASP VAL ALA VAL ASN THR TYR GLY VAL ASP LEU SEQRES 16 A 370 GLY GLU GLY MET PHE GLY GLU ASP ASN VAL GLN THR HIS SEQRES 17 A 370 PHE THR ILE GLY ASP GLU VAL ILE ALA THR ALA ASP ASP SEQRES 18 A 370 ASN THR LYS ILE LEU THR VAL ARG VAL ASN GLY GLU VAL SEQRES 19 A 370 VAL LYS SER MET PRO THR SER MET GLY LYS ASP SER THR SEQRES 20 A 370 PRO THR ALA ASN GLY ILE TYR ILE VAL GLY SER ARG TYR SEQRES 21 A 370 LYS HIS ILE ILE MET ASP SER SER THR TYR GLY VAL PRO SEQRES 22 A 370 VAL ASN SER PRO ASN GLY TYR ARG THR ASP VAL ASP TRP SEQRES 23 A 370 ALA THR GLN ILE SER TYR SER GLY VAL PHE VAL HIS SER SEQRES 24 A 370 ALA PRO TRP SER VAL GLY ALA GLN GLY HIS THR ASN THR SEQRES 25 A 370 SER HIS GLY CYS LEU ASN VAL SER PRO SER ASN ALA GLN SEQRES 26 A 370 TRP PHE TYR ASP HIS VAL LYS ARG GLY ASP ILE VAL GLU SEQRES 27 A 370 VAL VAL ASN THR VAL GLY GLY THR LEU PRO GLY ILE ASP SEQRES 28 A 370 GLY LEU GLY ASP TRP ASN ILE PRO TRP ASP GLN TRP ARG SEQRES 29 A 370 ALA GLY ASN ALA LYS ALA SEQRES 1 B 370 GLY HIS MET ALA PRO ILE LYS VAL ILE ALA ASP LYS GLY SEQRES 2 B 370 THR PRO PHE ALA ASP LEU LEU VAL PRO LYS LEU THR ALA SEQRES 3 B 370 SER VAL THR ASP GLY ALA VAL GLY VAL THR VAL ASP ALA SEQRES 4 B 370 PRO VAL SER VAL THR ALA ALA ASP GLY VAL LEU ALA ALA SEQRES 5 B 370 VAL THR MET VAL ASN ASP ASN GLY ARG PRO VAL ALA GLY SEQRES 6 B 370 ARG LEU SER PRO ASP GLY LEU ARG TRP SER THR THR GLU SEQRES 7 B 370 GLN LEU GLY TYR ASN ARG ARG TYR THR LEU ASN ALA THR SEQRES 8 B 370 ALA LEU GLY LEU GLY GLY ALA ALA THR ARG GLN LEU THR SEQRES 9 B 370 PHE GLN THR SER SER PRO ALA HIS LEU THR MET PRO TYR SEQRES 10 B 370 VAL MET PRO GLY ASP GLY GLU VAL VAL GLY VAL GLY GLU SEQRES 11 B 370 PRO VAL ALA ILE ARG PHE ASP GLU ASN ILE ALA ASP ARG SEQRES 12 B 370 GLY ALA ALA GLU LYS ALA ILE LYS ILE THR THR ASN PRO SEQRES 13 B 370 PRO VAL GLU GLY ALA PHE TYR TRP LEU ASN ASN ARG GLU SEQRES 14 B 370 VAL ARG TRP ARG PRO GLU HIS PHE TRP LYS PRO GLY THR SEQRES 15 B 370 ALA VAL ASP VAL ALA VAL ASN THR TYR GLY VAL ASP LEU SEQRES 16 B 370 GLY GLU GLY MET PHE GLY GLU ASP ASN VAL GLN THR HIS SEQRES 17 B 370 PHE THR ILE GLY ASP GLU VAL ILE ALA THR ALA ASP ASP SEQRES 18 B 370 ASN THR LYS ILE LEU THR VAL ARG VAL ASN GLY GLU VAL SEQRES 19 B 370 VAL LYS SER MET PRO THR SER MET GLY LYS ASP SER THR SEQRES 20 B 370 PRO THR ALA ASN GLY ILE TYR ILE VAL GLY SER ARG TYR SEQRES 21 B 370 LYS HIS ILE ILE MET ASP SER SER THR TYR GLY VAL PRO SEQRES 22 B 370 VAL ASN SER PRO ASN GLY TYR ARG THR ASP VAL ASP TRP SEQRES 23 B 370 ALA THR GLN ILE SER TYR SER GLY VAL PHE VAL HIS SER SEQRES 24 B 370 ALA PRO TRP SER VAL GLY ALA GLN GLY HIS THR ASN THR SEQRES 25 B 370 SER HIS GLY CYS LEU ASN VAL SER PRO SER ASN ALA GLN SEQRES 26 B 370 TRP PHE TYR ASP HIS VAL LYS ARG GLY ASP ILE VAL GLU SEQRES 27 B 370 VAL VAL ASN THR VAL GLY GLY THR LEU PRO GLY ILE ASP SEQRES 28 B 370 GLY LEU GLY ASP TRP ASN ILE PRO TRP ASP GLN TRP ARG SEQRES 29 B 370 ALA GLY ASN ALA LYS ALA HET 59I A 601 20 HET GOL A 602 6 HET GLU A 603 10 HET GOL A 604 6 HET 56X A 605 23 HET GOL B 501 6 HETNAM 59I (2R,3R)-3-METHYL-4-(2-OXIDANYLIDENE-2-PROPAN-2-YLOXY- HETNAM 2 59I ETHYL)SULFANYL-2-[(2R)-3-OXIDANYL-1-OXIDANYLIDENE- HETNAM 3 59I BUTAN-2-YL]-2,3-DIHYDRO-1H-PYRROLE-5-CARBOXYLIC ACID HETNAM GOL GLYCEROL HETNAM GLU GLUTAMIC ACID HETNAM 56X (4R,5S,6S)-6-((R)-1-HYDROXYETHYL)-3-((2-ISOPROPOXY-2- HETNAM 2 56X OXOETHYL)THIO)-4-METHYL-7-OXO-1-AZABICYCLO[3.2.0]HEPT- HETNAM 3 56X 2-ENE-2-CARBOXYLIC ACID HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 59I C15 H23 N O6 S FORMUL 4 GOL 3(C3 H8 O3) FORMUL 5 GLU C5 H9 N O4 FORMUL 7 56X C15 H21 N O6 S FORMUL 9 HOH *854(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 ASN A 127 N THR A 92 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 GLU A 162 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 257 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 ASN B 95 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 224 O THR B 245 SHEET 4 AB3 4 ILE B 188 ASN B 193 -1 N THR B 191 O ASP B 223 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 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 CYS A 354 C5 59I A 601 1555 1555 1.77 CISPEP 1 MET A 157 PRO A 158 0 0.60 CISPEP 2 ASN A 193 PRO A 194 0 0.46 CISPEP 3 MET B 157 PRO B 158 0 -0.59 CISPEP 4 ASN B 193 PRO B 194 0 0.65 CRYST1 60.799 94.278 75.707 90.00 93.14 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 0.016448 0.000000 0.000901 0.00000 SCALE2 0.000000 0.010607 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013229 0.00000