HEADER TRANSFERASE 19-APR-18 6D5A TITLE CRYSTAL STRUCTURE OF L,D-TRANSPEPTIDASE 5 FROM MYCOBACTERIUM TITLE 2 TUBERCULOSIS IN APO FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: L,D-TRANSPEPTIDASE 5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 50-416; COMPND 5 SYNONYM: LDT 5,LDT(MT5); COMPND 6 EC: 2.3.2.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: ATCC 25618 / H37RV; SOURCE 5 GENE: LPRQ, RV0483, MTCY20G9.09; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS L, D TRANSPEPTIDATION, APO FORM, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.A.LIBREROS,M.V.DIAS REVDAT 4 04-OCT-23 6D5A 1 REMARK REVDAT 3 01-JAN-20 6D5A 1 REMARK REVDAT 2 06-NOV-19 6D5A 1 REMARK REVDAT 1 27-FEB-19 6D5A 0 JRNL AUTH G.A.LIBREROS-ZUNIGA,C.DOS SANTOS SILVA,R.SALGADO FERREIRA, JRNL AUTH 2 M.V.B.DIAS JRNL TITL STRUCTURAL BASIS FOR THE INTERACTION AND PROCESSING OF JRNL TITL 2 BETA-LACTAM ANTIBIOTICS BY L,D-TRANSPEPTIDASE 3 (LDTMT3) JRNL TITL 3 FROM MYCOBACTERIUM TUBERCULOSIS. JRNL REF ACS INFECT DIS V. 5 260 2019 JRNL REFN ESSN 2373-8227 JRNL PMID 30556998 JRNL DOI 10.1021/ACSINFECDIS.8B00244 REMARK 2 REMARK 2 RESOLUTION. 2.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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) : 2.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.54 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.2 REMARK 3 NUMBER OF REFLECTIONS : 15879 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.940 REMARK 3 FREE R VALUE TEST SET COUNT : 785 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 43.5438 - 4.7632 0.90 2620 137 0.1792 0.1934 REMARK 3 2 4.7632 - 3.7814 0.93 2526 138 0.1639 0.2572 REMARK 3 3 3.7814 - 3.3036 0.94 2535 114 0.2057 0.2963 REMARK 3 4 3.3036 - 3.0016 0.94 2504 127 0.2474 0.2924 REMARK 3 5 3.0016 - 2.7865 0.95 2482 133 0.2948 0.3399 REMARK 3 6 2.7865 - 2.6223 0.93 2427 136 0.3558 0.4242 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) : 0.470 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.270 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 60.69 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 72.66 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 : 0.010 2705 REMARK 3 ANGLE : 1.154 3706 REMARK 3 CHIRALITY : 0.059 408 REMARK 3 PLANARITY : 0.013 486 REMARK 3 DIHEDRAL : 18.278 1570 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): -80.7830 87.0816 31.0168 REMARK 3 T TENSOR REMARK 3 T11: 0.5389 T22: 0.3395 REMARK 3 T33: 0.4598 T12: 0.0959 REMARK 3 T13: 0.0535 T23: 0.0095 REMARK 3 L TENSOR REMARK 3 L11: 0.6370 L22: 0.2848 REMARK 3 L33: 1.5544 L12: 0.1042 REMARK 3 L13: -0.3331 L23: -0.2330 REMARK 3 S TENSOR REMARK 3 S11: -0.0989 S12: -0.0324 S13: -0.0773 REMARK 3 S21: -0.1376 S22: 0.0495 S23: -0.2793 REMARK 3 S31: -0.1087 S32: 0.0849 S33: 0.0471 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 6D5A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-APR-18. REMARK 100 THE DEPOSITION ID IS D_1000234019. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-MAY-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS REMARK 200 BEAMLINE : W01B-MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.458 REMARK 200 MONOCHROMATOR : NULL 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 0.5.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15940 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.620 REMARK 200 RESOLUTION RANGE LOW (A) : 43.540 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.11500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.62 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.8 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.89600 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 REMARK 200 STARTING MODEL: 5DU7 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000 22% (W/V), SODIUM ACETATE 100 REMARK 280 MM, AMMONIUM SULPHATE 200 MM, PH 6.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 7555 Y,X,-Z+2/3 REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z+1/3 REMARK 290 10555 -Y,-X,-Z+2/3 REMARK 290 11555 -X+Y,Y,-Z REMARK 290 12555 X,X-Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 129.31467 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 64.65733 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 129.31467 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 64.65733 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 129.31467 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 64.65733 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 129.31467 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 64.65733 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 651 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 29 REMARK 465 GLY A 30 REMARK 465 SER A 31 REMARK 465 SER A 32 REMARK 465 HIS A 33 REMARK 465 HIS A 34 REMARK 465 HIS A 35 REMARK 465 HIS A 36 REMARK 465 HIS A 37 REMARK 465 HIS A 38 REMARK 465 SER A 39 REMARK 465 SER A 40 REMARK 465 GLY A 41 REMARK 465 LEU A 42 REMARK 465 VAL A 43 REMARK 465 PRO A 44 REMARK 465 ARG A 45 REMARK 465 GLY A 46 REMARK 465 SER A 47 REMARK 465 HIS A 48 REMARK 465 MET A 49 REMARK 465 ALA A 50 REMARK 465 GLY A 51 REMARK 465 LYS A 52 REMARK 465 VAL A 53 REMARK 465 THR A 54 REMARK 465 HIS A 325 REMARK 465 ILE A 326 REMARK 465 HIS A 327 REMARK 465 MET A 346 REMARK 465 SER A 347 REMARK 465 ALA A 348 REMARK 465 GLY A 349 REMARK 465 ALA A 350 REMARK 465 GLN A 351 REMARK 465 GLY A 352 REMARK 465 ASN A 353 REMARK 465 SER A 354 REMARK 465 ASN A 355 REMARK 465 VAL A 356 REMARK 465 THR A 357 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 60 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 66 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 104 CG CD CE NZ REMARK 470 ARG A 112 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 113 CG OD1 OD2 REMARK 470 LYS A 237 CG CD CE NZ REMARK 470 ASN A 298 CG OD1 ND2 REMARK 470 MET A 316 CG SD CE REMARK 470 ASN A 318 CG OD1 ND2 REMARK 470 TYR A 323 CG CD1 CD2 CE1 CE2 CZ OH 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 PHE A 162 O HOH A 601 2.04 REMARK 500 OE1 GLU A 309 O HOH A 602 2.07 REMARK 500 OH TYR A 311 O HOH A 602 2.10 REMARK 500 OG SER A 132 O HOH A 603 2.12 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 644 O HOH A 687 12575 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 PHE A 314 CB - CG - CD1 ANGL. DEV. = -4.3 DEGREES REMARK 500 PRO A 415 C - N - CD ANGL. DEV. = -18.3 DEGREES 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 LEU A 56 -133.69 -107.08 REMARK 500 ALA A 57 -77.01 -80.89 REMARK 500 SER A 74 -4.38 79.06 REMARK 500 ASP A 113 80.62 48.57 REMARK 500 ARG A 114 62.86 -42.94 REMARK 500 ILE A 172 3.74 -65.60 REMARK 500 PRO A 183 170.04 -57.22 REMARK 500 ASP A 186 70.69 -114.90 REMARK 500 THR A 278 -158.75 -115.65 REMARK 500 ASP A 294 -82.41 -48.32 REMARK 500 THR A 308 -71.77 -117.76 REMARK 500 PRO A 319 103.63 -50.90 REMARK 500 ALA A 320 -51.94 -178.18 REMARK 500 ALA A 321 -74.11 -172.28 REMARK 500 PRO A 415 42.02 -105.73 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 686 DISTANCE = 6.12 ANGSTROMS REMARK 525 HOH A 687 DISTANCE = 6.85 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PG4 A 501 DBREF 6D5A A 50 416 UNP P9WKV3 LDT5_MYCTU 50 416 SEQADV 6D5A MET A 29 UNP P9WKV3 INITIATING METHIONINE SEQADV 6D5A GLY A 30 UNP P9WKV3 EXPRESSION TAG SEQADV 6D5A SER A 31 UNP P9WKV3 EXPRESSION TAG SEQADV 6D5A SER A 32 UNP P9WKV3 EXPRESSION TAG SEQADV 6D5A HIS A 33 UNP P9WKV3 EXPRESSION TAG SEQADV 6D5A HIS A 34 UNP P9WKV3 EXPRESSION TAG SEQADV 6D5A HIS A 35 UNP P9WKV3 EXPRESSION TAG SEQADV 6D5A HIS A 36 UNP P9WKV3 EXPRESSION TAG SEQADV 6D5A HIS A 37 UNP P9WKV3 EXPRESSION TAG SEQADV 6D5A HIS A 38 UNP P9WKV3 EXPRESSION TAG SEQADV 6D5A SER A 39 UNP P9WKV3 EXPRESSION TAG SEQADV 6D5A SER A 40 UNP P9WKV3 EXPRESSION TAG SEQADV 6D5A GLY A 41 UNP P9WKV3 EXPRESSION TAG SEQADV 6D5A LEU A 42 UNP P9WKV3 EXPRESSION TAG SEQADV 6D5A VAL A 43 UNP P9WKV3 EXPRESSION TAG SEQADV 6D5A PRO A 44 UNP P9WKV3 EXPRESSION TAG SEQADV 6D5A ARG A 45 UNP P9WKV3 EXPRESSION TAG SEQADV 6D5A GLY A 46 UNP P9WKV3 EXPRESSION TAG SEQADV 6D5A SER A 47 UNP P9WKV3 EXPRESSION TAG SEQADV 6D5A HIS A 48 UNP P9WKV3 EXPRESSION TAG SEQADV 6D5A MET A 49 UNP P9WKV3 EXPRESSION TAG SEQRES 1 A 388 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 388 LEU VAL PRO ARG GLY SER HIS MET ALA GLY LYS VAL THR SEQRES 3 A 388 LYS LEU ALA GLU LYS ARG PRO PRO PRO ALA PRO ARG LEU SEQRES 4 A 388 THR PHE ARG PRO ALA ASP SER ALA ALA ASP VAL VAL PRO SEQRES 5 A 388 ILE ALA PRO ILE SER VAL GLU VAL GLY ASP GLY TRP PHE SEQRES 6 A 388 GLN ARG VAL ALA LEU THR ASN SER ALA GLY LYS VAL VAL SEQRES 7 A 388 ALA GLY ALA TYR SER ARG ASP ARG THR ILE TYR THR ILE SEQRES 8 A 388 THR GLU PRO LEU GLY TYR ASP THR THR TYR THR TRP SER SEQRES 9 A 388 GLY SER ALA VAL GLY HIS ASP GLY LYS ALA VAL PRO VAL SEQRES 10 A 388 ALA GLY LYS PHE THR THR VAL ALA PRO VAL LYS THR ILE SEQRES 11 A 388 ASN ALA GLY PHE GLN LEU ALA ASP GLY GLN THR VAL GLY SEQRES 12 A 388 ILE ALA ALA PRO VAL ILE ILE GLN PHE ASP SER PRO ILE SEQRES 13 A 388 SER ASP LYS ALA ALA VAL GLU ARG ALA LEU THR VAL THR SEQRES 14 A 388 THR ASP PRO PRO VAL GLU GLY GLY TRP ALA TRP LEU PRO SEQRES 15 A 388 ASP GLU ALA GLN GLY ALA ARG VAL HIS TRP ARG PRO ARG SEQRES 16 A 388 GLU TYR TYR PRO ALA GLY THR THR VAL ASP VAL ASP ALA SEQRES 17 A 388 LYS LEU TYR GLY LEU PRO PHE GLY ASP GLY ALA TYR GLY SEQRES 18 A 388 ALA GLN ASP MET SER LEU HIS PHE GLN ILE GLY ARG ARG SEQRES 19 A 388 GLN VAL VAL LYS ALA GLU VAL SER SER HIS ARG ILE GLN SEQRES 20 A 388 VAL VAL THR ASP ALA GLY VAL ILE MET ASP PHE PRO CYS SEQRES 21 A 388 SER TYR GLY GLU ALA ASP LEU ALA ARG ASN VAL THR ARG SEQRES 22 A 388 ASN GLY ILE HIS VAL VAL THR GLU LYS TYR SER ASP PHE SEQRES 23 A 388 TYR MET SER ASN PRO ALA ALA GLY TYR SER HIS ILE HIS SEQRES 24 A 388 GLU ARG TRP ALA VAL ARG ILE SER ASN ASN GLY GLU PHE SEQRES 25 A 388 ILE HIS ALA ASN PRO MET SER ALA GLY ALA GLN GLY ASN SEQRES 26 A 388 SER ASN VAL THR ASN GLY CYS ILE ASN LEU SER THR GLU SEQRES 27 A 388 ASN ALA GLU GLN TYR TYR ARG SER ALA VAL TYR GLY ASP SEQRES 28 A 388 PRO VAL GLU VAL THR GLY SER SER ILE GLN LEU SER TYR SEQRES 29 A 388 ALA ASP GLY ASP ILE TRP ASP TRP ALA VAL ASP TRP ASP SEQRES 30 A 388 THR TRP VAL SER MET SER ALA LEU PRO PRO PRO HET PG4 A 501 13 HETNAM PG4 TETRAETHYLENE GLYCOL FORMUL 2 PG4 C8 H18 O5 FORMUL 3 HOH *87(H2 O) HELIX 1 AA1 ASP A 186 ARG A 192 1 7 HELIX 2 AA2 LEU A 295 VAL A 299 5 5 HELIX 3 AA3 SER A 364 ALA A 375 1 12 HELIX 4 AA4 SER A 391 GLY A 395 5 5 HELIX 5 AA5 TRP A 398 VAL A 402 5 5 HELIX 6 AA6 ASP A 403 SER A 409 1 7 SHEET 1 AA1 4 ARG A 66 ARG A 70 0 SHEET 2 AA1 4 SER A 85 GLY A 89 -1 O SER A 85 N ARG A 70 SHEET 3 AA1 4 ILE A 116 ILE A 119 -1 O TYR A 117 N VAL A 86 SHEET 4 AA1 4 GLY A 108 SER A 111 -1 N ALA A 109 O THR A 118 SHEET 1 AA2 4 VAL A 105 VAL A 106 0 SHEET 2 AA2 4 TRP A 92 THR A 99 -1 N LEU A 98 O VAL A 106 SHEET 3 AA2 4 THR A 128 VAL A 136 -1 O SER A 134 N GLN A 94 SHEET 4 AA2 4 ALA A 142 PRO A 144 -1 O VAL A 143 N ALA A 135 SHEET 1 AA3 4 VAL A 105 VAL A 106 0 SHEET 2 AA3 4 TRP A 92 THR A 99 -1 N LEU A 98 O VAL A 106 SHEET 3 AA3 4 THR A 128 VAL A 136 -1 O SER A 134 N GLN A 94 SHEET 4 AA3 4 GLY A 147 THR A 150 -1 O GLY A 147 N TRP A 131 SHEET 1 AA4 3 LYS A 156 ILE A 158 0 SHEET 2 AA4 3 ALA A 247 GLY A 249 1 O TYR A 248 N ILE A 158 SHEET 3 AA4 3 PRO A 242 GLY A 244 -1 N GLY A 244 O ALA A 247 SHEET 1 AA5 4 ALA A 160 PHE A 162 0 SHEET 2 AA5 4 VAL A 176 PHE A 180 -1 O GLN A 179 N GLY A 161 SHEET 3 AA5 4 ARG A 217 PRO A 222 -1 O VAL A 218 N ILE A 178 SHEET 4 AA5 4 GLY A 204 LEU A 209 -1 N ALA A 207 O HIS A 219 SHEET 1 AA6 4 THR A 169 VAL A 170 0 SHEET 2 AA6 4 MET A 253 ILE A 259 1 O GLN A 258 N VAL A 170 SHEET 3 AA6 4 THR A 231 ALA A 236 -1 N VAL A 232 O PHE A 257 SHEET 4 AA6 4 LEU A 194 ASP A 199 -1 N THR A 195 O ASP A 235 SHEET 1 AA7 5 GLY A 281 PRO A 287 0 SHEET 2 AA7 5 ARG A 273 THR A 278 -1 N VAL A 276 O ILE A 283 SHEET 3 AA7 5 VAL A 264 GLU A 268 -1 N LYS A 266 O GLN A 275 SHEET 4 AA7 5 PRO A 380 THR A 384 1 O GLU A 382 N ALA A 267 SHEET 5 AA7 5 GLY A 303 VAL A 306 -1 N HIS A 305 O VAL A 381 SHEET 1 AA8 4 LYS A 310 ASP A 313 0 SHEET 2 AA8 4 ARG A 329 SER A 335 -1 O ALA A 331 N TYR A 311 SHEET 3 AA8 4 GLU A 339 ALA A 343 -1 O GLU A 339 N ILE A 334 SHEET 4 AA8 4 ILE A 361 LEU A 363 1 O ILE A 361 N PHE A 340 CISPEP 1 ARG A 70 PRO A 71 0 1.88 CISPEP 2 ASP A 199 PRO A 200 0 2.65 CISPEP 3 ASP A 396 ILE A 397 0 -7.89 SITE 1 AC1 2 ASP A 211 TYR A 392 CRYST1 97.446 97.446 193.972 90.00 90.00 120.00 P 62 2 2 12 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 0.010262 0.005925 0.000000 0.00000 SCALE2 0.000000 0.011850 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005155 0.00000