HEADER TRANSFERASE 18-SEP-15 5DUJ TITLE CRYSTAL STRUCTURE OF LDTMT2 IN COMPLEX WITH FAROPENEM ADDUCT COMPND MOL_ID: 1; COMPND 2 MOLECULE: L,D-TRANSPEPTIDASE 2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RESIDUES 42-408; COMPND 5 SYNONYM: LDT 2,LDT(MT2); COMPND 6 EC: 2.3.2.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83331; SOURCE 4 STRAIN: CDC 1551 / OSHKOSH; SOURCE 5 GENE: LDTB, MT2594, V735_02606; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS LD-TRANSPEPTIDASE, PEPTIDOGLYCAN SYNTHESIS ENZYME, CELL WALL ENZYME, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR P.KUMAR,G.LAMICHHANE REVDAT 6 27-SEP-23 5DUJ 1 REMARK REVDAT 5 20-SEP-17 5DUJ 1 REMARK REVDAT 4 28-DEC-16 5DUJ 1 JRNL REVDAT 3 23-NOV-16 5DUJ 1 JRNL REVDAT 2 09-NOV-16 5DUJ 1 JRNL REVDAT 1 28-SEP-16 5DUJ 0 JRNL AUTH P.KUMAR,A.KAUSHIK,E.P.LLOYD,S.G.LI,R.MATTOO,N.C.AMMERMAN, JRNL AUTH 2 D.T.BELL,A.L.PERRYMAN,T.A.ZANDI,S.EKINS,S.L.GINELL, JRNL AUTH 3 C.A.TOWNSEND,J.S.FREUNDLICH,G.LAMICHHANE JRNL TITL NON-CLASSICAL TRANSPEPTIDASES YIELD INSIGHT INTO NEW JRNL TITL 2 ANTIBACTERIALS. JRNL REF NAT. CHEM. BIOL. V. 13 54 2017 JRNL REFN ESSN 1552-4469 JRNL PMID 27820797 JRNL DOI 10.1038/NCHEMBIO.2237 REMARK 2 REMARK 2 RESOLUTION. 2.17 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.17 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 40491 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2153 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.17 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2504 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 80.87 REMARK 3 BIN R VALUE (WORKING SET) : 0.2160 REMARK 3 BIN FREE R VALUE SET COUNT : 147 REMARK 3 BIN FREE R VALUE : 0.2860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5292 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 25 REMARK 3 SOLVENT ATOMS : 462 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.03 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.66000 REMARK 3 B22 (A**2) : 1.39000 REMARK 3 B33 (A**2) : -1.97000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.75000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.234 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.199 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.138 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.402 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.948 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.914 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5458 ; 0.017 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5032 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7460 ; 1.929 ; 1.928 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11538 ; 1.079 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 701 ; 7.274 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 237 ;31.579 ;24.093 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 785 ;16.383 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 33 ;17.548 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 838 ; 0.128 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6322 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1263 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2807 ; 1.954 ; 2.497 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2806 ; 1.954 ; 2.496 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3507 ; 2.878 ; 3.734 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3508 ; 2.878 ; 3.735 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2651 ; 2.748 ; 2.793 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2651 ; 2.743 ; 2.793 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3954 ; 4.071 ; 4.059 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6298 ; 5.876 ;20.843 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6299 ; 5.876 ;20.846 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5DUJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 21-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000213831. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-OCT-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0-8.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL 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 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944+ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42667 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.170 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.6 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : 0.05600 REMARK 200 FOR THE DATA SET : 20.8600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.17 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 59.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.18600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.190 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: 3VYN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% 5000MME, 200MM AMMONIUM SULFATE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 46.96450 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, 3 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -26.0 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 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 -3.56934 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 -46.96450 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 75.13026 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 613 O HOH B 793 2.18 REMARK 500 ND1 HIS A 300 O HOH A 601 2.19 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 GLU B 162 CG GLU B 162 CD 0.131 REMARK 500 GLY B 353 N GLY B 353 CA -0.116 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 ARG A 99 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 209 CD - NE - CZ ANGL. DEV. = 13.8 DEGREES REMARK 500 ARG A 209 NE - CZ - NH1 ANGL. DEV. = 9.7 DEGREES REMARK 500 ARG A 209 NE - CZ - NH2 ANGL. DEV. = -12.3 DEGREES REMARK 500 ASP A 232 CB - CG - OD1 ANGL. DEV. = 7.2 DEGREES REMARK 500 ARG A 267 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 297 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG A 319 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 371 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG B 99 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 209 CD - NE - CZ ANGL. DEV. = 9.8 DEGREES REMARK 500 ARG B 209 NE - CZ - NH1 ANGL. DEV. = 7.4 DEGREES REMARK 500 ARG B 209 NE - CZ - NH2 ANGL. DEV. = -9.0 DEGREES REMARK 500 ASP B 232 CB - CG - OD1 ANGL. DEV. = 8.9 DEGREES REMARK 500 ARG B 319 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 HIS B 352 CA - C - N ANGL. DEV. = 15.0 DEGREES REMARK 500 HIS B 352 O - C - N ANGL. DEV. = -10.9 DEGREES REMARK 500 ARG B 371 NE - CZ - NH2 ANGL. DEV. = -3.4 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 ASP A 96 21.62 -76.85 REMARK 500 ASN A 97 34.14 -145.63 REMARK 500 ALA A 102 122.52 87.47 REMARK 500 ASN A 204 -175.33 -170.78 REMARK 500 ASN A 227 64.07 -103.08 REMARK 500 HIS A 347 -59.56 -137.57 REMARK 500 ASN A 405 40.66 -149.25 REMARK 500 MET B 280 -169.21 -102.57 REMARK 500 HIS B 347 -59.19 -126.71 REMARK 500 ASN B 405 38.72 -151.47 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 209 0.10 SIDE CHAIN REMARK 500 ARG B 209 0.07 SIDE CHAIN 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 B 830 DISTANCE = 6.25 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 DGF A 503 REMARK 610 DGF B 502 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BME A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue DGF A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BME B 501 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5DU7 RELATED DB: PDB DBREF 5DUJ A 42 408 UNP O53223 LDT2_MYCTO 42 408 DBREF 5DUJ B 42 408 UNP O53223 LDT2_MYCTO 42 408 SEQADV 5DUJ GLY A 39 UNP O53223 EXPRESSION TAG SEQADV 5DUJ HIS A 40 UNP O53223 EXPRESSION TAG SEQADV 5DUJ MET A 41 UNP O53223 EXPRESSION TAG SEQADV 5DUJ GLY B 39 UNP O53223 EXPRESSION TAG SEQADV 5DUJ HIS B 40 UNP O53223 EXPRESSION TAG SEQADV 5DUJ MET B 41 UNP O53223 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 SO4 A 501 5 HET BME A 502 4 HET DGF A 503 6 HET BME B 501 4 HET DGF B 502 6 HETNAM SO4 SULFATE ION HETNAM BME BETA-MERCAPTOETHANOL HETNAM DGF (2R,5R)-2-[(2S,3R)-3-HYDROXY-1-OXOBUTAN-2-YL]-5-[(2R)- HETNAM 2 DGF TETRAHYDROFURAN-2-YL]-2,5-DIHYDRO-1,3-THIAZOLE-4- HETNAM 3 DGF CARBOXYLIC ACID HETSYN DGF FAROPENEM PRODUCT, BOUND FORM FORMUL 3 SO4 O4 S 2- FORMUL 4 BME 2(C2 H6 O S) FORMUL 5 DGF 2(C12 H17 N O5 S) FORMUL 8 HOH *462(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 ALA A 84 N LYS A 61 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 THR A 125 N VAL A 94 SHEET 3 AA2 3 GLY A 135 GLN A 144 -1 O LEU A 141 N LEU A 126 SHEET 1 AA3 2 HIS A 150 THR A 152 0 SHEET 2 AA3 2 MET A 237 GLY A 239 1 O PHE A 238 N HIS A 150 SHEET 1 AA4 4 PRO A 154 MET A 157 0 SHEET 2 AA4 4 VAL A 170 PHE A 174 -1 O ARG A 173 N TYR A 155 SHEET 3 AA4 4 GLU A 207 PRO A 212 -1 O TRP A 210 N VAL A 170 SHEET 4 AA4 4 GLY A 198 TRP A 202 -1 N TYR A 201 O ARG A 209 SHEET 1 AA5 4 VAL A 163 VAL A 164 0 SHEET 2 AA5 4 VAL A 243 ILE A 249 1 O THR A 248 N VAL A 164 SHEET 3 AA5 4 ALA A 221 VAL A 226 -1 N VAL A 226 O VAL A 243 SHEET 4 AA5 4 ILE A 188 ASN A 193 -1 N LYS A 189 O ALA A 225 SHEET 1 AA6 5 GLU A 271 PRO A 277 0 SHEET 2 AA6 5 ILE A 263 VAL A 268 -1 N VAL A 266 O LYS A 274 SHEET 3 AA6 5 VAL A 253 ASP A 258 -1 N THR A 256 O THR A 265 SHEET 4 AA6 5 ILE A 374 VAL A 378 1 O GLU A 376 N ALA A 255 SHEET 5 AA6 5 GLY A 290 ILE A 293 -1 N TYR A 292 O VAL A 375 SHEET 1 AA7 4 ARG A 297 ASP A 304 0 SHEET 2 AA7 4 ARG A 319 GLN A 327 -1 O THR A 320 N MET A 303 SHEET 3 AA7 4 PHE A 334 SER A 337 -1 O VAL A 335 N THR A 326 SHEET 4 AA7 4 LEU A 355 VAL A 357 1 O LEU A 355 N PHE A 334 SHEET 1 AA8 4 LYS B 61 ALA B 64 0 SHEET 2 AA8 4 SER B 80 ALA B 84 -1 O 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 VAL B 94 0 SHEET 2 AA9 3 ARG B 123 GLY B 132 -1 O ASN B 127 N THR B 92 SHEET 3 AA9 3 GLY B 135 GLN B 144 -1 O ALA B 137 N ALA B 130 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 LYS B 189 O ALA B 225 SHEET 1 AB4 5 GLU B 271 PRO B 277 0 SHEET 2 AB4 5 ILE B 263 VAL B 268 -1 N LEU B 264 O MET B 276 SHEET 3 AB4 5 VAL B 253 ASP B 258 -1 N THR B 256 O THR B 265 SHEET 4 AB4 5 ILE B 374 VAL B 378 1 O ILE B 374 N ALA B 255 SHEET 5 AB4 5 GLY B 290 ILE B 293 -1 N TYR B 292 O VAL B 375 SHEET 1 AB5 4 ARG B 297 ASP B 304 0 SHEET 2 AB5 4 ARG B 319 GLN B 327 -1 O THR B 320 N MET B 303 SHEET 3 AB5 4 PHE B 334 SER B 337 -1 O VAL B 335 N THR B 326 SHEET 4 AB5 4 LEU B 355 VAL B 357 1 O LEU B 355 N PHE B 334 LINK SG CYS A 354 CAT DGF A 503 1555 1555 1.71 LINK SG CYS B 354 CAT DGF B 502 1555 1555 1.73 CISPEP 1 MET A 157 PRO A 158 0 -2.58 CISPEP 2 ASN A 193 PRO A 194 0 -0.68 CISPEP 3 MET B 157 PRO B 158 0 -4.42 CISPEP 4 ASN B 193 PRO B 194 0 15.98 CISPEP 5 HIS B 352 GLY B 353 0 16.23 SITE 1 AC1 5 ARG A 297 ARG A 371 HOH A 625 HOH A 716 SITE 2 AC1 5 HOH A 738 SITE 1 AC2 5 MET A 303 TYR A 318 HIS A 352 CYS A 354 SITE 2 AC2 5 DGF A 503 SITE 1 AC3 7 TYR A 318 SER A 331 GLY A 332 HIS A 352 SITE 2 AC3 7 GLY A 353 CYS A 354 BME A 502 SITE 1 AC4 6 MET B 303 HIS B 336 SER B 351 HIS B 352 SITE 2 AC4 6 CYS B 354 DGF B 502 CRYST1 61.051 93.929 75.215 90.00 92.72 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 0.016380 0.000000 0.000778 0.00000 SCALE2 0.000000 0.010646 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013310 0.00000