HEADER TRANSFERASE 25-NOV-04 1Y3I TITLE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS NAD KINASE-NAD COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: INORGANIC POLYPHOSPHATE/ATP-NAD KINASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: POLY(P)/ATP NAD KINASE; COMPND 5 EC: 2.7.1.23; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 1773; SOURCE 4 GENE: PPNK; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PSK27 KEYWDS NAD KINASE, POLYPHOSPHATE, NAD, MYCOBACTERIUM TUBERCULOSIS, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.MORI,M.YAMASAKI,Y.MARUYAMA,K.MOMMA,S.KAWAI,W.HASHIMOTO,B.MIKAMI, AUTHOR 2 K.MURATA REVDAT 4 13-MAR-24 1Y3I 1 REMARK REVDAT 3 13-JUL-11 1Y3I 1 VERSN REVDAT 2 24-FEB-09 1Y3I 1 VERSN REVDAT 1 18-JAN-05 1Y3I 0 JRNL AUTH S.MORI,M.YAMASAKI,Y.MARUYAMA,K.MOMMA,S.KAWAI,W.HASHIMOTO, JRNL AUTH 2 B.MIKAMI,K.MURATA JRNL TITL NAD-BINDING MODE AND THE SIGNIFICANCE OF INTERSUBUNIT JRNL TITL 2 CONTACT REVEALED BY THE CRYSTAL STRUCTURE OF MYCOBACTERIUM JRNL TITL 3 TUBERCULOSIS NAD KINASE-NAD COMPLEX JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 327 500 2005 JRNL REFN ISSN 0006-291X JRNL PMID 15629142 JRNL DOI 10.1016/J.BBRC.2004.11.163 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.0 REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.191 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL REMARK 3 FREE R VALUE (NO CUTOFF) : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.166 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 14577 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3476 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 117 REMARK 3 SOLVENT ATOMS : 43 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 3636.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 14548 REMARK 3 NUMBER OF RESTRAINTS : 19678 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.026 REMARK 3 ANGLE DISTANCES (A) : 0.029 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.058 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.026 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.025 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.028 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.073 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.078 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1Y3I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-DEC-04. REMARK 100 THE DEPOSITION ID IS D_1000031069. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-MAY-04 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 22375 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: SHELX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, HEPES-NA, NAD, PH REMARK 280 8.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 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 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 72.62133 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 36.31067 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 72.62133 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 36.31067 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 300 REMARK: THE BIOLOGICAL UNIT IS A TETRAMER GENERATED FROM THE DIMER REMARK 300 IN THE ASYMMETRIC UNIT BY THE OPERATIONS: -X, -Y, Z. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 16960 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -116.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 BIOMT1 2 -1.000000 0.000000 0.000000 110.45000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PQS REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 MET A 1 REMARK 465 THR A 2 REMARK 465 ALA A 3 REMARK 465 HIS A 4 REMARK 465 ARG A 5 REMARK 465 SER A 6 REMARK 465 THR A 13 REMARK 465 GLY A 14 REMARK 465 ARG A 15 REMARK 465 ASP A 16 REMARK 465 GLU A 17 REMARK 465 ALA A 18 REMARK 465 THR A 19 REMARK 465 GLU A 20 REMARK 465 THR A 21 REMARK 465 ALA A 22 REMARK 465 ARG A 23 REMARK 465 ARG A 24 REMARK 465 VAL A 25 REMARK 465 GLU A 26 REMARK 465 LYS A 27 REMARK 465 VAL A 28 REMARK 465 LEU A 29 REMARK 465 GLY A 30 REMARK 465 ASP A 31 REMARK 465 ASN A 32 REMARK 465 LYS A 33 REMARK 465 ILE A 34 REMARK 465 ALA A 35 REMARK 465 LEU A 36 REMARK 465 ARG A 37 REMARK 465 VAL A 38 REMARK 465 LEU A 39 REMARK 465 SER A 40 REMARK 465 ALA A 41 REMARK 465 GLU A 42 REMARK 465 ALA A 43 REMARK 465 VAL A 44 REMARK 465 ASP A 45 REMARK 465 ARG A 46 REMARK 465 GLY A 47 REMARK 465 SER A 48 REMARK 465 LEU A 49 REMARK 465 HIS A 50 REMARK 465 LEU A 51 REMARK 465 ALA A 52 REMARK 465 PRO A 53 REMARK 465 ASP A 54 REMARK 465 ASP A 55 REMARK 465 MET A 56 REMARK 465 ARG A 57 REMARK 465 ALA A 58 REMARK 465 MET A 59 REMARK 465 GLY A 60 REMARK 465 VAL A 61 REMARK 465 GLU A 62 REMARK 465 ILE A 63 REMARK 465 GLU A 64 REMARK 465 VAL A 65 REMARK 465 VAL A 66 REMARK 465 ASP A 67 REMARK 465 ALA A 68 REMARK 465 ASP A 69 REMARK 465 GLN A 70 REMARK 465 HIS A 71 REMARK 465 ALA A 72 REMARK 465 ALA A 73 REMARK 465 ASP A 74 REMARK 465 GLY A 75 REMARK 465 CYS A 76 REMARK 465 GLU A 77 REMARK 465 GLY A 303 REMARK 465 TRP A 304 REMARK 465 ARG A 305 REMARK 465 GLY A 306 REMARK 465 LYS A 307 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 465 ALA B 3 REMARK 465 HIS B 4 REMARK 465 ARG B 5 REMARK 465 SER B 6 REMARK 465 THR B 13 REMARK 465 GLY B 14 REMARK 465 ARG B 15 REMARK 465 ASP B 16 REMARK 465 GLU B 17 REMARK 465 ALA B 18 REMARK 465 THR B 19 REMARK 465 GLU B 20 REMARK 465 THR B 21 REMARK 465 ALA B 22 REMARK 465 ARG B 23 REMARK 465 ARG B 24 REMARK 465 VAL B 25 REMARK 465 GLU B 26 REMARK 465 LYS B 27 REMARK 465 VAL B 28 REMARK 465 LEU B 29 REMARK 465 GLY B 30 REMARK 465 ASP B 31 REMARK 465 ASN B 32 REMARK 465 LYS B 33 REMARK 465 ILE B 34 REMARK 465 ALA B 35 REMARK 465 LEU B 36 REMARK 465 ARG B 37 REMARK 465 VAL B 38 REMARK 465 LEU B 39 REMARK 465 SER B 40 REMARK 465 ALA B 41 REMARK 465 GLU B 42 REMARK 465 ALA B 43 REMARK 465 VAL B 44 REMARK 465 ASP B 45 REMARK 465 ARG B 46 REMARK 465 GLY B 47 REMARK 465 SER B 48 REMARK 465 LEU B 49 REMARK 465 HIS B 50 REMARK 465 LEU B 51 REMARK 465 ALA B 52 REMARK 465 PRO B 53 REMARK 465 ASP B 54 REMARK 465 ASP B 55 REMARK 465 MET B 56 REMARK 465 ARG B 57 REMARK 465 ALA B 58 REMARK 465 MET B 59 REMARK 465 GLY B 60 REMARK 465 VAL B 61 REMARK 465 GLU B 62 REMARK 465 ILE B 63 REMARK 465 GLU B 64 REMARK 465 VAL B 65 REMARK 465 VAL B 66 REMARK 465 ASP B 67 REMARK 465 ALA B 68 REMARK 465 ASP B 69 REMARK 465 GLN B 70 REMARK 465 HIS B 71 REMARK 465 ALA B 72 REMARK 465 ALA B 73 REMARK 465 ASP B 74 REMARK 465 GLY B 75 REMARK 465 CYS B 76 REMARK 465 GLU B 77 REMARK 465 GLY B 303 REMARK 465 TRP B 304 REMARK 465 ARG B 305 REMARK 465 GLY B 306 REMARK 465 LYS B 307 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 VAL A 7 CA VAL A 7 CB 0.867 REMARK 500 VAL A 7 CB VAL A 7 CG1 0.894 REMARK 500 VAL A 7 CB VAL A 7 CG2 0.889 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 VAL A 7 N - CA - CB ANGL. DEV. = -17.9 DEGREES REMARK 500 VAL A 7 CG1 - CB - CG2 ANGL. DEV. = -29.4 DEGREES REMARK 500 VAL A 7 CA - CB - CG1 ANGL. DEV. = -29.3 DEGREES REMARK 500 VAL A 7 CA - CB - CG2 ANGL. DEV. = -28.8 DEGREES REMARK 500 ARG A 96 CD - NE - CZ ANGL. DEV. = 9.1 DEGREES REMARK 500 ARG A 96 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 TYR A 202 CB - CG - CD2 ANGL. DEV. = -8.0 DEGREES REMARK 500 TYR A 202 CB - CG - CD1 ANGL. DEV. = 8.4 DEGREES REMARK 500 ARG A 260 CD - NE - CZ ANGL. DEV. = 21.3 DEGREES REMARK 500 ARG A 260 NE - CZ - NH1 ANGL. DEV. = 7.9 DEGREES REMARK 500 ARG A 260 NE - CZ - NH2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ARG B 96 CD - NE - CZ ANGL. DEV. = 10.1 DEGREES REMARK 500 ARG B 96 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 TYR B 202 CB - CG - CD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 TYR B 202 CB - CG - CD1 ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG B 231 NE - CZ - NH1 ANGL. DEV. = -3.5 DEGREES REMARK 500 ARG B 260 CD - NE - CZ ANGL. DEV. = 18.8 DEGREES REMARK 500 ARG B 260 NE - CZ - NH1 ANGL. DEV. = -6.5 DEGREES REMARK 500 ARG B 260 NE - CZ - NH2 ANGL. DEV. = 8.3 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 ALA A 91 -72.53 -51.67 REMARK 500 SER A 99 0.75 45.52 REMARK 500 PRO A 101 130.84 -32.08 REMARK 500 LEU A 107 71.56 -113.91 REMARK 500 ILE A 110 125.03 -24.96 REMARK 500 ALA A 120 55.66 -110.52 REMARK 500 LEU A 125 -52.82 -15.00 REMARK 500 TYR A 133 -176.35 178.05 REMARK 500 ASN A 153 154.78 177.84 REMARK 500 ASN A 159 -70.40 -78.16 REMARK 500 SER A 184 138.17 -179.23 REMARK 500 ALA A 201 -119.78 -107.20 REMARK 500 ALA A 217 160.39 178.86 REMARK 500 GLU A 238 38.16 -76.62 REMARK 500 ALA A 252 -157.68 -106.89 REMARK 500 ARG A 259 -151.17 -78.14 REMARK 500 ARG A 260 45.80 32.92 REMARK 500 SER A 268 -178.19 -54.37 REMARK 500 ALA B 91 -70.85 -47.92 REMARK 500 ALA B 92 -36.61 -38.78 REMARK 500 SER B 99 39.50 36.42 REMARK 500 LEU B 107 62.47 -116.44 REMARK 500 ALA B 120 68.52 -100.12 REMARK 500 VAL B 124 -70.97 -51.62 REMARK 500 GLN B 131 68.04 64.39 REMARK 500 TYR B 133 -172.21 172.56 REMARK 500 ASP B 137 85.15 -69.96 REMARK 500 ASN B 153 147.10 -172.83 REMARK 500 ALA B 157 142.31 -174.74 REMARK 500 ASN B 159 -73.41 -74.71 REMARK 500 ALA B 201 -131.09 -114.02 REMARK 500 ASN B 224 80.17 38.85 REMARK 500 ARG B 259 -157.43 -115.47 REMARK 500 SER B 268 -164.83 -64.39 REMARK 500 ARG B 269 115.41 -164.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 B 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD B 1501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1601 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1Y3H RELATED DB: PDB REMARK 900 THE SAME PROTEIN AT 2.8 ANGSTROM DBREF 1Y3I A 1 307 UNP P0A5S6 PPNK_MYCTU 1 307 DBREF 1Y3I B 1 307 UNP P0A5S6 PPNK_MYCTU 1 307 SEQRES 1 A 307 MET THR ALA HIS ARG SER VAL LEU LEU VAL VAL HIS THR SEQRES 2 A 307 GLY ARG ASP GLU ALA THR GLU THR ALA ARG ARG VAL GLU SEQRES 3 A 307 LYS VAL LEU GLY ASP ASN LYS ILE ALA LEU ARG VAL LEU SEQRES 4 A 307 SER ALA GLU ALA VAL ASP ARG GLY SER LEU HIS LEU ALA SEQRES 5 A 307 PRO ASP ASP MET ARG ALA MET GLY VAL GLU ILE GLU VAL SEQRES 6 A 307 VAL ASP ALA ASP GLN HIS ALA ALA ASP GLY CYS GLU LEU SEQRES 7 A 307 VAL LEU VAL LEU GLY GLY ASP GLY THR PHE LEU ARG ALA SEQRES 8 A 307 ALA GLU LEU ALA ARG ASN ALA SER ILE PRO VAL LEU GLY SEQRES 9 A 307 VAL ASN LEU GLY ARG ILE GLY PHE LEU ALA GLU ALA GLU SEQRES 10 A 307 ALA GLU ALA ILE ASP ALA VAL LEU GLU HIS VAL VAL ALA SEQRES 11 A 307 GLN ASP TYR ARG VAL GLU ASP ARG LEU THR LEU ASP VAL SEQRES 12 A 307 VAL VAL ARG GLN GLY GLY ARG ILE VAL ASN ARG GLY TRP SEQRES 13 A 307 ALA LEU ASN GLU VAL SER LEU GLU LYS GLY PRO ARG LEU SEQRES 14 A 307 GLY VAL LEU GLY VAL VAL VAL GLU ILE ASP GLY ARG PRO SEQRES 15 A 307 VAL SER ALA PHE GLY CYS ASP GLY VAL LEU VAL SER THR SEQRES 16 A 307 PRO THR GLY SER THR ALA TYR ALA PHE SER ALA GLY GLY SEQRES 17 A 307 PRO VAL LEU TRP PRO ASP LEU GLU ALA ILE LEU VAL VAL SEQRES 18 A 307 PRO ASN ASN ALA HIS ALA LEU PHE GLY ARG PRO MET VAL SEQRES 19 A 307 THR SER PRO GLU ALA THR ILE ALA ILE GLU ILE GLU ALA SEQRES 20 A 307 ASP GLY HIS ASP ALA LEU VAL PHE CYS ASP GLY ARG ARG SEQRES 21 A 307 GLU MET LEU ILE PRO ALA GLY SER ARG LEU GLU VAL THR SEQRES 22 A 307 ARG CYS VAL THR SER VAL LYS TRP ALA ARG LEU ASP SER SEQRES 23 A 307 ALA PRO PHE THR ASP ARG LEU VAL ARG LYS PHE ARG LEU SEQRES 24 A 307 PRO VAL THR GLY TRP ARG GLY LYS SEQRES 1 B 307 MET THR ALA HIS ARG SER VAL LEU LEU VAL VAL HIS THR SEQRES 2 B 307 GLY ARG ASP GLU ALA THR GLU THR ALA ARG ARG VAL GLU SEQRES 3 B 307 LYS VAL LEU GLY ASP ASN LYS ILE ALA LEU ARG VAL LEU SEQRES 4 B 307 SER ALA GLU ALA VAL ASP ARG GLY SER LEU HIS LEU ALA SEQRES 5 B 307 PRO ASP ASP MET ARG ALA MET GLY VAL GLU ILE GLU VAL SEQRES 6 B 307 VAL ASP ALA ASP GLN HIS ALA ALA ASP GLY CYS GLU LEU SEQRES 7 B 307 VAL LEU VAL LEU GLY GLY ASP GLY THR PHE LEU ARG ALA SEQRES 8 B 307 ALA GLU LEU ALA ARG ASN ALA SER ILE PRO VAL LEU GLY SEQRES 9 B 307 VAL ASN LEU GLY ARG ILE GLY PHE LEU ALA GLU ALA GLU SEQRES 10 B 307 ALA GLU ALA ILE ASP ALA VAL LEU GLU HIS VAL VAL ALA SEQRES 11 B 307 GLN ASP TYR ARG VAL GLU ASP ARG LEU THR LEU ASP VAL SEQRES 12 B 307 VAL VAL ARG GLN GLY GLY ARG ILE VAL ASN ARG GLY TRP SEQRES 13 B 307 ALA LEU ASN GLU VAL SER LEU GLU LYS GLY PRO ARG LEU SEQRES 14 B 307 GLY VAL LEU GLY VAL VAL VAL GLU ILE ASP GLY ARG PRO SEQRES 15 B 307 VAL SER ALA PHE GLY CYS ASP GLY VAL LEU VAL SER THR SEQRES 16 B 307 PRO THR GLY SER THR ALA TYR ALA PHE SER ALA GLY GLY SEQRES 17 B 307 PRO VAL LEU TRP PRO ASP LEU GLU ALA ILE LEU VAL VAL SEQRES 18 B 307 PRO ASN ASN ALA HIS ALA LEU PHE GLY ARG PRO MET VAL SEQRES 19 B 307 THR SER PRO GLU ALA THR ILE ALA ILE GLU ILE GLU ALA SEQRES 20 B 307 ASP GLY HIS ASP ALA LEU VAL PHE CYS ASP GLY ARG ARG SEQRES 21 B 307 GLU MET LEU ILE PRO ALA GLY SER ARG LEU GLU VAL THR SEQRES 22 B 307 ARG CYS VAL THR SER VAL LYS TRP ALA ARG LEU ASP SER SEQRES 23 B 307 ALA PRO PHE THR ASP ARG LEU VAL ARG LYS PHE ARG LEU SEQRES 24 B 307 PRO VAL THR GLY TRP ARG GLY LYS HET NAD A 501 44 HET GOL A 601 6 HET GOL A 602 6 HET SO4 B 701 5 HET NAD B1501 44 HET GOL B 603 6 HET GOL B1601 6 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 NAD 2(C21 H27 N7 O14 P2) FORMUL 4 GOL 4(C3 H8 O3) FORMUL 6 SO4 O4 S 2- FORMUL 10 HOH *43(H2 O) HELIX 1 1 GLY A 84 ALA A 98 1 15 HELIX 2 2 ALA A 120 ALA A 130 1 11 HELIX 3 3 PRO A 196 THR A 200 5 5 HELIX 4 4 ALA A 201 ALA A 206 1 6 HELIX 5 5 PRO A 288 ARG A 298 1 11 HELIX 6 6 GLY B 84 ALA B 98 1 15 HELIX 7 7 ALA B 120 GLN B 131 1 12 HELIX 8 8 PRO B 196 SER B 199 5 4 HELIX 9 9 ALA B 201 ALA B 206 1 6 HELIX 10 10 PRO B 288 ARG B 298 1 11 SHEET 1 A 3 LEU A 8 VAL A 11 0 SHEET 2 A 3 VAL A 79 GLY A 83 1 O LEU A 80 N LEU A 8 SHEET 3 A 3 VAL A 105 ASN A 106 1 O VAL A 105 N VAL A 81 SHEET 1 B 9 ILE A 151 ALA A 157 0 SHEET 2 B 9 ASP A 137 ARG A 146 -1 N VAL A 143 O GLY A 155 SHEET 3 B 9 ARG A 269 LYS A 280 -1 O CYS A 275 N THR A 140 SHEET 4 B 9 THR A 240 ILE A 245 -1 N ILE A 243 O LEU A 270 SHEET 5 B 9 LEU A 172 ILE A 178 -1 N GLU A 177 O ALA A 242 SHEET 6 B 9 ARG A 181 SER A 194 -1 O SER A 184 N VAL A 176 SHEET 7 B 9 GLU A 160 GLU A 164 -1 N VAL A 161 O VAL A 193 SHEET 8 B 9 ALA A 252 CYS A 256 -1 O LEU A 253 N GLU A 164 SHEET 9 B 9 ARG A 259 ILE A 264 -1 O MET A 262 N VAL A 254 SHEET 1 C 9 ILE A 151 ALA A 157 0 SHEET 2 C 9 ASP A 137 ARG A 146 -1 N VAL A 143 O GLY A 155 SHEET 3 C 9 ARG A 269 LYS A 280 -1 O CYS A 275 N THR A 140 SHEET 4 C 9 THR A 240 ILE A 245 -1 N ILE A 243 O LEU A 270 SHEET 5 C 9 LEU A 172 ILE A 178 -1 N GLU A 177 O ALA A 242 SHEET 6 C 9 ARG A 181 SER A 194 -1 O SER A 184 N VAL A 176 SHEET 7 C 9 ILE A 218 ALA A 225 -1 O VAL A 221 N LEU A 192 SHEET 8 C 9 MET A 233 THR A 235 -1 O MET A 233 N VAL A 220 SHEET 9 C 9 VAL B 210 LEU B 211 1 O VAL B 210 N VAL A 234 SHEET 1 D 9 VAL A 210 LEU A 211 0 SHEET 2 D 9 MET B 233 THR B 235 1 O VAL B 234 N VAL A 210 SHEET 3 D 9 ILE B 218 HIS B 226 -1 N ILE B 218 O THR B 235 SHEET 4 D 9 ARG B 181 SER B 194 -1 N GLY B 190 O ASN B 223 SHEET 5 D 9 LEU B 172 ILE B 178 -1 N VAL B 176 O SER B 184 SHEET 6 D 9 ILE B 241 ILE B 245 -1 O GLU B 244 N VAL B 175 SHEET 7 D 9 ARG B 269 ARG B 274 -1 O LEU B 270 N ILE B 243 SHEET 8 D 9 LEU B 141 GLN B 147 -1 N ASP B 142 O THR B 273 SHEET 9 D 9 ARG B 150 ALA B 157 -1 O ASN B 153 N VAL B 145 SHEET 1 E 7 VAL A 210 LEU A 211 0 SHEET 2 E 7 MET B 233 THR B 235 1 O VAL B 234 N VAL A 210 SHEET 3 E 7 ILE B 218 HIS B 226 -1 N ILE B 218 O THR B 235 SHEET 4 E 7 ARG B 181 SER B 194 -1 N GLY B 190 O ASN B 223 SHEET 5 E 7 GLU B 160 GLU B 164 -1 N LEU B 163 O VAL B 191 SHEET 6 E 7 ALA B 252 CYS B 256 -1 O PHE B 255 N SER B 162 SHEET 7 E 7 ARG B 259 ILE B 264 -1 O ILE B 264 N ALA B 252 SHEET 1 F 3 LEU B 8 VAL B 11 0 SHEET 2 F 3 VAL B 79 GLY B 83 1 O LEU B 80 N LEU B 8 SHEET 3 F 3 VAL B 102 ASN B 106 1 O VAL B 105 N VAL B 81 SHEET 1 G 2 VAL B 135 ARG B 138 0 SHEET 2 G 2 VAL B 279 ALA B 282 -1 O TRP B 281 N GLU B 136 SITE 1 AC1 4 LEU B 228 PHE B 229 GLY B 230 ARG B 231 SITE 1 AC2 18 ASP A 85 GLY A 86 LEU A 89 ARG A 109 SITE 2 AC2 18 ILE A 110 PHE A 112 LEU A 113 ASN A 159 SITE 3 AC2 18 GLU A 160 VAL A 171 ASP A 189 THR A 197 SITE 4 AC2 18 THR A 200 ALA A 201 TYR A 202 SER A 205 SITE 5 AC2 18 ASN A 224 HOH A 619 SITE 1 AC3 19 ASP B 85 GLY B 86 LEU B 89 ARG B 109 SITE 2 AC3 19 PHE B 112 LEU B 113 ASN B 159 GLU B 160 SITE 3 AC3 19 GLY B 170 VAL B 171 ASP B 189 GLY B 198 SITE 4 AC3 19 THR B 200 ALA B 201 TYR B 202 SER B 205 SITE 5 AC3 19 ASN B 224 ASP B 257 GLY B 258 SITE 1 AC4 1 HOH A 613 SITE 1 AC5 5 HIS A 226 ALA A 227 LEU A 228 LYS A 296 SITE 2 AC5 5 PHE A 297 SITE 1 AC6 3 GLY A 207 HOH A 620 ARG B 231 SITE 1 AC7 5 HIS B 226 ALA B 227 LEU B 228 PHE B 297 SITE 2 AC7 5 ARG B 298 CRYST1 110.450 110.450 108.932 90.00 90.00 120.00 P 62 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 0.009054 0.005227 0.000000 0.00000 SCALE2 0.000000 0.010455 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009180 0.00000