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 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 : 3636.00 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 RCSB ID CODE IS RCSB031069. 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. = -29.3 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. = 4.6 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 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 618 DISTANCE = 6.19 ANGSTROMS 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 SO4 B 701 5 HET NAD A 501 44 HET NAD B1501 44 HET GOL A 601 6 HET GOL A 602 6 HET GOL B 603 6 HET GOL B1601 6 HETNAM SO4 SULFATE ION HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 SO4 O4 S 2- FORMUL 4 NAD 2(C21 H27 N7 O14 P2) FORMUL 6 GOL 4(C3 H8 O3) 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 MASTER 516 0 7 10 42 0 17 6 0 0 0 48 END