HEADER TRANSFERASE 02-MAY-13 3WAG TITLE CRYSTAL STRUCTURE OF GLYCOSYLTRANSFERASE VINC IN COMPLEX WITH DTDP COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLYCOSYLTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES HALSTEDII; SOURCE 3 ORGANISM_TAXID: 1944; SOURCE 4 GENE: VINC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLYCOSYLTRANSFERASE, VICENISAMINYLTRANSFERASE, VICENISTATIN KEYWDS 2 BIOSYNTHESIS, ANTIBIOTIC, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR E.NANGO,A.MINAMI,T.KUMASAKA,T.EGUCHI REVDAT 2 08-NOV-23 3WAG 1 REMARK REVDAT 1 04-JUN-14 3WAG 0 JRNL AUTH E.NANGO,A.MINAMI,T.KUMASAKA,T.EGUCHI JRNL TITL CRYSTAL STRUCTURE OF GLYCOSYLTRANSFERASE VINC INVOLVED IN JRNL TITL 2 THE BIOSYNTHESIS OF VICENISTATIN JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0117 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.75 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 92.8 REMARK 3 NUMBER OF REFLECTIONS : 46427 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2467 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2469 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 70.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2400 REMARK 3 BIN FREE R VALUE SET COUNT : 152 REMARK 3 BIN FREE R VALUE : 0.3360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6191 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 372 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.04000 REMARK 3 B22 (A**2) : 0.02000 REMARK 3 B33 (A**2) : 0.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.241 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.212 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.156 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.039 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.956 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.923 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6413 ; 0.017 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8792 ; 2.029 ; 1.958 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 794 ; 6.920 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 290 ;35.900 ;23.379 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 941 ;18.402 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 51 ;19.335 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 997 ; 0.124 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4943 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : BABINET MODEL WITH 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 3WAG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000096089. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAY-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI 111 DCM REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48895 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL 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) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 74.6 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: REFMAC 5.6.0117 REMARK 200 STARTING MODEL: 3WAD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20 %(W/V) PEG 3350, 0.2M MGCL2, 100MM REMARK 280 TRIS, 10MM DTDP, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 1.000000 0.000000 0.000000 49.41450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 65.08100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 69.89350 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 49.41450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 65.08100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 69.89350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 49.41450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 65.08100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 69.89350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 49.41450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 65.08100 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 69.89350 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -51.0 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 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 MG MG A 502 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 759 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 783 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 LEU A 62 REMARK 465 ALA A 63 REMARK 465 GLN A 64 REMARK 465 SER A 65 REMARK 465 THR A 66 REMARK 465 PRO A 67 REMARK 465 ARG A 68 REMARK 465 GLU A 69 REMARK 465 GLU A 70 REMARK 465 MET A 71 REMARK 465 VAL A 72 REMARK 465 ASN A 73 REMARK 465 GLY A 74 REMARK 465 GLY A 75 REMARK 465 ALA A 260 REMARK 465 ASP A 261 REMARK 465 ASP A 262 REMARK 465 ARG A 417 REMARK 465 SER A 418 REMARK 465 LEU A 419 REMARK 465 LEU B 62 REMARK 465 ALA B 63 REMARK 465 GLN B 64 REMARK 465 SER B 65 REMARK 465 THR B 66 REMARK 465 PRO B 67 REMARK 465 ARG B 68 REMARK 465 GLU B 69 REMARK 465 GLU B 70 REMARK 465 MET B 71 REMARK 465 VAL B 72 REMARK 465 ASN B 73 REMARK 465 GLY B 74 REMARK 465 GLY B 75 REMARK 465 ALA B 260 REMARK 465 ASP B 261 REMARK 465 ASP B 262 REMARK 465 LEU B 419 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 MET A 60 CB CG SD CE REMARK 470 ASP A 175 OD1 OD2 REMARK 470 ARG A 257 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 287 CG CD OE1 OE2 REMARK 470 ARG B 257 NE CZ NH1 NH2 REMARK 470 GLU B 258 CG CD OE1 OE2 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 HIS A 13 CG HIS A 13 CD2 0.055 REMARK 500 HIS A 163 CG HIS A 163 CD2 0.055 REMARK 500 TRP A 238 CE2 TRP A 238 CD2 0.081 REMARK 500 TRP A 342 CE2 TRP A 342 CD2 0.085 REMARK 500 HIS B 13 CG HIS B 13 CD2 0.060 REMARK 500 TRP B 89 CE2 TRP B 89 CD2 0.085 REMARK 500 TRP B 129 CE2 TRP B 129 CD2 0.082 REMARK 500 HIS B 147 CG HIS B 147 CD2 0.057 REMARK 500 HIS B 308 CG HIS B 308 CD2 0.072 REMARK 500 TRP B 342 CE2 TRP B 342 CD2 0.073 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 331 NE - CZ - NH2 ANGL. DEV. = -4.8 DEGREES REMARK 500 MET B 213 CG - SD - CE ANGL. DEV. = -10.9 DEGREES REMARK 500 ARG B 240 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG B 326 NE - CZ - NH1 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG B 378 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG B 378 NE - CZ - NH2 ANGL. DEV. = -3.0 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 56 130.87 -34.44 REMARK 500 ASN A 58 65.81 38.72 REMARK 500 ASP A 108 -169.65 -74.67 REMARK 500 GLU A 170 65.10 -101.42 REMARK 500 ALA A 172 120.16 -33.35 REMARK 500 ALA A 173 -16.99 -45.67 REMARK 500 ARG A 176 57.72 -93.06 REMARK 500 ASP A 275 54.45 -60.69 REMARK 500 SER A 285 153.51 -18.89 REMARK 500 ALA A 290 -74.15 -51.36 REMARK 500 GLU A 291 34.23 -82.88 REMARK 500 ASP A 297 -5.59 -53.10 REMARK 500 PHE A 304 138.37 -174.89 REMARK 500 TRP A 344 -58.50 -143.79 REMARK 500 ASP A 345 15.50 -152.58 REMARK 500 ALA B 9 91.75 -64.81 REMARK 500 MET B 60 49.91 -86.27 REMARK 500 ALA B 107 77.56 -155.99 REMARK 500 GLN B 123 69.34 37.75 REMARK 500 ARG B 176 45.03 -148.73 REMARK 500 PRO B 232 133.60 -38.74 REMARK 500 LEU B 252 16.97 -147.58 REMARK 500 GLU B 258 10.08 -153.46 REMARK 500 TRP B 344 -68.00 -160.30 REMARK 500 ASP B 345 14.18 -147.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 502 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 351 OE2 REMARK 620 2 GLU A 355 OE2 62.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TYD A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TYD B 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 B 502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WAD RELATED DB: PDB REMARK 900 THE SAME PROTEIN (NATIVE) DBREF 3WAG A 1 419 UNP Q76KZ6 Q76KZ6_STRHA 1 419 DBREF 3WAG B 1 419 UNP Q76KZ6 Q76KZ6_STRHA 1 419 SEQRES 1 A 419 MET ARG VAL LEU MET THR VAL PHE ALA ASN ARG SER HIS SEQRES 2 A 419 LEU TYR ASN MET VAL PRO LEU ALA TRP ALA LEU THR THR SEQRES 3 A 419 ALA GLY HIS GLU VAL HIS ILE ALA SER HIS PRO ASP ASN SEQRES 4 A 419 VAL GLN ALA ILE SER ASP SER GLY LEU THR ALA VAL PRO SEQRES 5 A 419 VAL GLY ASN ASP LEU ASN ILE MET ALA LEU ALA GLN SER SEQRES 6 A 419 THR PRO ARG GLU GLU MET VAL ASN GLY GLY ALA LEU THR SEQRES 7 A 419 LEU ASN GLU THR ARG PRO GLU LYS LEU THR TRP GLN TYR SEQRES 8 A 419 ILE HIS ASP VAL PHE ALA GLN TYR SER GLN ILE TYR GLU SEQRES 9 A 419 TYR MET ALA ASP SER THR MET THR ALA ASP LEU VAL ALA SEQRES 10 A 419 HIS ALA ARG GLN TRP GLN PRO ASP LEU VAL ILE TRP ASP SEQRES 11 A 419 ALA LEU THR TYR ALA GLY PRO ILE ALA ALA GLU ALA VAL SEQRES 12 A 419 GLY ALA PRO HIS VAL ARG MET LEU PHE GLY LEU ASP GLN SEQRES 13 A 419 TRP GLY ARG MET ARG ASP HIS PHE ASN ARG LEU THR GLY SEQRES 14 A 419 GLU ARG ALA ALA ASP ASP ARG HIS ASP PRO LEU ALA ASP SEQRES 15 A 419 TRP LEU ALA THR LYS GLY GLU PRO HIS GLY VAL ALA PHE SEQRES 16 A 419 THR GLU SER LEU VAL THR GLY THR THR THR LEU ALA VAL SEQRES 17 A 419 ALA PRO PRO TRP MET SER PHE PRO SER GLU GLN PRO ALA SEQRES 18 A 419 LEU SER MET ARG HIS LEU PRO PHE ASN GLY PRO ALA VAL SEQRES 19 A 419 LEU PRO ASP TRP LEU ARG GLU ALA PRO SER ARG PRO ARG SEQRES 20 A 419 VAL CYS LEU THR LEU GLY LEU THR LEU ARG GLU LEU ALA SEQRES 21 A 419 ASP ASP ASN VAL THR LEU ALA ASP PHE VAL ASN ALA VAL SEQRES 22 A 419 ALA ASP ILE ASP ALA ASP VAL VAL ALA THR PHE SER ALA SEQRES 23 A 419 GLU GLN VAL ALA GLU ILE GLY ASP LEU PRO ASP ASN VAL SEQRES 24 A 419 ARG ALA VAL ASP PHE VAL PRO LEU HIS ALA LEU LEU PRO SEQRES 25 A 419 SER CYS ALA ALA ILE VAL HIS HIS GLY GLY GLY GLY THR SEQRES 26 A 419 ARG THR ASN ALA ILE ARG TYR GLY VAL PRO GLN LEU ILE SEQRES 27 A 419 VAL PRO ASN TRP LEU TRP ASP GLU GLY TYR VAL ALA GLU SEQRES 28 A 419 ARG PHE ALA GLU ARG GLY ALA ALA LEU VAL THR GLU VAL SEQRES 29 A 419 PRO ASP LEU THR PRO ASP ARG LEU ARG ASP GLN LEU ARG SEQRES 30 A 419 ARG LEU ILE ALA GLU PRO SER PHE LYS ALA ALA ALA GLU SEQRES 31 A 419 GLN ILE GLN LYS GLU TYR ASP ALA LEU PRO SER LEU THR SEQRES 32 A 419 GLU THR VAL GLY GLU LEU VAL ARG VAL ALA GLU ARG GLY SEQRES 33 A 419 ARG SER LEU SEQRES 1 B 419 MET ARG VAL LEU MET THR VAL PHE ALA ASN ARG SER HIS SEQRES 2 B 419 LEU TYR ASN MET VAL PRO LEU ALA TRP ALA LEU THR THR SEQRES 3 B 419 ALA GLY HIS GLU VAL HIS ILE ALA SER HIS PRO ASP ASN SEQRES 4 B 419 VAL GLN ALA ILE SER ASP SER GLY LEU THR ALA VAL PRO SEQRES 5 B 419 VAL GLY ASN ASP LEU ASN ILE MET ALA LEU ALA GLN SER SEQRES 6 B 419 THR PRO ARG GLU GLU MET VAL ASN GLY GLY ALA LEU THR SEQRES 7 B 419 LEU ASN GLU THR ARG PRO GLU LYS LEU THR TRP GLN TYR SEQRES 8 B 419 ILE HIS ASP VAL PHE ALA GLN TYR SER GLN ILE TYR GLU SEQRES 9 B 419 TYR MET ALA ASP SER THR MET THR ALA ASP LEU VAL ALA SEQRES 10 B 419 HIS ALA ARG GLN TRP GLN PRO ASP LEU VAL ILE TRP ASP SEQRES 11 B 419 ALA LEU THR TYR ALA GLY PRO ILE ALA ALA GLU ALA VAL SEQRES 12 B 419 GLY ALA PRO HIS VAL ARG MET LEU PHE GLY LEU ASP GLN SEQRES 13 B 419 TRP GLY ARG MET ARG ASP HIS PHE ASN ARG LEU THR GLY SEQRES 14 B 419 GLU ARG ALA ALA ASP ASP ARG HIS ASP PRO LEU ALA ASP SEQRES 15 B 419 TRP LEU ALA THR LYS GLY GLU PRO HIS GLY VAL ALA PHE SEQRES 16 B 419 THR GLU SER LEU VAL THR GLY THR THR THR LEU ALA VAL SEQRES 17 B 419 ALA PRO PRO TRP MET SER PHE PRO SER GLU GLN PRO ALA SEQRES 18 B 419 LEU SER MET ARG HIS LEU PRO PHE ASN GLY PRO ALA VAL SEQRES 19 B 419 LEU PRO ASP TRP LEU ARG GLU ALA PRO SER ARG PRO ARG SEQRES 20 B 419 VAL CYS LEU THR LEU GLY LEU THR LEU ARG GLU LEU ALA SEQRES 21 B 419 ASP ASP ASN VAL THR LEU ALA ASP PHE VAL ASN ALA VAL SEQRES 22 B 419 ALA ASP ILE ASP ALA ASP VAL VAL ALA THR PHE SER ALA SEQRES 23 B 419 GLU GLN VAL ALA GLU ILE GLY ASP LEU PRO ASP ASN VAL SEQRES 24 B 419 ARG ALA VAL ASP PHE VAL PRO LEU HIS ALA LEU LEU PRO SEQRES 25 B 419 SER CYS ALA ALA ILE VAL HIS HIS GLY GLY GLY GLY THR SEQRES 26 B 419 ARG THR ASN ALA ILE ARG TYR GLY VAL PRO GLN LEU ILE SEQRES 27 B 419 VAL PRO ASN TRP LEU TRP ASP GLU GLY TYR VAL ALA GLU SEQRES 28 B 419 ARG PHE ALA GLU ARG GLY ALA ALA LEU VAL THR GLU VAL SEQRES 29 B 419 PRO ASP LEU THR PRO ASP ARG LEU ARG ASP GLN LEU ARG SEQRES 30 B 419 ARG LEU ILE ALA GLU PRO SER PHE LYS ALA ALA ALA GLU SEQRES 31 B 419 GLN ILE GLN LYS GLU TYR ASP ALA LEU PRO SER LEU THR SEQRES 32 B 419 GLU THR VAL GLY GLU LEU VAL ARG VAL ALA GLU ARG GLY SEQRES 33 B 419 ARG SER LEU HET TYD A 500 25 HET PO4 A 501 5 HET MG A 502 1 HET TYD B 500 25 HET PO4 B 501 5 HET PO4 B 502 5 HETNAM TYD THYMIDINE-5'-DIPHOSPHATE HETNAM PO4 PHOSPHATE ION HETNAM MG MAGNESIUM ION FORMUL 3 TYD 2(C10 H16 N2 O11 P2) FORMUL 4 PO4 3(O4 P 3-) FORMUL 5 MG MG 2+ FORMUL 9 HOH *372(H2 O) HELIX 1 1 ASN A 10 ALA A 27 1 18 HELIX 2 2 HIS A 36 ASP A 38 5 3 HELIX 3 3 ASN A 39 SER A 46 1 8 HELIX 4 4 THR A 88 ALA A 107 1 20 HELIX 5 5 ASP A 108 GLN A 123 1 16 HELIX 6 6 TYR A 134 VAL A 143 1 10 HELIX 7 7 ASP A 155 GLU A 170 1 16 HELIX 8 8 ASP A 178 GLU A 189 1 12 HELIX 9 9 PRO A 190 GLY A 192 5 3 HELIX 10 10 GLU A 197 GLY A 202 1 6 HELIX 11 11 PRO A 210 SER A 214 5 5 HELIX 12 12 PRO A 236 GLU A 241 5 6 HELIX 13 13 LEU A 252 LEU A 259 1 8 HELIX 14 14 THR A 265 ASP A 275 1 11 HELIX 15 15 SER A 285 GLU A 291 1 7 HELIX 16 16 PRO A 306 LEU A 311 1 6 HELIX 17 17 GLY A 322 TYR A 332 1 11 HELIX 18 18 ASP A 345 ARG A 356 1 12 HELIX 19 19 GLU A 363 LEU A 367 5 5 HELIX 20 20 THR A 368 GLU A 382 1 15 HELIX 21 21 GLU A 382 ALA A 398 1 17 HELIX 22 22 SER A 401 GLY A 416 1 16 HELIX 23 23 ASN B 10 ALA B 27 1 18 HELIX 24 24 HIS B 36 ASP B 38 5 3 HELIX 25 25 ASN B 39 ASP B 45 1 7 HELIX 26 26 ARG B 83 LEU B 87 5 5 HELIX 27 27 THR B 88 ALA B 107 1 20 HELIX 28 28 ASP B 108 GLN B 123 1 16 HELIX 29 29 TYR B 134 ALA B 142 1 9 HELIX 30 30 ASP B 155 GLY B 169 1 15 HELIX 31 31 ASP B 178 GLU B 189 1 12 HELIX 32 32 PRO B 190 GLY B 192 5 3 HELIX 33 33 THR B 196 GLY B 202 1 7 HELIX 34 34 PRO B 210 SER B 214 5 5 HELIX 35 35 PRO B 236 GLU B 241 1 6 HELIX 36 36 LEU B 252 ARG B 257 1 6 HELIX 37 37 THR B 265 ASP B 275 1 11 HELIX 38 38 SER B 285 GLY B 293 1 9 HELIX 39 39 PRO B 306 LEU B 311 1 6 HELIX 40 40 GLY B 322 TYR B 332 1 11 HELIX 41 41 ASP B 345 ARG B 356 1 12 HELIX 42 42 GLU B 363 LEU B 367 5 5 HELIX 43 43 THR B 368 GLU B 382 1 15 HELIX 44 44 PRO B 383 ALA B 398 1 16 HELIX 45 45 SER B 401 GLY B 416 1 16 SHEET 1 A 7 THR A 204 LEU A 206 0 SHEET 2 A 7 HIS A 147 MET A 150 1 N ARG A 149 O LEU A 206 SHEET 3 A 7 LEU A 126 ASP A 130 1 N TRP A 129 O MET A 150 SHEET 4 A 7 ARG A 2 THR A 6 1 N THR A 6 O ASP A 130 SHEET 5 A 7 GLU A 30 SER A 35 1 O HIS A 32 N MET A 5 SHEET 6 A 7 THR A 49 PRO A 52 1 O THR A 49 N ILE A 33 SHEET 7 A 7 ALA B 233 VAL B 234 1 O ALA B 233 N ALA A 50 SHEET 1 B 7 ALA A 233 VAL A 234 0 SHEET 2 B 7 THR B 49 PRO B 52 1 O ALA B 50 N ALA A 233 SHEET 3 B 7 GLU B 30 SER B 35 1 N ILE B 33 O VAL B 51 SHEET 4 B 7 ARG B 2 THR B 6 1 N MET B 5 O ALA B 34 SHEET 5 B 7 LEU B 126 ASP B 130 1 O ASP B 130 N THR B 6 SHEET 6 B 7 HIS B 147 MET B 150 1 O VAL B 148 N VAL B 127 SHEET 7 B 7 THR B 204 LEU B 206 1 O THR B 204 N ARG B 149 SHEET 1 C 6 VAL A 299 VAL A 302 0 SHEET 2 C 6 ASP A 279 THR A 283 1 N ALA A 282 O ARG A 300 SHEET 3 C 6 ARG A 247 THR A 251 1 N VAL A 248 O ASP A 279 SHEET 4 C 6 CYS A 314 HIS A 319 1 O ALA A 315 N ARG A 247 SHEET 5 C 6 GLN A 336 ILE A 338 1 O LEU A 337 N ILE A 317 SHEET 6 C 6 ALA A 359 VAL A 361 1 O LEU A 360 N ILE A 338 SHEET 1 D 6 VAL B 299 VAL B 302 0 SHEET 2 D 6 ASP B 279 THR B 283 1 N ALA B 282 O ARG B 300 SHEET 3 D 6 ARG B 247 THR B 251 1 N LEU B 250 O VAL B 281 SHEET 4 D 6 CYS B 314 HIS B 319 1 O ALA B 315 N ARG B 247 SHEET 5 D 6 GLN B 336 ILE B 338 1 O LEU B 337 N ILE B 317 SHEET 6 D 6 ALA B 359 VAL B 361 1 O LEU B 360 N GLN B 336 LINK OE2 GLU A 351 MG MG A 502 1555 1555 2.18 LINK OE2 GLU A 355 MG MG A 502 1555 1555 2.49 SITE 1 AC1 16 SER A 12 ASN A 230 THR A 283 PHE A 304 SITE 2 AC1 16 VAL A 305 PRO A 306 LEU A 307 HIS A 320 SITE 3 AC1 16 GLY A 322 GLY A 323 GLY A 324 THR A 325 SITE 4 AC1 16 ASN A 328 HOH A 724 HOH A 747 HOH A 748 SITE 1 AC2 6 LEU A 227 PRO A 228 PHE A 229 ASN A 230 SITE 2 AC2 6 HIS A 308 HOH A 611 SITE 1 AC3 2 GLU A 351 GLU A 355 SITE 1 AC4 14 SER B 12 ASN B 230 THR B 283 PHE B 304 SITE 2 AC4 14 VAL B 305 PRO B 306 LEU B 307 HIS B 320 SITE 3 AC4 14 GLY B 322 GLY B 324 THR B 325 ASN B 328 SITE 4 AC4 14 HOH B 654 HOH B 763 SITE 1 AC5 8 LEU B 227 PRO B 228 PHE B 229 ASN B 230 SITE 2 AC5 8 HIS B 308 ARG B 331 HOH B 680 HOH B 701 SITE 1 AC6 4 ASP A 45 ASP A 174 ASP B 45 HOH B 789 CRYST1 98.829 130.162 139.787 90.00 90.00 90.00 I 2 2 2 16 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 0.010118 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007683 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007154 0.00000