HEADER TRANSFERASE 12-MAR-12 3VPS TITLE STRUCTURE OF A NOVEL NAD DEPENDENT-NDP-HEXOSAMINE 5,6-DEHYDRATASE, TITLE 2 TUNA, INVOLVED IN TUNICAMYCIN BIOSYNTHESIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NAD-DEPENDENT EPIMERASE/DEHYDRATASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TUNA; COMPND 5 EC: 4.2.1.- SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES CHARTREUSIS; SOURCE 3 ORGANISM_TAXID: 1079985; SOURCE 4 STRAIN: NLLR 3882 KEYWDS TUNICAMYCINS, BIOSYNTHESIS, EXO-GLYCAL, DEHYDRATASE, ROSSMANN FOLD, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR F.J.WYSZYNSKI,S.S.LEE,T.YABE,H.WANG,J.P.GOMEZ-ESCRIBANO,M.J.BIBB, AUTHOR 2 S.J.LEE,G.J.DAVIES,B.G.DAVIS REVDAT 2 20-MAR-24 3VPS 1 REMARK REVDAT 1 18-APR-12 3VPS 0 JRNL AUTH F.J.WYSZYNSKI,S.S.LEE,T.YABE,H.WANG,J.P.GOMEZ-ESCRIBANO, JRNL AUTH 2 M.J.BIBB,S.J.LEE,G.J.DAVIES,B.G.DAVIS JRNL TITL BIOSYNTHESIS OF NUCLEOSIDE ANTIBIOTIC TUNICAMYCIN PROCEEDS JRNL TITL 2 VIA UNIQUE EXO-GLYCAL INTERMEDIATES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.26 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 42667 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) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2283 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3092 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.55 REMARK 3 BIN R VALUE (WORKING SET) : 0.2080 REMARK 3 BIN FREE R VALUE SET COUNT : 175 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4618 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 166 REMARK 3 SOLVENT ATOMS : 219 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.81 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.10000 REMARK 3 B22 (A**2) : 0.08000 REMARK 3 B33 (A**2) : -0.10000 REMARK 3 B12 (A**2) : 0.28000 REMARK 3 B13 (A**2) : -0.26000 REMARK 3 B23 (A**2) : 0.68000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.156 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.112 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 8.434 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.935 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4887 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6682 ; 2.002 ; 2.027 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 601 ; 6.289 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 208 ;30.756 ;23.462 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 767 ;17.104 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 46 ;23.079 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 771 ; 0.128 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3678 ; 0.011 ; 0.022 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): 3011 ; 2.127 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4877 ; 3.537 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1876 ; 4.014 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1805 ; 6.278 ; 4.500 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): 4887 ; 2.302 ; 3.000 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 7 A 309 REMARK 3 RESIDUE RANGE : A 400 A 401 REMARK 3 ORIGIN FOR THE GROUP (A): -21.0385 -5.1583 -2.2697 REMARK 3 T TENSOR REMARK 3 T11: 0.0159 T22: 0.0259 REMARK 3 T33: 0.0257 T12: -0.0037 REMARK 3 T13: 0.0088 T23: -0.0223 REMARK 3 L TENSOR REMARK 3 L11: 0.0006 L22: 0.0024 REMARK 3 L33: 0.0044 L12: -0.0012 REMARK 3 L13: -0.0016 L23: 0.0032 REMARK 3 S TENSOR REMARK 3 S11: 0.0006 S12: 0.0001 S13: 0.0003 REMARK 3 S21: -0.0008 S22: 0.0003 S23: -0.0006 REMARK 3 S31: -0.0007 S32: 0.0001 S33: -0.0009 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 8 B 310 REMARK 3 RESIDUE RANGE : B 400 B 401 REMARK 3 ORIGIN FOR THE GROUP (A): -34.9369 -11.5418 -35.5177 REMARK 3 T TENSOR REMARK 3 T11: 0.0162 T22: 0.0285 REMARK 3 T33: 0.0275 T12: -0.0046 REMARK 3 T13: 0.0088 T23: -0.0218 REMARK 3 L TENSOR REMARK 3 L11: 0.0036 L22: 0.0014 REMARK 3 L33: 0.0495 L12: -0.0022 REMARK 3 L13: 0.0133 L23: -0.0084 REMARK 3 S TENSOR REMARK 3 S11: 0.0013 S12: -0.0007 S13: 0.0001 REMARK 3 S21: -0.0013 S22: 0.0004 S23: 0.0002 REMARK 3 S31: 0.0062 S32: -0.0007 S33: -0.0017 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3VPS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-MAR-12. REMARK 100 THE DEPOSITION ID IS D_1000095348. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6 REMARK 200 NUMBER OF CRYSTALS USED : 1 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 FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL 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-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42667 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 22.260 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 3.700 REMARK 200 R MERGE (I) : 0.18782 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 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 : 1.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% POLYETHYLENE GLYCOL 3350, 100MM REMARK 280 8V/V TASCIMATE, PH 6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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 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 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 GLN A 2 REMARK 465 ARG A 3 REMARK 465 ASN A 4 REMARK 465 THR A 5 REMARK 465 LEU A 6 REMARK 465 ILE A 310 REMARK 465 ARG A 311 REMARK 465 GLN A 312 REMARK 465 ARG A 313 REMARK 465 ILE A 314 REMARK 465 PHE A 315 REMARK 465 GLN A 316 REMARK 465 GLU A 317 REMARK 465 GLU A 318 REMARK 465 GLY A 319 REMARK 465 ALA A 320 REMARK 465 ASP A 321 REMARK 465 MET B 1 REMARK 465 GLN B 2 REMARK 465 ARG B 3 REMARK 465 ASN B 4 REMARK 465 THR B 5 REMARK 465 LEU B 6 REMARK 465 LYS B 7 REMARK 465 ARG B 285 REMARK 465 SER B 286 REMARK 465 ARG B 311 REMARK 465 GLN B 312 REMARK 465 ARG B 313 REMARK 465 ILE B 314 REMARK 465 PHE B 315 REMARK 465 GLN B 316 REMARK 465 GLU B 317 REMARK 465 GLU B 318 REMARK 465 GLY B 319 REMARK 465 ALA B 320 REMARK 465 ASP B 321 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 285 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 597 O HOH A 617 1655 1.79 REMARK 500 O HOH A 595 O HOH B 581 1656 1.98 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 VAL A 36 CB VAL A 36 CG2 -0.150 REMARK 500 GLU A 49 CB GLU A 49 CG -0.117 REMARK 500 GLU A 63 CB GLU A 63 CG -0.118 REMARK 500 GLU A 63 CD GLU A 63 OE1 -0.077 REMARK 500 GLN A 262 CB GLN A 262 CG -0.193 REMARK 500 GLN A 262 CG GLN A 262 CD -0.191 REMARK 500 ASP A 309 CB ASP A 309 CG -0.153 REMARK 500 VAL B 36 CB VAL B 36 CG1 -0.138 REMARK 500 ARG B 71 NE ARG B 71 CZ -0.080 REMARK 500 GLU B 257 CG GLU B 257 CD -0.092 REMARK 500 GLU B 284 CG GLU B 284 CD -0.144 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 9 NE - CZ - NH2 ANGL. DEV. = -4.0 DEGREES REMARK 500 VAL A 36 CG1 - CB - CG2 ANGL. DEV. = -11.8 DEGREES REMARK 500 ARG A 187 NE - CZ - NH1 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG A 187 NE - CZ - NH2 ANGL. DEV. = 5.8 DEGREES REMARK 500 GLN A 262 N - CA - CB ANGL. DEV. = -12.8 DEGREES REMARK 500 ARG B 71 CG - CD - NE ANGL. DEV. = -14.1 DEGREES REMARK 500 ARG B 71 CD - NE - CZ ANGL. DEV. = -8.6 DEGREES REMARK 500 ARG B 71 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 VAL B 169 CG1 - CB - CG2 ANGL. DEV. = -10.3 DEGREES REMARK 500 ARG B 187 NE - CZ - NH1 ANGL. DEV. = -6.3 DEGREES REMARK 500 ARG B 187 NE - CZ - NH2 ANGL. DEV. = 7.1 DEGREES REMARK 500 ARG B 264 NE - CZ - NH1 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 HIS A 8 -19.62 -145.52 REMARK 500 SER A 118 -156.04 -126.49 REMARK 500 SER A 161 59.29 -92.87 REMARK 500 PRO A 181 33.65 -84.81 REMARK 500 ARG A 195 -2.46 -142.03 REMARK 500 ASP B 38 127.18 -170.20 REMARK 500 SER B 118 -158.00 -130.04 REMARK 500 PRO B 181 33.75 -83.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 SER B 78 HIS B 79 149.89 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 UD1 A 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE UD1 B 400 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD B 401 DBREF 3VPS A 1 321 UNP E5KJ94 E5KJ94_STRCX 1 321 DBREF 3VPS B 1 321 UNP E5KJ94 E5KJ94_STRCX 1 321 SEQRES 1 A 321 MET GLN ARG ASN THR LEU LYS HIS ARG ILE LEU ILE THR SEQRES 2 A 321 GLY GLY ALA GLY PHE ILE GLY GLY HIS LEU ALA ARG ALA SEQRES 3 A 321 LEU VAL ALA SER GLY GLU GLU VAL THR VAL LEU ASP ASP SEQRES 4 A 321 LEU ARG VAL PRO PRO MET ILE PRO PRO GLU GLY THR GLY SEQRES 5 A 321 LYS PHE LEU GLU LYS PRO VAL LEU GLU LEU GLU GLU ARG SEQRES 6 A 321 ASP LEU SER ASP VAL ARG LEU VAL TYR HIS LEU ALA SER SEQRES 7 A 321 HIS LYS SER VAL PRO ARG SER PHE LYS GLN PRO LEU ASP SEQRES 8 A 321 TYR LEU ASP ASN VAL ASP SER GLY ARG HIS LEU LEU ALA SEQRES 9 A 321 LEU CYS THR SER VAL GLY VAL PRO LYS VAL VAL VAL GLY SEQRES 10 A 321 SER THR CYS GLU VAL TYR GLY GLN ALA ASP THR LEU PRO SEQRES 11 A 321 THR PRO GLU ASP SER PRO LEU SER PRO ARG SER PRO TYR SEQRES 12 A 321 ALA ALA SER LYS VAL GLY LEU GLU MET VAL ALA GLY ALA SEQRES 13 A 321 HIS GLN ARG ALA SER VAL ALA PRO GLU VAL GLY ILE VAL SEQRES 14 A 321 ARG PHE PHE ASN VAL TYR GLY PRO GLY GLU ARG PRO ASP SEQRES 15 A 321 ALA LEU VAL PRO ARG LEU CYS ALA ASN LEU LEU THR ARG SEQRES 16 A 321 ASN GLU LEU PRO VAL GLU GLY ASP GLY GLU GLN ARG ARG SEQRES 17 A 321 ASP PHE THR TYR ILE THR ASP VAL VAL ASP LYS LEU VAL SEQRES 18 A 321 ALA LEU ALA ASN ARG PRO LEU PRO SER VAL VAL ASN PHE SEQRES 19 A 321 GLY SER GLY GLN SER LEU SER VAL ASN ASP VAL ILE ARG SEQRES 20 A 321 ILE LEU GLN ALA THR SER PRO ALA ALA GLU VAL ALA ARG SEQRES 21 A 321 LYS GLN PRO ARG PRO ASN GLU ILE THR GLU PHE ARG ALA SEQRES 22 A 321 ASP THR ALA LEU GLN THR ARG GLN ILE GLY GLU ARG SER SEQRES 23 A 321 GLY GLY ILE GLY ILE GLU GLU GLY ILE ARG LEU THR LEU SEQRES 24 A 321 GLU TRP TRP GLN SER ARG ASP LEU ASP ASP ILE ARG GLN SEQRES 25 A 321 ARG ILE PHE GLN GLU GLU GLY ALA ASP SEQRES 1 B 321 MET GLN ARG ASN THR LEU LYS HIS ARG ILE LEU ILE THR SEQRES 2 B 321 GLY GLY ALA GLY PHE ILE GLY GLY HIS LEU ALA ARG ALA SEQRES 3 B 321 LEU VAL ALA SER GLY GLU GLU VAL THR VAL LEU ASP ASP SEQRES 4 B 321 LEU ARG VAL PRO PRO MET ILE PRO PRO GLU GLY THR GLY SEQRES 5 B 321 LYS PHE LEU GLU LYS PRO VAL LEU GLU LEU GLU GLU ARG SEQRES 6 B 321 ASP LEU SER ASP VAL ARG LEU VAL TYR HIS LEU ALA SER SEQRES 7 B 321 HIS LYS SER VAL PRO ARG SER PHE LYS GLN PRO LEU ASP SEQRES 8 B 321 TYR LEU ASP ASN VAL ASP SER GLY ARG HIS LEU LEU ALA SEQRES 9 B 321 LEU CYS THR SER VAL GLY VAL PRO LYS VAL VAL VAL GLY SEQRES 10 B 321 SER THR CYS GLU VAL TYR GLY GLN ALA ASP THR LEU PRO SEQRES 11 B 321 THR PRO GLU ASP SER PRO LEU SER PRO ARG SER PRO TYR SEQRES 12 B 321 ALA ALA SER LYS VAL GLY LEU GLU MET VAL ALA GLY ALA SEQRES 13 B 321 HIS GLN ARG ALA SER VAL ALA PRO GLU VAL GLY ILE VAL SEQRES 14 B 321 ARG PHE PHE ASN VAL TYR GLY PRO GLY GLU ARG PRO ASP SEQRES 15 B 321 ALA LEU VAL PRO ARG LEU CYS ALA ASN LEU LEU THR ARG SEQRES 16 B 321 ASN GLU LEU PRO VAL GLU GLY ASP GLY GLU GLN ARG ARG SEQRES 17 B 321 ASP PHE THR TYR ILE THR ASP VAL VAL ASP LYS LEU VAL SEQRES 18 B 321 ALA LEU ALA ASN ARG PRO LEU PRO SER VAL VAL ASN PHE SEQRES 19 B 321 GLY SER GLY GLN SER LEU SER VAL ASN ASP VAL ILE ARG SEQRES 20 B 321 ILE LEU GLN ALA THR SER PRO ALA ALA GLU VAL ALA ARG SEQRES 21 B 321 LYS GLN PRO ARG PRO ASN GLU ILE THR GLU PHE ARG ALA SEQRES 22 B 321 ASP THR ALA LEU GLN THR ARG GLN ILE GLY GLU ARG SER SEQRES 23 B 321 GLY GLY ILE GLY ILE GLU GLU GLY ILE ARG LEU THR LEU SEQRES 24 B 321 GLU TRP TRP GLN SER ARG ASP LEU ASP ASP ILE ARG GLN SEQRES 25 B 321 ARG ILE PHE GLN GLU GLU GLY ALA ASP HET UD1 A 400 39 HET NAD A 401 44 HET UD1 B 400 39 HET NAD B 401 44 HETNAM UD1 URIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE FORMUL 3 UD1 2(C17 H27 N3 O17 P2) FORMUL 4 NAD 2(C21 H27 N7 O14 P2) FORMUL 7 HOH *219(H2 O) HELIX 1 1 GLY A 17 SER A 30 1 14 HELIX 2 2 PRO A 58 LEU A 62 5 5 HELIX 3 3 GLU A 63 SER A 68 1 6 HELIX 4 4 SER A 81 PHE A 86 1 6 HELIX 5 5 TYR A 92 GLY A 110 1 19 HELIX 6 6 GLU A 121 GLY A 124 5 4 HELIX 7 7 SER A 141 ALA A 160 1 20 HELIX 8 8 ALA A 183 ASN A 196 1 14 HELIX 9 9 ILE A 213 LEU A 223 1 11 HELIX 10 10 ALA A 224 ARG A 226 5 3 HELIX 11 11 VAL A 242 ALA A 251 1 10 HELIX 12 12 THR A 275 GLY A 283 1 9 HELIX 13 13 GLY A 290 SER A 304 1 15 HELIX 14 14 GLY B 17 SER B 30 1 14 HELIX 15 15 PRO B 58 LEU B 62 5 5 HELIX 16 16 GLU B 63 LEU B 67 5 5 HELIX 17 17 SER B 81 PHE B 86 1 6 HELIX 18 18 LYS B 87 ASP B 91 5 5 HELIX 19 19 TYR B 92 GLY B 110 1 19 HELIX 20 20 GLU B 121 GLY B 124 5 4 HELIX 21 21 SER B 141 ALA B 160 1 20 HELIX 22 22 ALA B 183 ASN B 196 1 14 HELIX 23 23 ILE B 213 ALA B 224 1 12 HELIX 24 24 VAL B 242 ALA B 251 1 10 HELIX 25 25 THR B 275 GLY B 283 1 9 HELIX 26 26 GLY B 290 SER B 304 1 15 SHEET 1 A 7 LYS A 53 LEU A 55 0 SHEET 2 A 7 VAL A 34 LEU A 37 1 N VAL A 36 O LEU A 55 SHEET 3 A 7 ARG A 9 THR A 13 1 N ILE A 10 O THR A 35 SHEET 4 A 7 VAL A 70 HIS A 75 1 O TYR A 74 N LEU A 11 SHEET 5 A 7 LYS A 113 THR A 119 1 O VAL A 115 N HIS A 75 SHEET 6 A 7 GLU A 165 PHE A 171 1 O VAL A 169 N SER A 118 SHEET 7 A 7 VAL A 231 PHE A 234 1 O VAL A 232 N ARG A 170 SHEET 1 B 2 ASN A 173 TYR A 175 0 SHEET 2 B 2 PHE A 210 TYR A 212 1 O THR A 211 N ASN A 173 SHEET 1 C 2 GLU A 197 GLU A 201 0 SHEET 2 C 2 GLU A 257 LYS A 261 1 O LYS A 261 N VAL A 200 SHEET 1 D 2 ARG A 207 ARG A 208 0 SHEET 2 D 2 LEU A 240 SER A 241 -1 O LEU A 240 N ARG A 208 SHEET 1 E 7 LYS B 53 LEU B 55 0 SHEET 2 E 7 VAL B 34 LEU B 37 1 N VAL B 36 O LEU B 55 SHEET 3 E 7 ARG B 9 THR B 13 1 N ILE B 12 O THR B 35 SHEET 4 E 7 VAL B 70 HIS B 75 1 O TYR B 74 N LEU B 11 SHEET 5 E 7 LYS B 113 THR B 119 1 O VAL B 115 N HIS B 75 SHEET 6 E 7 GLU B 165 PHE B 171 1 O GLY B 167 N VAL B 116 SHEET 7 E 7 VAL B 231 PHE B 234 1 O PHE B 234 N ARG B 170 SHEET 1 F 2 ASN B 173 TYR B 175 0 SHEET 2 F 2 PHE B 210 TYR B 212 1 O THR B 211 N ASN B 173 SHEET 1 G 2 GLU B 197 GLU B 201 0 SHEET 2 G 2 GLU B 257 LYS B 261 1 O LYS B 261 N VAL B 200 SHEET 1 H 2 ARG B 207 ARG B 208 0 SHEET 2 H 2 LEU B 240 SER B 241 -1 O LEU B 240 N ARG B 208 CISPEP 1 LEU A 129 PRO A 130 0 -11.58 CISPEP 2 ALA A 163 PRO A 164 0 -0.33 CISPEP 3 LEU B 129 PRO B 130 0 -6.35 CISPEP 4 ALA B 163 PRO B 164 0 -0.36 SITE 1 AC1 25 LYS A 80 VAL A 82 THR A 119 CYS A 120 SITE 2 AC1 25 GLU A 121 TYR A 143 ASN A 173 GLU A 179 SITE 3 AC1 25 ASP A 182 ALA A 183 LEU A 184 ARG A 187 SITE 4 AC1 25 PRO A 199 VAL A 200 GLU A 201 GLN A 206 SITE 5 AC1 25 ARG A 208 VAL A 242 ARG A 264 GLU A 267 SITE 6 AC1 25 NAD A 401 HOH A 536 HOH A 579 HOH A 580 SITE 7 AC1 25 HOH A 590 SITE 1 AC2 36 GLY A 14 GLY A 17 PHE A 18 ILE A 19 SITE 2 AC2 36 LEU A 37 ASP A 38 ASP A 39 LEU A 40 SITE 3 AC2 36 ARG A 41 VAL A 42 LYS A 57 PRO A 58 SITE 4 AC2 36 VAL A 59 LEU A 76 ALA A 77 SER A 78 SITE 5 AC2 36 LYS A 80 ASP A 94 SER A 98 SER A 118 SITE 6 AC2 36 TYR A 143 LYS A 147 PHE A 171 PHE A 172 SITE 7 AC2 36 VAL A 174 GLU A 179 ARG A 180 UD1 A 400 SITE 8 AC2 36 HOH A 518 HOH A 519 HOH A 520 HOH A 521 SITE 9 AC2 36 HOH A 563 HOH A 574 HOH A 580 HOH A 588 SITE 1 AC3 24 LYS B 80 THR B 119 CYS B 120 GLU B 121 SITE 2 AC3 24 TYR B 143 ASN B 173 GLU B 179 ASP B 182 SITE 3 AC3 24 ALA B 183 LEU B 184 ARG B 187 PRO B 199 SITE 4 AC3 24 VAL B 200 GLU B 201 GLN B 206 ARG B 208 SITE 5 AC3 24 VAL B 242 ARG B 264 GLU B 267 NAD B 401 SITE 6 AC3 24 HOH B 507 HOH B 516 HOH B 547 HOH B 570 SITE 1 AC4 35 GLY B 14 GLY B 17 PHE B 18 ILE B 19 SITE 2 AC4 35 ASP B 38 ASP B 39 LEU B 40 ARG B 41 SITE 3 AC4 35 VAL B 42 LYS B 57 PRO B 58 VAL B 59 SITE 4 AC4 35 LEU B 76 ALA B 77 SER B 78 LYS B 80 SITE 5 AC4 35 ASP B 94 SER B 98 SER B 118 TYR B 143 SITE 6 AC4 35 LYS B 147 PHE B 171 PHE B 172 VAL B 174 SITE 7 AC4 35 GLU B 179 ARG B 180 UD1 B 400 HOH B 507 SITE 8 AC4 35 HOH B 533 HOH B 534 HOH B 542 HOH B 558 SITE 9 AC4 35 HOH B 559 HOH B 565 HOH B 567 CRYST1 45.453 51.061 67.804 98.13 106.65 94.36 P 1 2 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 0.022001 0.001677 0.006969 0.00000 SCALE2 0.000000 0.019641 0.003406 0.00000 SCALE3 0.000000 0.000000 0.015623 0.00000