HEADER TRANSFERASE 21-DEC-07 3BRK TITLE CRYSTAL STRUCTURE OF ADP-GLUCOSE PYROPHOSPHORYLASE FROM AGROBACTERIUM TITLE 2 TUMEFACIENS CAVEAT 3BRK CHIRALITY ERROR AT CA OF SER X98 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUCOSE-1-PHOSPHATE ADENYLYLTRANSFERASE; COMPND 3 CHAIN: X; COMPND 4 SYNONYM: ADP-GLUCOSE SYNTHASE, ADP-GLUCOSE PYROPHOSPHORYLASE, ADPGLC COMPND 5 PPASE; COMPND 6 EC: 2.7.7.27; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AGROBACTERIUM TUMEFACIENS; SOURCE 3 ORGANISM_TAXID: 358; SOURCE 4 GENE: GLGC; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ADP-GLUCOSE PYROPHOSPHORYLASE, AGROBACTERIUM TUMEFACIENS, ALLOSTERY, KEYWDS 2 KINETICS, STRUCTURE-FUNCTION RELATIONSHIPS, SITE-DIRECTED KEYWDS 3 MUTAGENESIS, GLYCOGEN BIOSYNTHESIS, NUCLEOTIDYLTRANSFERASE, KEYWDS 4 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.CUPP-VICKERY,C.MEYER,R.IGARASHI REVDAT 4 25-OCT-17 3BRK 1 REMARK REVDAT 3 24-FEB-09 3BRK 1 VERSN REVDAT 2 20-MAY-08 3BRK 1 JRNL REVDAT 1 22-APR-08 3BRK 0 JRNL AUTH J.R.CUPP-VICKERY,R.Y.IGARASHI,M.PEREZ,M.POLAND,C.R.MEYER JRNL TITL STRUCTURAL ANALYSIS OF ADP-GLUCOSE PYROPHOSPHORYLASE FROM JRNL TITL 2 THE BACTERIUM AGROBACTERIUM TUMEFACIENS. JRNL REF BIOCHEMISTRY V. 47 4439 2008 JRNL REFN ISSN 0006-2960 JRNL PMID 18355040 JRNL DOI 10.1021/BI701933Q REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON 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) : 46.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 33213 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) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.221 REMARK 3 FREE R VALUE : 0.267 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3336 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) : 2177 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE SET COUNT : 234 REMARK 3 BIN FREE R VALUE : 0.3280 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2974 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 238 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.82000 REMARK 3 B22 (A**2) : 1.67000 REMARK 3 B33 (A**2) : -2.50000 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): 0.209 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.191 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.143 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.400 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.900 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3054 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2771 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4150 ; 1.487 ; 1.948 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6403 ; 0.922 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 392 ; 7.856 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 454 ; 0.145 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3475 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 638 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 665 ; 0.214 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3261 ; 0.239 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1846 ; 0.084 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 158 ; 0.213 ; 0.200 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): 18 ; 0.101 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 64 ; 0.310 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.154 ; 0.200 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): 1951 ; 0.721 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3109 ; 1.299 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1103 ; 1.980 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1041 ; 3.082 ; 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): 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 : 1.40 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 3BRK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000045879. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM, DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33214 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 79.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06900 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5M LITHIUM SULFATE, PH 7.5, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 298K 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 42.69000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.89650 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 70.14650 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 42.69000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.89650 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 70.14650 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 42.69000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.89650 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 70.14650 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 42.69000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 46.89650 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 70.14650 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: X 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3960 ANGSTROM**2 REMARK 350 APPLY THE FOLLOWING TO CHAINS: X 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 85.38000 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 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 HOH X 674 LIES ON A SPECIAL POSITION. REMARK 375 HOH X 677 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 MET X 1 REMARK 465 SER X 2 REMARK 465 GLU X 3 REMARK 465 LYS X 4 REMARK 465 ARG X 5 REMARK 465 VAL X 6 REMARK 465 GLN X 99 REMARK 465 ARG X 100 REMARK 465 VAL X 101 REMARK 465 SER X 102 REMARK 465 GLU X 103 REMARK 465 THR X 104 REMARK 465 GLN X 105 REMARK 465 ASP X 226 REMARK 465 PRO X 227 REMARK 465 THR X 228 REMARK 465 SER X 229 REMARK 465 SER X 230 REMARK 465 ARG X 231 REMARK 465 ASP X 232 REMARK 465 PHE X 233 REMARK 465 GLY X 234 REMARK 465 LYS X 235 REMARK 465 ASP X 419 REMARK 465 LEU X 420 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 X 22 CB CG CD NE CZ NH1 NH2 REMARK 470 TYR X 68 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 LYS X 69 CG CD CE NZ REMARK 470 TRP X 106 CB CG CD1 CD2 NE1 CE2 CE3 REMARK 470 TRP X 106 CZ2 CZ3 CH2 REMARK 470 TYR X 107 CB CG CD1 CD2 CE1 CE2 CZ REMARK 470 TYR X 107 OH REMARK 470 GLU X 108 CB CG CD OE1 OE2 REMARK 470 GLU X 127 CG CD OE1 OE2 REMARK 470 ARG X 165 CG CD NE CZ NH1 NH2 REMARK 470 GLU X 167 CG CD OE1 OE2 REMARK 470 VAL X 176 CG1 CG2 REMARK 470 GLU X 178 CG CD OE1 OE2 REMARK 470 LYS X 179 CG CD CE NZ REMARK 470 GLU X 187 CG CD OE1 OE2 REMARK 470 LYS X 214 CG CD CE NZ REMARK 470 GLU X 218 CB CG CD OE1 OE2 REMARK 470 ALA X 219 CB REMARK 470 VAL X 220 CG1 CG2 REMARK 470 ARG X 221 CB CG CD NE CZ NH1 NH2 REMARK 470 ARG X 222 CB CG CD NE CZ NH1 NH2 REMARK 470 ASP X 223 CB CG OD1 OD2 REMARK 470 ALA X 224 CB REMARK 470 ALA X 225 CB REMARK 470 ASP X 236 CB CG OD1 OD2 REMARK 470 ILE X 237 CB CG1 CG2 CD1 REMARK 470 TYR X 240 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 HIS X 244 CG ND1 CD2 CE1 NE2 REMARK 470 GLU X 316 CG CD OE1 OE2 REMARK 470 ARG X 354 CG CD NE CZ NH1 NH2 REMARK 470 GLU X 356 CG CD OE1 OE2 REMARK 470 GLU X 404 CG CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 N ASP X 236 O HOH X 742 2.16 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 ASP X 12 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP X 93 CB - CG - OD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 SER X 98 CB - CA - C ANGL. DEV. = 12.6 DEGREES REMARK 500 SER X 98 N - CA - CB ANGL. DEV. = 9.0 DEGREES REMARK 500 ASP X 294 CB - CG - OD2 ANGL. DEV. = 7.0 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 PRO X 8 123.60 -38.59 REMARK 500 LYS X 27 -123.86 60.14 REMARK 500 ALA X 44 -178.99 179.91 REMARK 500 GLN X 67 -92.60 -140.37 REMARK 500 LYS X 69 54.08 35.86 REMARK 500 TRP X 81 56.43 -109.73 REMARK 500 PRO X 96 4.69 -66.48 REMARK 500 TYR X 107 -79.00 119.10 REMARK 500 GLU X 108 -18.81 89.16 REMARK 500 ASN X 177 -160.35 -121.45 REMARK 500 ASN X 198 53.60 -150.36 REMARK 500 ARG X 221 51.86 -100.01 REMARK 500 ARG X 222 47.31 -170.21 REMARK 500 ASP X 223 -9.21 144.94 REMARK 500 ALA X 224 -102.76 -64.63 REMARK 500 ILE X 237 138.56 -173.61 REMARK 500 ILE X 238 55.26 -94.49 REMARK 500 VAL X 270 54.33 28.60 REMARK 500 HIS X 313 131.01 73.29 REMARK 500 HIS X 369 -1.21 68.48 REMARK 500 LYS X 417 55.74 -94.71 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 ALA X 97 SER X 98 -122.83 REMARK 500 ILE X 238 PRO X 239 137.73 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 X 600 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 X 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 X 601 DBREF 3BRK X 1 420 UNP P39669 GLGC_AGRTU 1 420 SEQRES 1 X 420 MET SER GLU LYS ARG VAL GLN PRO LEU ALA ARG ASP ALA SEQRES 2 X 420 MSE ALA TYR VAL LEU ALA GLY GLY ARG GLY SER ARG LEU SEQRES 3 X 420 LYS GLU LEU THR ASP ARG ARG ALA LYS PRO ALA VAL TYR SEQRES 4 X 420 PHE GLY GLY LYS ALA ARG ILE ILE ASP PHE ALA LEU SER SEQRES 5 X 420 ASN ALA LEU ASN SER GLY ILE ARG ARG ILE GLY VAL ALA SEQRES 6 X 420 THR GLN TYR LYS ALA HIS SER LEU ILE ARG HIS LEU GLN SEQRES 7 X 420 ARG GLY TRP ASP PHE PHE ARG PRO GLU ARG ASN GLU SER SEQRES 8 X 420 PHE ASP ILE LEU PRO ALA SER GLN ARG VAL SER GLU THR SEQRES 9 X 420 GLN TRP TYR GLU GLY THR ALA ASP ALA VAL TYR GLN ASN SEQRES 10 X 420 ILE ASP ILE ILE GLU PRO TYR ALA PRO GLU TYR MSE VAL SEQRES 11 X 420 ILE LEU ALA GLY ASP HIS ILE TYR LYS MSE ASP TYR GLU SEQRES 12 X 420 TYR MSE LEU GLN GLN HIS VAL ASP SER GLY ALA ASP VAL SEQRES 13 X 420 THR ILE GLY CYS LEU GLU VAL PRO ARG MSE GLU ALA THR SEQRES 14 X 420 GLY PHE GLY VAL MSE HIS VAL ASN GLU LYS ASP GLU ILE SEQRES 15 X 420 ILE ASP PHE ILE GLU LYS PRO ALA ASP PRO PRO GLY ILE SEQRES 16 X 420 PRO GLY ASN GLU GLY PHE ALA LEU ALA SER MSE GLY ILE SEQRES 17 X 420 TYR VAL PHE HIS THR LYS PHE LEU MSE GLU ALA VAL ARG SEQRES 18 X 420 ARG ASP ALA ALA ASP PRO THR SER SER ARG ASP PHE GLY SEQRES 19 X 420 LYS ASP ILE ILE PRO TYR ILE VAL GLU HIS GLY LYS ALA SEQRES 20 X 420 VAL ALA HIS ARG PHE ALA ASP SER CYS VAL ARG SER ASP SEQRES 21 X 420 PHE GLU HIS GLU PRO TYR TRP ARG ASP VAL GLY THR ILE SEQRES 22 X 420 ASP ALA TYR TRP GLN ALA ASN ILE ASP LEU THR ASP VAL SEQRES 23 X 420 VAL PRO ASP LEU ASP ILE TYR ASP LYS SER TRP PRO ILE SEQRES 24 X 420 TRP THR TYR ALA GLU ILE THR PRO PRO ALA LYS PHE VAL SEQRES 25 X 420 HIS ASP ASP GLU ASP ARG ARG GLY SER ALA VAL SER SER SEQRES 26 X 420 VAL VAL SER GLY ASP CYS ILE ILE SER GLY ALA ALA LEU SEQRES 27 X 420 ASN ARG SER LEU LEU PHE THR GLY VAL ARG ALA ASN SER SEQRES 28 X 420 TYR SER ARG LEU GLU ASN ALA VAL VAL LEU PRO SER VAL SEQRES 29 X 420 LYS ILE GLY ARG HIS ALA GLN LEU SER ASN VAL VAL ILE SEQRES 30 X 420 ASP HIS GLY VAL VAL ILE PRO GLU GLY LEU ILE VAL GLY SEQRES 31 X 420 GLU ASP PRO GLU LEU ASP ALA LYS ARG PHE ARG ARG THR SEQRES 32 X 420 GLU SER GLY ILE CYS LEU ILE THR GLN SER MSE ILE ASP SEQRES 33 X 420 LYS LEU ASP LEU MODRES 3BRK MSE X 14 MET SELENOMETHIONINE MODRES 3BRK MSE X 129 MET SELENOMETHIONINE MODRES 3BRK MSE X 140 MET SELENOMETHIONINE MODRES 3BRK MSE X 145 MET SELENOMETHIONINE MODRES 3BRK MSE X 166 MET SELENOMETHIONINE MODRES 3BRK MSE X 174 MET SELENOMETHIONINE MODRES 3BRK MSE X 206 MET SELENOMETHIONINE MODRES 3BRK MSE X 217 MET SELENOMETHIONINE MODRES 3BRK MSE X 414 MET SELENOMETHIONINE HET MSE X 14 8 HET MSE X 129 8 HET MSE X 140 8 HET MSE X 145 8 HET MSE X 166 8 HET MSE X 174 8 HET MSE X 206 8 HET MSE X 217 8 HET MSE X 414 8 HET SO4 X 600 5 HET SO4 X 602 5 HET SO4 X 601 5 HETNAM MSE SELENOMETHIONINE HETNAM SO4 SULFATE ION FORMUL 1 MSE 9(C5 H11 N O2 SE) FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 HOH *238(H2 O) HELIX 1 1 PRO X 8 ARG X 11 5 4 HELIX 2 2 GLY X 23 ASP X 31 5 9 HELIX 3 3 ALA X 34 ALA X 37 5 4 HELIX 4 4 ILE X 47 SER X 57 1 11 HELIX 5 5 ALA X 70 TRP X 81 1 12 HELIX 6 6 ARG X 85 ASN X 89 5 5 HELIX 7 7 GLY X 109 GLN X 116 1 8 HELIX 8 8 ASN X 117 ALA X 125 1 9 HELIX 9 9 TYR X 142 SER X 152 1 11 HELIX 10 10 MSE X 166 GLY X 170 5 5 HELIX 11 11 THR X 213 ARG X 221 1 9 HELIX 12 12 PRO X 239 GLY X 245 1 7 HELIX 13 13 PHE X 252 CYS X 256 1 5 HELIX 14 14 THR X 272 LEU X 283 1 12 HELIX 15 15 ASP X 392 PHE X 400 1 9 HELIX 16 16 THR X 411 LYS X 417 1 7 SHEET 1 A 7 SER X 91 LEU X 95 0 SHEET 2 A 7 ARG X 61 THR X 66 1 N ILE X 62 O SER X 91 SHEET 3 A 7 ALA X 13 ALA X 19 1 N VAL X 17 O GLY X 63 SHEET 4 A 7 TYR X 128 ALA X 133 1 O VAL X 130 N TYR X 16 SHEET 5 A 7 PHE X 201 HIS X 212 -1 O TYR X 209 N ILE X 131 SHEET 6 A 7 GLY X 172 VAL X 176 -1 N MSE X 174 O LEU X 203 SHEET 7 A 7 ILE X 182 GLU X 187 -1 O ILE X 186 N VAL X 173 SHEET 1 B 7 SER X 91 LEU X 95 0 SHEET 2 B 7 ARG X 61 THR X 66 1 N ILE X 62 O SER X 91 SHEET 3 B 7 ALA X 13 ALA X 19 1 N VAL X 17 O GLY X 63 SHEET 4 B 7 TYR X 128 ALA X 133 1 O VAL X 130 N TYR X 16 SHEET 5 B 7 PHE X 201 HIS X 212 -1 O TYR X 209 N ILE X 131 SHEET 6 B 7 VAL X 156 PRO X 164 -1 N VAL X 163 O ALA X 202 SHEET 7 B 7 ALA X 247 ARG X 251 1 O HIS X 250 N ILE X 158 SHEET 1 C 2 TYR X 39 PHE X 40 0 SHEET 2 C 2 ALA X 44 ARG X 45 -1 O ALA X 44 N PHE X 40 SHEET 1 D 2 ILE X 137 TYR X 138 0 SHEET 2 D 2 TRP X 267 ARG X 268 -1 O ARG X 268 N ILE X 137 SHEET 1 E 5 LYS X 310 VAL X 312 0 SHEET 2 E 5 ILE X 332 SER X 334 1 O ILE X 333 N LYS X 310 SHEET 3 E 5 ARG X 348 ALA X 349 1 O ALA X 349 N SER X 334 SHEET 4 E 5 LYS X 365 ILE X 366 1 O ILE X 366 N ARG X 348 SHEET 5 E 5 VAL X 382 ILE X 383 1 O ILE X 383 N LYS X 365 SHEET 1 F 5 SER X 321 VAL X 323 0 SHEET 2 F 5 ALA X 337 ASN X 339 1 O LEU X 338 N SER X 321 SHEET 3 F 5 ARG X 354 VAL X 360 1 O LEU X 355 N ALA X 337 SHEET 4 F 5 GLN X 371 ILE X 377 1 O ILE X 377 N VAL X 359 SHEET 5 F 5 ILE X 388 VAL X 389 1 O VAL X 389 N GLN X 371 SHEET 1 G 6 VAL X 326 VAL X 327 0 SHEET 2 G 6 LEU X 342 LEU X 343 1 O LEU X 343 N VAL X 326 SHEET 3 G 6 ARG X 354 VAL X 360 1 O VAL X 360 N LEU X 342 SHEET 4 G 6 GLN X 371 ILE X 377 1 O ILE X 377 N VAL X 359 SHEET 5 G 6 CYS X 408 ILE X 410 1 O ILE X 410 N VAL X 376 SHEET 6 G 6 ARG X 401 ARG X 402 -1 N ARG X 401 O LEU X 409 LINK C ALA X 13 N MSE X 14 1555 1555 1.32 LINK C MSE X 14 N ALA X 15 1555 1555 1.33 LINK C TYR X 128 N MSE X 129 1555 1555 1.34 LINK C MSE X 129 N VAL X 130 1555 1555 1.33 LINK C LYS X 139 N MSE X 140 1555 1555 1.33 LINK C MSE X 140 N ASP X 141 1555 1555 1.34 LINK C TYR X 144 N MSE X 145 1555 1555 1.33 LINK C MSE X 145 N LEU X 146 1555 1555 1.34 LINK C ARG X 165 N MSE X 166 1555 1555 1.32 LINK C MSE X 166 N GLU X 167 1555 1555 1.33 LINK C VAL X 173 N MSE X 174 1555 1555 1.33 LINK C MSE X 174 N HIS X 175 1555 1555 1.34 LINK C SER X 205 N MSE X 206 1555 1555 1.34 LINK C MSE X 206 N GLY X 207 1555 1555 1.33 LINK C LEU X 216 N MSE X 217 1555 1555 1.34 LINK C MSE X 217 N GLU X 218 1555 1555 1.34 LINK C SER X 413 N MSE X 414 1555 1555 1.33 LINK C MSE X 414 N ILE X 415 1555 1555 1.33 SITE 1 AC1 6 SER X 334 ASN X 350 SER X 351 ARG X 368 SITE 2 AC1 6 HOH X 712 HOH X 812 SITE 1 AC2 2 ARG X 318 ARG X 368 SITE 1 AC3 4 ARG X 33 TYR X 39 ARG X 45 SER X 72 CRYST1 85.380 93.793 140.293 90.00 90.00 90.00 I 2 2 2 8 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 0.011712 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010662 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007128 0.00000