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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
