HEADER ISOMERASE 04-DEC-20 7DMM TITLE STRUCTURE OF A GLUCOSE ISOMERASE CRYSTAL GROWN IN AN AQUEOUS GLYCEROL TITLE 2 SOLUTION WITHOUT ANY PRECIPITANTS COMPND MOL_ID: 1; COMPND 2 MOLECULE: XYLOSE ISOMERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GLUCOSE ISOMERASE; COMPND 5 EC: 5.3.1.5 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES RUBIGINOSUS; SOURCE 3 ORGANISM_TAXID: 1929 KEYWDS ISOMERASE(INTRAMOLEC, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.SUZUKI,N.MAITA REVDAT 2 29-NOV-23 7DMM 1 REMARK REVDAT 1 08-DEC-21 7DMM 0 JRNL AUTH Y.SUZUKI,N.IKEMITSU,N.MAITA JRNL TITL EXTRAORDINARILY FAST GROWTH OF HIGH-QUALITY GLUCOSE JRNL TITL 2 ISOMERASE CRYSTALS SIMPLY BY CONCENTRATION IN A JRNL TITL 3 PRECIPITANT-FREE SOLUTION WITH A CRYOPROTECTANT JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 0.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0189 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) : 0.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 51.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 242981 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) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.157 REMARK 3 FREE R VALUE : 0.166 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 13077 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) : 0.99 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.02 REMARK 3 REFLECTION IN BIN (WORKING SET) : 17907 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.31 REMARK 3 BIN R VALUE (WORKING SET) : 0.2330 REMARK 3 BIN FREE R VALUE SET COUNT : 882 REMARK 3 BIN FREE R VALUE : 0.2520 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3039 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 303 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.19000 REMARK 3 B22 (A**2) : 0.36000 REMARK 3 B33 (A**2) : -0.17000 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): 0.019 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.020 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.013 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.246 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.973 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.970 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3242 ; 0.029 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2948 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4408 ; 2.290 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6822 ; 1.124 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 418 ; 5.690 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 179 ;33.056 ;23.240 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 523 ;10.761 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;16.980 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 455 ; 0.130 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3754 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 738 ; 0.003 ; 0.020 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): 1582 ; 0.953 ; 0.826 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1581 ; 0.921 ; 0.825 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1985 ; 1.284 ; 1.250 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1986 ; 1.292 ; 1.251 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1660 ; 2.307 ; 1.047 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1660 ; 2.303 ; 1.047 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2409 ; 3.193 ; 1.507 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3755 ; 3.626 ;10.587 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3699 ; 3.532 ;10.340 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 : 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 ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 7DMM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1300019265. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AIMLESS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 256074 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.990 REMARK 200 RESOLUTION RANGE LOW (A) : 70.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.04600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.01 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.30800 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: MOLREP REMARK 200 STARTING MODEL: 1XIB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PRECIPITANT-FREE IN 30(V/V)% AQUEOUS REMARK 280 GLYCEROL SOLUTION, BATCH MODE, 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 46.30500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.23000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 51.15000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 46.30500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.23000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.15000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 46.30500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.23000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.15000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 46.30500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.23000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 51.15000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 34390 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -222.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 -102.30000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 -102.30000 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 A 752 LIES ON A SPECIAL POSITION. 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 778 O HOH A 797 4554 1.93 REMARK 500 O HOH A 622 O HOH A 797 4554 2.11 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 PHE A 26 CB PHE A 26 CG 0.137 REMARK 500 PHE A 26 CG PHE A 26 CD2 -0.105 REMARK 500 ASP A 56 CB ASP A 56 CG 0.198 REMARK 500 ARG A 68 CZ ARG A 68 NH2 -0.084 REMARK 500 GLU A 70 CG GLU A 70 CD 0.112 REMARK 500 ARG A 76 CZ ARG A 76 NH1 -0.081 REMARK 500 ARG A 113 CZ ARG A 113 NH1 -0.121 REMARK 500 GLY A 130 N GLY A 130 CA -0.099 REMARK 500 GLU A 160 CD GLU A 160 OE2 0.074 REMARK 500 VAL A 169 CB VAL A 169 CG2 -0.174 REMARK 500 ASN A 250 C ASN A 250 O 0.147 REMARK 500 ARG A 266 CZ ARG A 266 NH2 -0.099 REMARK 500 SER A 277 CB SER A 277 OG 0.080 REMARK 500 SER A 281 CB SER A 281 OG -0.090 REMARK 500 PHE A 296 CD1 PHE A 296 CE1 0.123 REMARK 500 GLU A 315 CD GLU A 315 OE1 -0.068 REMARK 500 ARG A 340 CD ARG A 340 NE -0.104 REMARK 500 ARG A 340 NE ARG A 340 CZ 0.091 REMARK 500 ARG A 340 CZ ARG A 340 NH1 0.089 REMARK 500 ARG A 340 CZ ARG A 340 NH1 -0.131 REMARK 500 ARG A 368 CZ ARG A 368 NH1 0.122 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 A 56 CB - CG - OD2 ANGL. DEV. = -8.3 DEGREES REMARK 500 PHE A 61 CB - CG - CD2 ANGL. DEV. = 5.3 DEGREES REMARK 500 ASP A 65 CB - CG - OD1 ANGL. DEV. = 7.1 DEGREES REMARK 500 ARG A 68 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 113 NE - CZ - NH1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG A 113 NE - CZ - NH2 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 117 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG A 121 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 152 NE - CZ - NH2 ANGL. DEV. = -6.4 DEGREES REMARK 500 ARG A 177 NE - CZ - NH1 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG A 188 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 208 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG A 208 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 TYR A 212 CB - CG - CD2 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 266 CD - NE - CZ ANGL. DEV. = 11.4 DEGREES REMARK 500 ARG A 266 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 PHE A 296 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 PHE A 296 CB - CG - CD1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG A 316 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 340 CG - CD - NE ANGL. DEV. = 14.0 DEGREES REMARK 500 ARG A 340 CD - NE - CZ ANGL. DEV. = 9.4 DEGREES REMARK 500 ARG A 340 NH1 - CZ - NH2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ARG A 340 NE - CZ - NH1 ANGL. DEV. = 7.9 DEGREES REMARK 500 ARG A 340 NE - CZ - NH1 ANGL. DEV. = 7.6 DEGREES REMARK 500 ARG A 340 NE - CZ - NH2 ANGL. DEV. = -9.4 DEGREES REMARK 500 ASP A 352 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ASP A 361 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 ASP A 361 CB - CG - OD2 ANGL. DEV. = -6.8 DEGREES REMARK 500 ARG A 368 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 368 NE - CZ - NH2 ANGL. DEV. = -8.7 DEGREES REMARK 500 ARG A 374 NE - CZ - NH1 ANGL. DEV. = -5.5 DEGREES REMARK 500 ARG A 374 NE - CZ - NH2 ANGL. DEV. = 7.1 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 THR A 17 -76.44 -83.96 REMARK 500 PHE A 26 14.80 -143.45 REMARK 500 PHE A 94 -28.81 -140.35 REMARK 500 GLU A 186 101.15 83.23 REMARK 500 ASN A 215 76.55 -119.69 REMARK 500 ASN A 247 -168.15 -171.51 REMARK 500 TYR A 254 158.47 -49.26 REMARK 500 ALA A 343 61.83 -150.55 REMARK 500 PHE A 357 -78.09 -154.55 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 117 0.08 SIDE CHAIN 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 MN A 405 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 181 OE2 REMARK 620 2 GLU A 217 OE1 92.0 REMARK 620 3 ASP A 245 OD2 94.2 105.3 REMARK 620 4 ASP A 287 OD2 164.3 87.0 101.2 REMARK 620 5 GOL A 401 O1 83.1 94.6 160.0 81.3 REMARK 620 6 GOL A 401 O2 88.8 168.7 85.8 89.2 74.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 404 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 217 OE2 REMARK 620 2 HIS A 220 NE2 80.3 REMARK 620 3 ASP A 255 OD1 102.8 88.3 REMARK 620 4 ASP A 255 OD2 159.7 92.1 57.9 REMARK 620 5 ASP A 257 OD1 89.8 163.8 81.4 92.8 REMARK 620 6 HOH A 521 O 106.7 108.2 148.1 93.5 86.8 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 403 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 261 O REMARK 620 2 GLY A 263 O 111.4 REMARK 620 N 1 DBREF 7DMM A 2 387 UNP P24300 XYLA_STRRU 2 387 SEQADV 7DMM GLN A 41 UNP P24300 ARG 41 VARIANT SEQRES 1 A 386 ASN TYR GLN PRO THR PRO GLU ASP ARG PHE THR PHE GLY SEQRES 2 A 386 LEU TRP THR VAL GLY TRP GLN GLY ARG ASP PRO PHE GLY SEQRES 3 A 386 ASP ALA THR ARG ARG ALA LEU ASP PRO VAL GLU SER VAL SEQRES 4 A 386 GLN ARG LEU ALA GLU LEU GLY ALA HIS GLY VAL THR PHE SEQRES 5 A 386 HIS ASP ASP ASP LEU ILE PRO PHE GLY SER SER ASP SER SEQRES 6 A 386 GLU ARG GLU GLU HIS VAL LYS ARG PHE ARG GLN ALA LEU SEQRES 7 A 386 ASP ASP THR GLY MET LYS VAL PRO MET ALA THR THR ASN SEQRES 8 A 386 LEU PHE THR HIS PRO VAL PHE LYS ASP GLY GLY PHE THR SEQRES 9 A 386 ALA ASN ASP ARG ASP VAL ARG ARG TYR ALA LEU ARG LYS SEQRES 10 A 386 THR ILE ARG ASN ILE ASP LEU ALA VAL GLU LEU GLY ALA SEQRES 11 A 386 GLU THR TYR VAL ALA TRP GLY GLY ARG GLU GLY ALA GLU SEQRES 12 A 386 SER GLY GLY ALA LYS ASP VAL ARG ASP ALA LEU ASP ARG SEQRES 13 A 386 MET LYS GLU ALA PHE ASP LEU LEU GLY GLU TYR VAL THR SEQRES 14 A 386 SER GLN GLY TYR ASP ILE ARG PHE ALA ILE GLU PRO LYS SEQRES 15 A 386 PRO ASN GLU PRO ARG GLY ASP ILE LEU LEU PRO THR VAL SEQRES 16 A 386 GLY HIS ALA LEU ALA PHE ILE GLU ARG LEU GLU ARG PRO SEQRES 17 A 386 GLU LEU TYR GLY VAL ASN PRO GLU VAL GLY HIS GLU GLN SEQRES 18 A 386 MET ALA GLY LEU ASN PHE PRO HIS GLY ILE ALA GLN ALA SEQRES 19 A 386 LEU TRP ALA GLY LYS LEU PHE HIS ILE ASP LEU ASN GLY SEQRES 20 A 386 GLN ASN GLY ILE LYS TYR ASP GLN ASP LEU ARG PHE GLY SEQRES 21 A 386 ALA GLY ASP LEU ARG ALA ALA PHE TRP LEU VAL ASP LEU SEQRES 22 A 386 LEU GLU SER ALA GLY TYR SER GLY PRO ARG HIS PHE ASP SEQRES 23 A 386 PHE LYS PRO PRO ARG THR GLU ASP PHE ASP GLY VAL TRP SEQRES 24 A 386 ALA SER ALA ALA GLY CYS MET ARG ASN TYR LEU ILE LEU SEQRES 25 A 386 LYS GLU ARG ALA ALA ALA PHE ARG ALA ASP PRO GLU VAL SEQRES 26 A 386 GLN GLU ALA LEU ARG ALA SER ARG LEU ASP GLU LEU ALA SEQRES 27 A 386 ARG PRO THR ALA ALA ASP GLY LEU GLN ALA LEU LEU ASP SEQRES 28 A 386 ASP ARG SER ALA PHE GLU GLU PHE ASP VAL ASP ALA ALA SEQRES 29 A 386 ALA ALA ARG GLY MET ALA PHE GLU ARG LEU ASP GLN LEU SEQRES 30 A 386 ALA MET ASP HIS LEU LEU GLY ALA ARG HET GOL A 401 6 HET GOL A 402 6 HET CA A 403 1 HET MN A 404 1 HET MN A 405 1 HETNAM GOL GLYCEROL HETNAM CA CALCIUM ION HETNAM MN MANGANESE (II) ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 2(C3 H8 O3) FORMUL 4 CA CA 2+ FORMUL 5 MN 2(MN 2+) FORMUL 7 HOH *303(H2 O) HELIX 1 AA1 THR A 6 ASP A 9 5 4 HELIX 2 AA2 LEU A 15 GLY A 19 1 5 HELIX 3 AA3 ASP A 35 LEU A 46 1 12 HELIX 4 AA4 ASP A 55 ILE A 59 1 5 HELIX 5 AA5 SER A 64 GLY A 83 1 20 HELIX 6 AA6 HIS A 96 LYS A 100 5 5 HELIX 7 AA7 ASP A 108 LEU A 129 1 22 HELIX 8 AA8 ASP A 150 GLY A 173 1 24 HELIX 9 AA9 THR A 195 GLU A 204 1 10 HELIX 10 AB1 ARG A 208 GLU A 210 5 3 HELIX 11 AB2 GLU A 217 MET A 223 1 7 HELIX 12 AB3 ASN A 227 ALA A 238 1 12 HELIX 13 AB4 ASP A 264 GLY A 279 1 16 HELIX 14 AB5 ASP A 295 ASP A 323 1 29 HELIX 15 AB6 ASP A 323 SER A 333 1 11 HELIX 16 AB7 ARG A 334 ALA A 339 1 6 HELIX 17 AB8 GLY A 346 ASP A 353 1 8 HELIX 18 AB9 ARG A 354 PHE A 357 5 4 HELIX 19 AC1 ASP A 361 ARG A 368 1 8 HELIX 20 AC2 ALA A 371 GLY A 385 1 15 SHEET 1 AA1 8 TYR A 212 VAL A 214 0 SHEET 2 AA1 8 ARG A 177 ILE A 180 1 N ILE A 180 O GLY A 213 SHEET 3 AA1 8 THR A 133 ALA A 136 1 N TYR A 134 O ARG A 177 SHEET 4 AA1 8 LYS A 85 THR A 90 1 N ALA A 89 O VAL A 135 SHEET 5 AA1 8 GLY A 50 HIS A 54 1 N VAL A 51 O LYS A 85 SHEET 6 AA1 8 PHE A 11 GLY A 14 1 N PHE A 13 O THR A 52 SHEET 7 AA1 8 ARG A 284 PHE A 286 1 O PHE A 286 N THR A 12 SHEET 8 AA1 8 ASP A 245 LEU A 246 1 N LEU A 246 O HIS A 285 SHEET 1 AA2 2 GLY A 142 ALA A 143 0 SHEET 2 AA2 2 ASP A 190 ILE A 191 -1 O ASP A 190 N ALA A 143 LINK OE2 GLU A 181 MN MN A 405 1555 1555 2.05 LINK OE2 GLU A 217 MN MN A 404 1555 1555 2.05 LINK OE1 GLU A 217 MN MN A 405 1555 1555 2.05 LINK NE2 HIS A 220 MN MN A 404 1555 1555 2.35 LINK OD2 ASP A 245 MN MN A 405 1555 1555 2.03 LINK OD1 ASP A 255 MN MN A 404 1555 1555 2.30 LINK OD2 ASP A 255 MN MN A 404 1555 1555 2.24 LINK OD1 ASP A 257 MN MN A 404 1555 1555 2.20 LINK O GLY A 261 CA CA A 403 1555 1555 2.79 LINK O GLY A 263 CA CA A 403 1555 1555 2.83 LINK OD2 ASP A 287 MN MN A 405 1555 1555 2.09 LINK O1 GOL A 401 MN MN A 405 1555 1555 2.27 LINK O2 GOL A 401 MN MN A 405 1555 1555 2.22 LINK MN MN A 404 O HOH A 521 1555 1555 2.19 CISPEP 1 GLU A 186 PRO A 187 0 21.01 CRYST1 92.610 98.460 102.300 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 0.010798 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010156 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009775 0.00000