HEADER ISOMERASE 15-SEP-23 8WDG TITLE SUBATOMIC CRYSTAL STRUCTURE OF GLUCOSE ISOMERASE FROM STREPTOMYCES TITLE 2 RUBIGINOSUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: XYLOSE ISOMERASE; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES RUBIGINOSUS; SOURCE 3 ORGANISM_TAXID: 1929 KEYWDS GLUCOSE ISOMERASE, SUBATOMIC RESOLUTION, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR K.H.NAM REVDAT 2 17-APR-24 8WDG 1 JRNL REVDAT 1 04-OCT-23 8WDG 0 JRNL AUTH Y.XU,K.H.NAM JRNL TITL XYLITOL BINDING TO THE M1 SITE OF GLUCOSE ISOMERASE INDUCES JRNL TITL 2 A CONFORMATIONAL CHANGE IN THE SUBSTRATE BINDING CHANNEL. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 682 21 2023 JRNL REFN ESSN 1090-2104 JRNL PMID 37793321 JRNL DOI 10.1016/J.BBRC.2023.09.087 REMARK 2 REMARK 2 RESOLUTION. 0.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 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) : 40.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 243532 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) : 0.159 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.171 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 12883 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) : 17153 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.57 REMARK 3 BIN R VALUE (WORKING SET) : 0.3070 REMARK 3 BIN FREE R VALUE SET COUNT : 952 REMARK 3 BIN FREE R VALUE : 0.3140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3033 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 13 REMARK 3 SOLVENT ATOMS : 502 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.42000 REMARK 3 B33 (A**2) : -0.43000 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): 0.020 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.021 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.018 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.353 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.980 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.976 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3232 ; 0.018 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2972 ; 0.001 ; 0.015 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4389 ; 2.043 ; 1.647 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6826 ; 1.677 ; 1.588 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 406 ; 6.098 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 210 ;29.957 ;20.810 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 510 ;11.187 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 36 ;13.805 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 391 ; 0.120 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3800 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 816 ; 0.002 ; 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): 1597 ; 0.943 ; 0.894 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1596 ; 0.907 ; 0.892 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2012 ; 1.277 ; 1.349 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2013 ; 1.285 ; 1.350 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1635 ; 2.306 ; 1.153 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1636 ; 2.306 ; 1.154 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2378 ; 3.397 ; 1.650 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3904 ; 4.745 ;12.775 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3768 ; 4.383 ;11.834 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 8WDG COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1300041072. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-DEC-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 11C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8265 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 255970 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.990 REMARK 200 RESOLUTION RANGE LOW (A) : 40.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2000 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 (%) : 94.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS-HCL, PH 8.0, PEG400, MGCL2, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 295K 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 46.33750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.31300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 51.06850 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 46.33750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.31300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.06850 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 46.33750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.31300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.06850 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 46.33750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.31300 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 51.06850 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: 32710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 45730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -224.0 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 92.67500 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 92.67500 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 102.13700 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 102.13700 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 888 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 917 LIES ON A SPECIAL POSITION. 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 HD1 HIS A 96 H VAL A 98 1.13 REMARK 500 HD22 ASN A 122 HH TYR A 134 1.33 REMARK 500 HH21 ARG A 152 O HOH A 501 1.37 REMARK 500 HH21 ARG A 42 O HOH A 503 1.44 REMARK 500 O HOH A 871 O HOH A 898 1.49 REMARK 500 O HOH A 873 O HOH A 959 1.94 REMARK 500 O HOH A 833 O HOH A 991 2.02 REMARK 500 O HOH A 619 O HOH A 700 2.02 REMARK 500 O HOH A 672 O HOH A 847 2.09 REMARK 500 O HOH A 740 O HOH A 782 2.10 REMARK 500 O HOH A 523 O HOH A 600 2.13 REMARK 500 O HOH A 998 O HOH A 1002 2.15 REMARK 500 NH2 ARG A 152 O HOH A 501 2.16 REMARK 500 OE2 GLU A 358 O HOH A 502 2.16 REMARK 500 OE1 GLU A 358 O HOH A 502 2.16 REMARK 500 O HOH A 862 O HOH A 935 2.17 REMARK 500 O HOH A 733 O HOH A 957 2.18 REMARK 500 O HOH A 543 O HOH A 882 2.19 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 HIS A 220 CE1 HIS A 220 NE2 -0.097 REMARK 500 ASN A 250 C ASN A 250 O 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 24 O - C - N ANGL. DEV. = -12.0 DEGREES REMARK 500 ARG A 42 CD - NE - CZ ANGL. DEV. = 10.6 DEGREES REMARK 500 ARG A 42 NE - CZ - NH1 ANGL. DEV. = 8.0 DEGREES REMARK 500 ARG A 42 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 76 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 113 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 TYR A 212 CB - CG - CD2 ANGL. DEV. = 4.8 DEGREES REMARK 500 TYR A 212 CB - CG - CD1 ANGL. DEV. = -4.0 DEGREES REMARK 500 ARG A 266 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 ARG A 340 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 340 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 340 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ALA A 386 O - C - N ANGL. DEV. = -11.8 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 -75.94 -84.09 REMARK 500 PHE A 94 -27.00 -141.66 REMARK 500 GLU A 186 100.64 83.45 REMARK 500 GLU A 186 99.03 81.12 REMARK 500 GLU A 186 97.05 78.84 REMARK 500 ASN A 215 76.40 -119.45 REMARK 500 ASN A 247 -167.10 -168.01 REMARK 500 LYS A 253 -179.01 -173.14 REMARK 500 TYR A 254 155.87 -48.87 REMARK 500 ALA A 343 62.02 -150.14 REMARK 500 PHE A 357 -74.52 -155.95 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 PRO A 25 PHE A 26 148.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASP A 24 15.88 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A1000 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A1001 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A1002 DISTANCE = 6.01 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 402 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 181 OE2 REMARK 620 2 GLU A 217 OE1 97.5 REMARK 620 3 ASP A 245 OD2 93.6 98.0 REMARK 620 4 ASP A 287 OD2 160.2 84.6 105.6 REMARK 620 5 XYL A 403 O4 86.6 172.0 88.5 89.2 REMARK 620 6 XYL A 403 O2 85.3 90.1 171.9 75.0 83.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 401 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 217 OE2 REMARK 620 2 ASP A 255 OD1 115.5 REMARK 620 3 ASP A 255 OD2 168.5 55.7 REMARK 620 4 ASP A 255 OD2 172.1 56.6 6.8 REMARK 620 5 ASP A 257 OD1 93.2 78.9 92.2 85.9 REMARK 620 6 HOH A 552 O 93.5 147.1 97.1 94.2 84.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 404 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 222 OE1 REMARK 620 2 HOH A 742 O 101.0 REMARK 620 N 1 DBREF 8WDG A 3 387 UNP P24300 XYLA_STRRU 3 387 SEQRES 1 A 385 TYR GLN PRO THR PRO GLU ASP ARG PHE THR PHE GLY LEU SEQRES 2 A 385 TRP THR VAL GLY TRP GLN GLY ARG ASP PRO PHE GLY ASP SEQRES 3 A 385 ALA THR ARG ARG ALA LEU ASP PRO VAL GLU SER VAL ARG SEQRES 4 A 385 ARG LEU ALA GLU LEU GLY ALA HIS GLY VAL THR PHE HIS SEQRES 5 A 385 ASP ASP ASP LEU ILE PRO PHE GLY SER SER ASP SER GLU SEQRES 6 A 385 ARG GLU GLU HIS VAL LYS ARG PHE ARG GLN ALA LEU ASP SEQRES 7 A 385 ASP THR GLY MET LYS VAL PRO MET ALA THR THR ASN LEU SEQRES 8 A 385 PHE THR HIS PRO VAL PHE LYS ASP GLY GLY PHE THR ALA SEQRES 9 A 385 ASN ASP ARG ASP VAL ARG ARG TYR ALA LEU ARG LYS THR SEQRES 10 A 385 ILE ARG ASN ILE ASP LEU ALA VAL GLU LEU GLY ALA GLU SEQRES 11 A 385 THR TYR VAL ALA TRP GLY GLY ARG GLU GLY ALA GLU SER SEQRES 12 A 385 GLY GLY ALA LYS ASP VAL ARG ASP ALA LEU ASP ARG MET SEQRES 13 A 385 LYS GLU ALA PHE ASP LEU LEU GLY GLU TYR VAL THR SER SEQRES 14 A 385 GLN GLY TYR ASP ILE ARG PHE ALA ILE GLU PRO LYS PRO SEQRES 15 A 385 ASN GLU PRO ARG GLY ASP ILE LEU LEU PRO THR VAL GLY SEQRES 16 A 385 HIS ALA LEU ALA PHE ILE GLU ARG LEU GLU ARG PRO GLU SEQRES 17 A 385 LEU TYR GLY VAL ASN PRO GLU VAL GLY HIS GLU GLN MET SEQRES 18 A 385 ALA GLY LEU ASN PHE PRO HIS GLY ILE ALA GLN ALA LEU SEQRES 19 A 385 TRP ALA GLY LYS LEU PHE HIS ILE ASP LEU ASN GLY GLN SEQRES 20 A 385 ASN GLY ILE LYS TYR ASP GLN ASP LEU ARG PHE GLY ALA SEQRES 21 A 385 GLY ASP LEU ARG ALA ALA PHE TRP LEU VAL ASP LEU LEU SEQRES 22 A 385 GLU SER ALA GLY TYR SER GLY PRO ARG HIS PHE ASP PHE SEQRES 23 A 385 LYS PRO PRO ARG THR GLU ASP PHE ASP GLY VAL TRP ALA SEQRES 24 A 385 SER ALA ALA GLY CYS MET ARG ASN TYR LEU ILE LEU LYS SEQRES 25 A 385 GLU ARG ALA ALA ALA PHE ARG ALA ASP PRO GLU VAL GLN SEQRES 26 A 385 GLU ALA LEU ARG ALA SER ARG LEU ASP GLU LEU ALA ARG SEQRES 27 A 385 PRO THR ALA ALA ASP GLY LEU GLN ALA LEU LEU ASP ASP SEQRES 28 A 385 ARG SER ALA PHE GLU GLU PHE ASP VAL ASP ALA ALA ALA SEQRES 29 A 385 ALA ARG GLY MET ALA PHE GLU ARG LEU ASP GLN LEU ALA SEQRES 30 A 385 MET ASP HIS LEU LEU GLY ALA ARG HET MG A 401 1 HET MG A 402 1 HET XYL A 403 22 HET MG A 404 1 HETNAM MG MAGNESIUM ION HETNAM XYL XYLITOL HETSYN XYL D-XYLITOL FORMUL 2 MG 3(MG 2+) FORMUL 4 XYL C5 H12 O5 FORMUL 6 HOH *502(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 GLY A 47 1 13 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 SER A 145 LYS A 149 5 5 HELIX 9 AA9 ASP A 150 GLY A 173 1 24 HELIX 10 AB1 THR A 195 GLU A 204 1 10 HELIX 11 AB2 ARG A 208 GLU A 210 5 3 HELIX 12 AB3 GLU A 217 MET A 223 1 7 HELIX 13 AB4 ASN A 227 ALA A 238 1 12 HELIX 14 AB5 ASP A 264 ALA A 278 1 15 HELIX 15 AB6 ASP A 295 ASP A 323 1 29 HELIX 16 AB7 ASP A 323 SER A 333 1 11 HELIX 17 AB8 ARG A 334 ALA A 339 1 6 HELIX 18 AB9 GLY A 346 ASP A 353 1 8 HELIX 19 AC1 ARG A 354 PHE A 357 5 4 HELIX 20 AC2 ASP A 361 ARG A 368 1 8 HELIX 21 AC3 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 MG MG A 402 1555 1555 2.13 LINK OE2 GLU A 217 MG MG A 401 1555 1555 2.07 LINK OE1 GLU A 217 MG MG A 402 1555 1555 2.03 LINK OE1 GLN A 222 MG MG A 404 1555 1555 2.69 LINK OD2 ASP A 245 MG MG A 402 1555 1555 2.19 LINK OD1AASP A 255 MG MG A 401 1555 1555 2.31 LINK OD2AASP A 255 MG MG A 401 1555 1555 2.31 LINK OD2BASP A 255 MG MG A 401 1555 1555 2.60 LINK OD1 ASP A 257 MG MG A 401 1555 1555 2.26 LINK OD2 ASP A 287 MG MG A 402 1555 1555 2.12 LINK MG MG A 401 O HOH A 552 1555 1555 2.21 LINK MG MG A 402 O4 XYL A 403 1555 1555 2.28 LINK MG MG A 402 O2 XYL A 403 1555 1555 2.12 LINK MG MG A 404 O HOH A 742 1555 1555 2.87 CISPEP 1 GLU A 186 PRO A 187 0 22.26 CISPEP 2 GLU A 186 PRO A 187 0 21.47 CISPEP 3 GLU A 186 PRO A 187 0 25.22 CRYST1 92.675 98.626 102.137 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 0.010790 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010139 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009791 0.00000