HEADER ISOMERASE 16-JUN-15 5AVH TITLE THE 0.90 ANGSTROM STRUCTURE (I222) OF GLUCOSE ISOMERASE CRYSTALLIZED TITLE 2 IN HIGH-STRENGTH AGAROSE HYDROGEL 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; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOMYCES RUBIGINOSUS; SOURCE 3 ORGANISM_TAXID: 1929; SOURCE 4 GENE: XYLA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_COMMON: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS XYLOSE ISOMERASE, HYDROGEL, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.SUGIYAMA,N.SHIMIZU,N.MARUYAMA,G.SAZAKI,H.ADACHI,K.TAKANO, AUTHOR 2 S.MURAKAMI,T.INOUE,Y.MORI,H.MATSUMURA REVDAT 3 20-MAR-24 5AVH 1 REMARK REVDAT 2 19-FEB-20 5AVH 1 SOURCE REMARK REVDAT 1 08-JUL-15 5AVH 0 JRNL AUTH S.SUGIYAMA,M.MARUYAMA,G.SAZAKI,M.HIROSE,H.ADACHI,K.TAKANO, JRNL AUTH 2 S.MURAKAMI,T.INOUE,Y.MORI,H.MATSUMURA JRNL TITL GROWTH OF PROTEIN CRYSTALS IN HYDROGELS PREVENTS OSMOTIC JRNL TITL 2 SHOCK JRNL REF J.AM.CHEM.SOC. V. 134 5786 2012 JRNL REFN ESSN 1520-5126 JRNL PMID 22435400 JRNL DOI 10.1021/JA301584Y REMARK 2 REMARK 2 RESOLUTION. 0.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 0.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 3 NUMBER OF REFLECTIONS : 300000 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) : 0.117 REMARK 3 R VALUE (WORKING SET) : 0.116 REMARK 3 FREE R VALUE : 0.127 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 16000 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 0.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 0.92 REMARK 3 REFLECTION IN BIN (WORKING SET) : 20000 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.15 REMARK 3 BIN R VALUE (WORKING SET) : 0.2250 REMARK 3 BIN FREE R VALUE SET COUNT : 1213 REMARK 3 BIN FREE R VALUE : 0.2370 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3042 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 515 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.06000 REMARK 3 B22 (A**2) : 0.13000 REMARK 3 B33 (A**2) : -0.20000 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): 0.013 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.014 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.009 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.344 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.981 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.979 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3492 ; 0.023 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3210 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4762 ; 2.122 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7383 ; 2.328 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 446 ; 5.823 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 196 ;33.326 ;23.112 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 562 ;11.994 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 42 ;17.250 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 478 ; 0.123 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4196 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 876 ; 0.011 ; 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): 1721 ; 0.849 ; 0.690 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1720 ; 0.828 ; 0.688 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2188 ; 0.976 ; 1.043 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2189 ; 1.001 ; 1.044 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1771 ; 1.913 ; 0.900 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1771 ; 1.905 ; 0.899 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2574 ; 2.182 ; 1.293 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4661 ; 2.420 ; 7.284 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4281 ; 1.954 ; 6.395 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 6702 ;11.590 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 155 ;17.766 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 7094 ; 5.589 ; 5.000 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 5AVH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1300000020. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.70000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS V REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 325304 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.92 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.35400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.380 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL 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 (%): 54.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL (PH 7.0), 10% (V/V) MPD, REMARK 280 0.1M CA ACETATE, MICROBATCH, 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 46.63400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 48.79400 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 51.24500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 46.63400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 48.79400 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 51.24500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 46.63400 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 48.79400 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 51.24500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 46.63400 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 48.79400 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 51.24500 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 562 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 787 LIES ON A SPECIAL POSITION. 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 GLU A 67 CD GLU A 67 OE2 0.071 REMARK 500 GLU A 186 CD GLU A 186 OE2 -0.094 REMARK 500 GLU A 207 CD GLU A 207 OE1 -0.089 REMARK 500 GLN A 249 C ASN A 250 N 0.159 REMARK 500 ASN A 250 N ASN A 250 CA 0.126 REMARK 500 ASN A 250 CG ASN A 250 ND2 0.203 REMARK 500 ASN A 250 C ASN A 250 O 0.503 REMARK 500 TYR A 254 CG TYR A 254 CD2 -0.100 REMARK 500 TYR A 254 CE1 TYR A 254 CZ -0.095 REMARK 500 SER A 277 CA SER A 277 CB -0.183 REMARK 500 SER A 277 CA SER A 277 CB 0.111 REMARK 500 SER A 277 CB SER A 277 OG -0.173 REMARK 500 ARG A 368 CZ ARG A 368 NH1 0.096 REMARK 500 ARG A 368 CZ ARG A 368 NH2 0.106 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 23 CG - CD - NE ANGL. DEV. = -15.7 DEGREES REMARK 500 ARG A 23 NE - CZ - NH1 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 41 NE - CZ - NH1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 41 NE - CZ - NH2 ANGL. DEV. = -6.4 DEGREES REMARK 500 ARG A 76 NE - CZ - NH2 ANGL. DEV. = -5.3 DEGREES REMARK 500 GLN A 249 O - C - N ANGL. DEV. = 13.8 DEGREES REMARK 500 ASN A 250 C - N - CA ANGL. DEV. = -18.5 DEGREES REMARK 500 ASP A 257 CB - CG - OD1 ANGL. DEV. = -5.7 DEGREES REMARK 500 SER A 277 CB - CA - C ANGL. DEV. = 13.8 DEGREES REMARK 500 ASP A 297 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 368 CD - NE - CZ ANGL. DEV. = 11.6 DEGREES REMARK 500 ARG A 368 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG A 368 NE - CZ - NH2 ANGL. DEV. = -9.3 DEGREES REMARK 500 ARG A 374 NE - CZ - NH1 ANGL. DEV. = -4.0 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 THR A 17 -75.86 -86.12 REMARK 500 PHE A 94 -39.91 -140.88 REMARK 500 PHE A 94 -16.56 -140.88 REMARK 500 GLU A 186 101.75 85.06 REMARK 500 GLU A 186 100.19 87.78 REMARK 500 GLU A 186 105.33 75.37 REMARK 500 ASN A 247 -169.83 -169.96 REMARK 500 LYS A 253 -171.36 -176.77 REMARK 500 TYR A 254 155.43 -46.88 REMARK 500 ALA A 343 64.54 -150.71 REMARK 500 PHE A 357 -80.62 -156.90 REMARK 500 PHE A 357 -76.29 -156.90 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 0.09 SIDE CHAIN REMARK 500 ARG A 284 0.08 SIDE CHAIN 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 GLY A 22 10.93 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 A 912 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A 913 DISTANCE = 5.87 ANGSTROMS REMARK 525 HOH A 914 DISTANCE = 6.35 ANGSTROMS REMARK 525 HOH A 915 DISTANCE = 6.98 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5AVD RELATED DB: PDB REMARK 900 THE 0.86 ANGSTROM STRUCTURE OF ELASTASE CRYSTALLIZED IN HIGH- REMARK 900 STRENGTH AGAROSE HYDROGEL REMARK 900 RELATED ID: 5AVG RELATED DB: PDB REMARK 900 THE 0.95 ANGSTROM STRUCTURE OF THAUMATIN CRYSTALLIZED IN HIGH- REMARK 900 STRENGTH AGAROSE HYDROGEL DBREF 5AVH A 2 387 UNP P24300 XYLA_STRRU 2 387 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 ARG 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 FORMUL 2 HOH *515(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 ALA A 278 1 15 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 PHE A 53 O THR A 90 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 CISPEP 1 GLU A 186 PRO A 187 0 24.25 CISPEP 2 GLU A 186 PRO A 187 0 21.98 CISPEP 3 GLU A 186 PRO A 187 0 22.74 CRYST1 93.268 97.588 102.490 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 0.010722 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010247 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009757 0.00000