HEADER ISOMERASE 23-JUN-15 5AVN TITLE THE 1.03 ANGSTROM STRUCTURE (P212121) OF GLUCOSE ISOMERASE TITLE 2 CRYSTALLIZED IN HIGH-STRENGTH AGAROSE HYDROGEL COMPND MOL_ID: 1; COMPND 2 MOLECULE: XYLOSE ISOMERASE; COMPND 3 CHAIN: A, B; 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_TAXID: 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 08-NOV-23 5AVN 1 LINK REVDAT 2 26-FEB-20 5AVN 1 SOURCE REMARK REVDAT 1 08-JUL-15 5AVN 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. 1.03 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) : 1.03 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 367026 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) : 0.129 REMARK 3 R VALUE (WORKING SET) : 0.127 REMARK 3 FREE R VALUE : 0.150 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) : 1.03 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.06 REMARK 3 REFLECTION IN BIN (WORKING SET) : 20000 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.76 REMARK 3 BIN R VALUE (WORKING SET) : 0.2290 REMARK 3 BIN FREE R VALUE SET COUNT : 1441 REMARK 3 BIN FREE R VALUE : 0.2420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6092 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 24 REMARK 3 SOLVENT ATOMS : 1058 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.58000 REMARK 3 B22 (A**2) : -0.29000 REMARK 3 B33 (A**2) : -0.29000 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): 0.022 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.023 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.017 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.743 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.980 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.974 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6721 ; 0.022 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 6191 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9160 ; 2.037 ; 1.956 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14231 ; 0.941 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 864 ; 5.807 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 366 ;33.478 ;22.923 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1081 ;11.579 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 81 ;15.552 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 923 ; 0.129 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8059 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 1690 ; 0.001 ; 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): 3330 ; 1.907 ; 0.863 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3329 ; 1.651 ; 0.859 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4236 ; 1.862 ; 1.298 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 4237 ; 1.863 ; 1.301 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3391 ; 2.132 ; 1.036 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3379 ; 2.063 ; 1.034 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4906 ; 2.722 ; 1.506 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 9480 ; 2.740 ; 8.918 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 8990 ; 2.463 ; 8.285 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 12912 ; 8.439 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 227 ;19.816 ; 5.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 13775 ; 6.062 ; 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 5AVN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JUN-15. REMARK 100 THE DEPOSITION ID IS D_1300000055. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-SEP-08 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 : 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) : 0.90 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 386570 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.030 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 (%) : 99.2 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.03 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.40700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 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: 1O1H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES-NAOH (PH 7.5), 1.75 M REMARK 280 (NH4)2SO4, MICROBATCH, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 47.04100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 49.14250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 47.04100 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 49.14250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2, 3 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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: 3 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 29310 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -108.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 513 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 938 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 515 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 PRO A 7 CA PRO A 7 C -0.154 REMARK 500 ASP A 24 C PRO A 25 N -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 ASN A 250 CA - C - N ANGL. DEV. = -12.8 DEGREES REMARK 500 ARG A 266 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 MET A 370 CG - SD - CE ANGL. DEV. = 16.9 DEGREES REMARK 500 ARG B 42 NE - CZ - NH1 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG B 266 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG B 266 NE - CZ - NH2 ANGL. DEV. = -6.8 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 -75.37 -86.18 REMARK 500 PHE A 94 -29.68 -142.01 REMARK 500 GLU A 186 102.75 83.70 REMARK 500 GLU A 186 106.82 83.29 REMARK 500 TYR A 254 156.35 -47.25 REMARK 500 TYR A 254 156.35 -45.94 REMARK 500 PHE A 357 -73.77 -147.27 REMARK 500 THR B 17 -74.56 -89.07 REMARK 500 PHE B 94 -29.38 -142.48 REMARK 500 GLU B 186 100.00 91.88 REMARK 500 GLU B 186 109.53 80.60 REMARK 500 ASN B 247 -170.37 -170.22 REMARK 500 TYR B 254 157.28 -48.78 REMARK 500 TYR B 254 157.28 -46.95 REMARK 500 ALA B 343 62.69 -152.04 REMARK 500 PHE B 357 -73.88 -152.20 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 B 284 0.08 SIDE CHAIN 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 A1031 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH A1032 DISTANCE = 6.45 ANGSTROMS REMARK 525 HOH B1026 DISTANCE = 6.18 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 CA A 402 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 181 OE2 REMARK 620 2 GLU A 217 OE1 108.0 REMARK 620 3 ASP A 245 OD2 106.3 123.5 REMARK 620 4 ASP A 287 OD2 116.0 98.8 104.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 401 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 217 OE2 REMARK 620 2 HIS A 220 NE2 78.3 REMARK 620 3 ASP A 255 OD1 104.9 90.3 REMARK 620 4 ASP A 255 OD2 158.5 89.0 57.3 REMARK 620 5 ASP A 257 OD1 90.8 168.0 87.7 99.8 REMARK 620 6 HOH A 675 O 95.8 87.7 158.4 101.1 98.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 402 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 181 OE2 REMARK 620 2 GLU B 217 OE1 110.0 REMARK 620 3 ASP B 245 OD2 104.1 121.7 REMARK 620 4 ASP B 287 OD2 117.0 99.8 105.0 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN B 401 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 217 OE2 REMARK 620 2 HIS B 220 NE2 78.0 REMARK 620 3 ASP B 255 OD1 104.6 89.9 REMARK 620 4 ASP B 255 OD2 158.9 89.5 58.0 REMARK 620 5 ASP B 257 OD1 90.8 167.6 87.7 99.5 REMARK 620 6 HOH B 687 O 94.9 87.5 159.3 101.5 98.9 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MN B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA B 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 404 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5AVH RELATED DB: PDB REMARK 900 THE 0.90 ANGSTROM STRUCTURE (I222) OF GLUCOSE ISOMERASE REMARK 900 CRYSTALLIZED IN HIGH-STRENGTH AGAROSE HYDROGEL 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 5AVN A 2 388 UNP P24300 XYLA_STRRU 2 388 DBREF 5AVN B 2 388 UNP P24300 XYLA_STRRU 2 388 SEQRES 1 A 387 ASN TYR GLN PRO THR PRO GLU ASP ARG PHE THR PHE GLY SEQRES 2 A 387 LEU TRP THR VAL GLY TRP GLN GLY ARG ASP PRO PHE GLY SEQRES 3 A 387 ASP ALA THR ARG ARG ALA LEU ASP PRO VAL GLU SER VAL SEQRES 4 A 387 ARG ARG LEU ALA GLU LEU GLY ALA HIS GLY VAL THR PHE SEQRES 5 A 387 HIS ASP ASP ASP LEU ILE PRO PHE GLY SER SER ASP SER SEQRES 6 A 387 GLU ARG GLU GLU HIS VAL LYS ARG PHE ARG GLN ALA LEU SEQRES 7 A 387 ASP ASP THR GLY MET LYS VAL PRO MET ALA THR THR ASN SEQRES 8 A 387 LEU PHE THR HIS PRO VAL PHE LYS ASP GLY GLY PHE THR SEQRES 9 A 387 ALA ASN ASP ARG ASP VAL ARG ARG TYR ALA LEU ARG LYS SEQRES 10 A 387 THR ILE ARG ASN ILE ASP LEU ALA VAL GLU LEU GLY ALA SEQRES 11 A 387 GLU THR TYR VAL ALA TRP GLY GLY ARG GLU GLY ALA GLU SEQRES 12 A 387 SER GLY GLY ALA LYS ASP VAL ARG ASP ALA LEU ASP ARG SEQRES 13 A 387 MET LYS GLU ALA PHE ASP LEU LEU GLY GLU TYR VAL THR SEQRES 14 A 387 SER GLN GLY TYR ASP ILE ARG PHE ALA ILE GLU PRO LYS SEQRES 15 A 387 PRO ASN GLU PRO ARG GLY ASP ILE LEU LEU PRO THR VAL SEQRES 16 A 387 GLY HIS ALA LEU ALA PHE ILE GLU ARG LEU GLU ARG PRO SEQRES 17 A 387 GLU LEU TYR GLY VAL ASN PRO GLU VAL GLY HIS GLU GLN SEQRES 18 A 387 MET ALA GLY LEU ASN PHE PRO HIS GLY ILE ALA GLN ALA SEQRES 19 A 387 LEU TRP ALA GLY LYS LEU PHE HIS ILE ASP LEU ASN GLY SEQRES 20 A 387 GLN ASN GLY ILE LYS TYR ASP GLN ASP LEU ARG PHE GLY SEQRES 21 A 387 ALA GLY ASP LEU ARG ALA ALA PHE TRP LEU VAL ASP LEU SEQRES 22 A 387 LEU GLU SER ALA GLY TYR SER GLY PRO ARG HIS PHE ASP SEQRES 23 A 387 PHE LYS PRO PRO ARG THR GLU ASP PHE ASP GLY VAL TRP SEQRES 24 A 387 ALA SER ALA ALA GLY CYS MET ARG ASN TYR LEU ILE LEU SEQRES 25 A 387 LYS GLU ARG ALA ALA ALA PHE ARG ALA ASP PRO GLU VAL SEQRES 26 A 387 GLN GLU ALA LEU ARG ALA SER ARG LEU ASP GLU LEU ALA SEQRES 27 A 387 ARG PRO THR ALA ALA ASP GLY LEU GLN ALA LEU LEU ASP SEQRES 28 A 387 ASP ARG SER ALA PHE GLU GLU PHE ASP VAL ASP ALA ALA SEQRES 29 A 387 ALA ALA ARG GLY MET ALA PHE GLU ARG LEU ASP GLN LEU SEQRES 30 A 387 ALA MET ASP HIS LEU LEU GLY ALA ARG GLY SEQRES 1 B 387 ASN TYR GLN PRO THR PRO GLU ASP ARG PHE THR PHE GLY SEQRES 2 B 387 LEU TRP THR VAL GLY TRP GLN GLY ARG ASP PRO PHE GLY SEQRES 3 B 387 ASP ALA THR ARG ARG ALA LEU ASP PRO VAL GLU SER VAL SEQRES 4 B 387 ARG ARG LEU ALA GLU LEU GLY ALA HIS GLY VAL THR PHE SEQRES 5 B 387 HIS ASP ASP ASP LEU ILE PRO PHE GLY SER SER ASP SER SEQRES 6 B 387 GLU ARG GLU GLU HIS VAL LYS ARG PHE ARG GLN ALA LEU SEQRES 7 B 387 ASP ASP THR GLY MET LYS VAL PRO MET ALA THR THR ASN SEQRES 8 B 387 LEU PHE THR HIS PRO VAL PHE LYS ASP GLY GLY PHE THR SEQRES 9 B 387 ALA ASN ASP ARG ASP VAL ARG ARG TYR ALA LEU ARG LYS SEQRES 10 B 387 THR ILE ARG ASN ILE ASP LEU ALA VAL GLU LEU GLY ALA SEQRES 11 B 387 GLU THR TYR VAL ALA TRP GLY GLY ARG GLU GLY ALA GLU SEQRES 12 B 387 SER GLY GLY ALA LYS ASP VAL ARG ASP ALA LEU ASP ARG SEQRES 13 B 387 MET LYS GLU ALA PHE ASP LEU LEU GLY GLU TYR VAL THR SEQRES 14 B 387 SER GLN GLY TYR ASP ILE ARG PHE ALA ILE GLU PRO LYS SEQRES 15 B 387 PRO ASN GLU PRO ARG GLY ASP ILE LEU LEU PRO THR VAL SEQRES 16 B 387 GLY HIS ALA LEU ALA PHE ILE GLU ARG LEU GLU ARG PRO SEQRES 17 B 387 GLU LEU TYR GLY VAL ASN PRO GLU VAL GLY HIS GLU GLN SEQRES 18 B 387 MET ALA GLY LEU ASN PHE PRO HIS GLY ILE ALA GLN ALA SEQRES 19 B 387 LEU TRP ALA GLY LYS LEU PHE HIS ILE ASP LEU ASN GLY SEQRES 20 B 387 GLN ASN GLY ILE LYS TYR ASP GLN ASP LEU ARG PHE GLY SEQRES 21 B 387 ALA GLY ASP LEU ARG ALA ALA PHE TRP LEU VAL ASP LEU SEQRES 22 B 387 LEU GLU SER ALA GLY TYR SER GLY PRO ARG HIS PHE ASP SEQRES 23 B 387 PHE LYS PRO PRO ARG THR GLU ASP PHE ASP GLY VAL TRP SEQRES 24 B 387 ALA SER ALA ALA GLY CYS MET ARG ASN TYR LEU ILE LEU SEQRES 25 B 387 LYS GLU ARG ALA ALA ALA PHE ARG ALA ASP PRO GLU VAL SEQRES 26 B 387 GLN GLU ALA LEU ARG ALA SER ARG LEU ASP GLU LEU ALA SEQRES 27 B 387 ARG PRO THR ALA ALA ASP GLY LEU GLN ALA LEU LEU ASP SEQRES 28 B 387 ASP ARG SER ALA PHE GLU GLU PHE ASP VAL ASP ALA ALA SEQRES 29 B 387 ALA ALA ARG GLY MET ALA PHE GLU ARG LEU ASP GLN LEU SEQRES 30 B 387 ALA MET ASP HIS LEU LEU GLY ALA ARG GLY HET MN A 401 1 HET CA A 402 1 HET SO4 A 403 5 HET SO4 A 404 5 HET MN B 401 1 HET CA B 402 1 HET SO4 B 403 5 HET SO4 B 404 5 HETNAM MN MANGANESE (II) ION HETNAM CA CALCIUM ION HETNAM SO4 SULFATE ION FORMUL 3 MN 2(MN 2+) FORMUL 4 CA 2(CA 2+) FORMUL 5 SO4 4(O4 S 2-) FORMUL 11 HOH *1058(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 GLY A 130 1 23 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 LEU A 384 1 14 HELIX 21 AC3 THR B 6 ASP B 9 5 4 HELIX 22 AC4 LEU B 15 GLY B 19 1 5 HELIX 23 AC5 ASP B 35 LEU B 46 1 12 HELIX 24 AC6 ASP B 55 ILE B 59 1 5 HELIX 25 AC7 SER B 64 GLY B 83 1 20 HELIX 26 AC8 HIS B 96 LYS B 100 5 5 HELIX 27 AC9 ASP B 108 LEU B 129 1 22 HELIX 28 AD1 SER B 145 LYS B 149 5 5 HELIX 29 AD2 ASP B 150 GLN B 172 1 23 HELIX 30 AD3 THR B 195 GLU B 204 1 10 HELIX 31 AD4 ARG B 208 GLU B 210 5 3 HELIX 32 AD5 GLU B 217 MET B 223 1 7 HELIX 33 AD6 ASN B 227 ALA B 238 1 12 HELIX 34 AD7 ASP B 264 GLY B 279 1 16 HELIX 35 AD8 ASP B 295 ASP B 323 1 29 HELIX 36 AD9 ASP B 323 SER B 333 1 11 HELIX 37 AE1 ARG B 334 ARG B 340 1 7 HELIX 38 AE2 GLY B 346 ASP B 353 1 8 HELIX 39 AE3 ARG B 354 PHE B 357 5 4 HELIX 40 AE4 ASP B 361 ARG B 368 1 8 HELIX 41 AE5 ALA B 371 GLY B 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 SHEET 1 AA3 8 TYR B 212 VAL B 214 0 SHEET 2 AA3 8 ARG B 177 ILE B 180 1 N ILE B 180 O GLY B 213 SHEET 3 AA3 8 THR B 133 ALA B 136 1 N TYR B 134 O ARG B 177 SHEET 4 AA3 8 LYS B 85 THR B 90 1 N ALA B 89 O VAL B 135 SHEET 5 AA3 8 GLY B 50 HIS B 54 1 N VAL B 51 O LYS B 85 SHEET 6 AA3 8 PHE B 11 GLY B 14 1 N PHE B 13 O THR B 52 SHEET 7 AA3 8 ARG B 284 PHE B 286 1 O PHE B 286 N THR B 12 SHEET 8 AA3 8 ILE B 244 LEU B 246 1 N LEU B 246 O HIS B 285 SHEET 1 AA4 2 GLY B 142 ALA B 143 0 SHEET 2 AA4 2 ASP B 190 ILE B 191 -1 O ASP B 190 N ALA B 143 LINK OE2 GLU A 181 CA CA A 402 1555 1555 1.92 LINK OE2 GLU A 217 MN MN A 401 1555 1555 2.10 LINK OE1 GLU A 217 CA CA A 402 1555 1555 1.90 LINK NE2 HIS A 220 MN MN A 401 1555 1555 2.38 LINK OD2 ASP A 245 CA CA A 402 1555 1555 1.95 LINK OD1 ASP A 255 MN MN A 401 1555 1555 2.30 LINK OD2 ASP A 255 MN MN A 401 1555 1555 2.25 LINK OD1 ASP A 257 MN MN A 401 1555 1555 2.17 LINK OD2 ASP A 287 CA CA A 402 1555 1555 1.98 LINK MN MN A 401 O HOH A 675 1555 1555 2.13 LINK OE2 GLU B 181 CA CA B 402 1555 1555 1.86 LINK OE2 GLU B 217 MN MN B 401 1555 1555 2.11 LINK OE1 GLU B 217 CA CA B 402 1555 1555 1.90 LINK NE2 HIS B 220 MN MN B 401 1555 1555 2.38 LINK OD2 ASP B 245 CA CA B 402 1555 1555 2.01 LINK OD1 ASP B 255 MN MN B 401 1555 1555 2.29 LINK OD2 ASP B 255 MN MN B 401 1555 1555 2.23 LINK OD1 ASP B 257 MN MN B 401 1555 1555 2.19 LINK OD2 ASP B 287 CA CA B 402 1555 1555 1.93 LINK MN MN B 401 O HOH B 687 1555 1555 2.13 CISPEP 1 GLU A 186 PRO A 187 0 24.67 CISPEP 2 GLU A 186 PRO A 187 0 15.58 CISPEP 3 GLU B 186 PRO B 187 0 23.31 CISPEP 4 GLU B 186 PRO B 187 0 13.11 SITE 1 AC1 5 GLU A 217 HIS A 220 ASP A 255 ASP A 257 SITE 2 AC1 5 HOH A 675 SITE 1 AC2 4 GLU A 181 GLU A 217 ASP A 245 ASP A 287 SITE 1 AC3 5 TRP A 20 GLN A 21 GLY A 22 ARG A 23 SITE 2 AC3 5 HOH A 531 SITE 1 AC4 5 ARG A 23 ASP A 28 ALA A 29 HOH A 551 SITE 2 AC4 5 HOH A 837 SITE 1 AC5 5 GLU B 217 HIS B 220 ASP B 255 ASP B 257 SITE 2 AC5 5 HOH B 687 SITE 1 AC6 4 GLU B 181 GLU B 217 ASP B 245 ASP B 287 SITE 1 AC7 6 TRP B 20 GLN B 21 GLY B 22 ARG B 23 SITE 2 AC7 6 HOH B 549 HOH B 767 SITE 1 AC8 5 ARG B 23 ASP B 28 ALA B 29 HOH B 518 SITE 2 AC8 5 HOH B 768 CRYST1 94.082 98.285 85.777 90.00 90.00 90.00 P 21 21 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 0.010629 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010174 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011658 0.00000