HEADER HYDROLASE 24-MAR-23 8IUB TITLE CRYSTAL STRUCTURE OF GH66 ENDODEXTRANASE FROM FLAVOBACTERIUM TITLE 2 JOHNSONIAE IN COMPLEX WITH ISOMALTOTRIOSE COMPND MOL_ID: 1; COMPND 2 MOLECULE: CANDIDATE DEXTRANASE GLYCOSIDE HYDROLASE FAMILY 66; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FLAVOBACTERIUM JOHNSONIAE UW101; SOURCE 3 ORGANISM_TAXID: 376686; SOURCE 4 ATCC: 17061; SOURCE 5 GENE: FJOH_4431; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS GLYCOSIDE HYDROLASE, GH66, DEXTRAN, TIM-BARREL, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.NAKAMURA,T.MIYAZAKI REVDAT 2 12-JUL-23 8IUB 1 JRNL REVDAT 1 14-JUN-23 8IUB 0 JRNL AUTH S.NAKAMURA,R.KURATA,T.TONOZUKA,K.FUNANE,E.Y.PARK,T.MIYAZAKI JRNL TITL BACTEROIDOTA POLYSACCHARIDE UTILIZATION SYSTEM FOR BRANCHED JRNL TITL 2 DEXTRAN EXOPOLYSACCHARIDES FROM LACTIC ACID BACTERIA. JRNL REF J.BIOL.CHEM. V. 299 04885 2023 JRNL REFN ESSN 1083-351X JRNL PMID 37269952 JRNL DOI 10.1016/J.JBC.2023.104885 REMARK 2 REMARK 2 RESOLUTION. 1.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0405 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.57 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 172910 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.163 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.016 REMARK 3 FREE R VALUE TEST SET COUNT : 8674 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) : 1.18 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.21 REMARK 3 REFLECTION IN BIN (WORKING SET) : 11947 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.06 REMARK 3 BIN R VALUE (WORKING SET) : 0.2320 REMARK 3 BIN FREE R VALUE SET COUNT : 597 REMARK 3 BIN FREE R VALUE : 0.2700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4341 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 42 REMARK 3 SOLVENT ATOMS : 540 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.53 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.31800 REMARK 3 B22 (A**2) : 0.52800 REMARK 3 B33 (A**2) : -0.21000 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): 0.040 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.040 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.031 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.542 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.964 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4542 ; 0.010 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 4122 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6182 ; 1.648 ; 1.644 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9498 ; 0.567 ; 1.574 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 557 ; 7.268 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 10 ;10.228 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 731 ;13.328 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 664 ; 0.086 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5335 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1089 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 870 ; 0.250 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 63 ; 0.158 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2254 ; 0.187 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 379 ; 0.126 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 7 ; 0.076 ; 0.200 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): 2213 ; 0.474 ; 0.648 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2213 ; 0.474 ; 0.648 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2775 ; 0.696 ; 1.167 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2776 ; 0.696 ; 1.167 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2329 ; 0.552 ; 0.766 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2326 ; 0.549 ; 0.764 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3407 ; 0.774 ; 1.358 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3402 ; 0.770 ; 1.354 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 8664 ; 3.339 ; 3.000 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 41 A 116 REMARK 3 ORIGIN FOR THE GROUP (A): -7.5920 34.1368 -51.7952 REMARK 3 T TENSOR REMARK 3 T11: 0.1875 T22: 0.0891 REMARK 3 T33: 0.0760 T12: -0.0185 REMARK 3 T13: -0.0067 T23: 0.0042 REMARK 3 L TENSOR REMARK 3 L11: 1.4980 L22: 2.5160 REMARK 3 L33: 2.4578 L12: 0.2330 REMARK 3 L13: -0.0242 L23: -0.2148 REMARK 3 S TENSOR REMARK 3 S11: -0.0308 S12: 0.2671 S13: 0.0147 REMARK 3 S21: -0.5477 S22: 0.0421 S23: -0.0758 REMARK 3 S31: -0.2715 S32: 0.1633 S33: -0.0113 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 117 A 586 REMARK 3 ORIGIN FOR THE GROUP (A): 0.8040 18.0762 -30.1620 REMARK 3 T TENSOR REMARK 3 T11: 0.0027 T22: 0.0156 REMARK 3 T33: 0.0746 T12: 0.0015 REMARK 3 T13: 0.0075 T23: 0.0165 REMARK 3 L TENSOR REMARK 3 L11: 0.3822 L22: 0.7579 REMARK 3 L33: 1.0095 L12: -0.0156 REMARK 3 L13: -0.0415 L23: 0.3579 REMARK 3 S TENSOR REMARK 3 S11: -0.0254 S12: -0.0021 S13: -0.0897 REMARK 3 S21: 0.0131 S22: 0.0172 S23: 0.0264 REMARK 3 S31: 0.0338 S32: 0.0206 S33: 0.0082 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 8IUB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-APR-23. REMARK 100 THE DEPOSITION ID IS D_1300036256. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAY-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5-9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 173012 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.180 REMARK 200 RESOLUTION RANGE LOW (A) : 45.780 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : 0.06300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.20 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.97500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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 (%): 39.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS-HCL, PH 8.5-9.0, 200MM REMARK 280 LITHIUM SULFATE, 20% PEG 4000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 20.95550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 68.67700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.52900 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 68.67700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.95550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.52900 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 11 REMARK 465 GLY A 12 REMARK 465 SER A 13 REMARK 465 SER A 14 REMARK 465 HIS A 15 REMARK 465 HIS A 16 REMARK 465 HIS A 17 REMARK 465 HIS A 18 REMARK 465 HIS A 19 REMARK 465 HIS A 20 REMARK 465 SER A 21 REMARK 465 SER A 22 REMARK 465 GLY A 23 REMARK 465 LEU A 24 REMARK 465 VAL A 25 REMARK 465 PRO A 26 REMARK 465 ARG A 27 REMARK 465 GLY A 28 REMARK 465 SER A 29 REMARK 465 HIS A 30 REMARK 465 MET A 31 REMARK 465 ALA A 32 REMARK 465 SER A 33 REMARK 465 ALA A 34 REMARK 465 GLU A 35 REMARK 465 ASP A 36 REMARK 465 ALA A 37 REMARK 465 VAL A 38 REMARK 465 THR A 39 REMARK 465 ALA A 40 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 173 H LEU A 224 1.35 REMARK 500 OD2 ASP A 310 HD21 ASN A 313 1.58 REMARK 500 HH11 ARG A 71 O HOH A 704 1.59 REMARK 500 REMARK 500 REMARK: NULL 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 941 O HOH A 972 1455 2.18 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 TYR A 134 CB - CG - CD1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 193 NE - CZ - NH1 ANGL. DEV. = -3.1 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 SER A 85 -94.80 -130.43 REMARK 500 SER A 85 -80.46 -147.28 REMARK 500 SER A 138 -6.23 -144.52 REMARK 500 GLN A 174 78.45 -156.63 REMARK 500 TYR A 221 25.48 -156.46 REMARK 500 ASN A 245 -76.26 -91.51 REMARK 500 ASP A 286 43.82 -84.56 REMARK 500 ASP A 310 75.35 18.86 REMARK 500 ALA A 394 0.11 -66.08 REMARK 500 GLU A 421 -17.68 -145.07 REMARK 500 ARG A 462 54.48 -150.19 REMARK 500 ASP A 476 4.67 -150.39 REMARK 500 SER A 483 -131.56 -127.08 REMARK 500 GLN A 578 -73.05 -118.27 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 193 0.12 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 NA A 602 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 119 O REMARK 620 2 THR A 119 OG1 77.6 REMARK 620 3 GLU A 449 OE1 166.7 92.2 REMARK 620 4 ASP A 452 OD2 88.2 115.3 104.0 REMARK 620 5 HOH A 805 O 84.8 83.3 85.6 158.2 REMARK 620 6 HOH A1145 O 90.5 157.6 96.2 82.7 76.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 604 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 139 O REMARK 620 2 TYR A 203 OH 116.4 REMARK 620 3 GLU A 424 OE1 94.2 116.9 REMARK 620 4 HOH A 889 O 119.2 104.5 105.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 603 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 293 OD1 REMARK 620 2 ASP A 293 OD2 54.5 REMARK 620 3 GLN A 294 O 82.7 94.9 REMARK 620 4 HOH A 933 O 140.6 163.9 93.3 REMARK 620 5 HOH A 986 O 83.0 92.4 155.9 85.6 REMARK 620 N 1 2 3 4 DBREF 8IUB A 34 586 UNP A5FBI2 A5FBI2_FLAJ1 34 586 SEQADV 8IUB MET A 11 UNP A5FBI2 INITIATING METHIONINE SEQADV 8IUB GLY A 12 UNP A5FBI2 EXPRESSION TAG SEQADV 8IUB SER A 13 UNP A5FBI2 EXPRESSION TAG SEQADV 8IUB SER A 14 UNP A5FBI2 EXPRESSION TAG SEQADV 8IUB HIS A 15 UNP A5FBI2 EXPRESSION TAG SEQADV 8IUB HIS A 16 UNP A5FBI2 EXPRESSION TAG SEQADV 8IUB HIS A 17 UNP A5FBI2 EXPRESSION TAG SEQADV 8IUB HIS A 18 UNP A5FBI2 EXPRESSION TAG SEQADV 8IUB HIS A 19 UNP A5FBI2 EXPRESSION TAG SEQADV 8IUB HIS A 20 UNP A5FBI2 EXPRESSION TAG SEQADV 8IUB SER A 21 UNP A5FBI2 EXPRESSION TAG SEQADV 8IUB SER A 22 UNP A5FBI2 EXPRESSION TAG SEQADV 8IUB GLY A 23 UNP A5FBI2 EXPRESSION TAG SEQADV 8IUB LEU A 24 UNP A5FBI2 EXPRESSION TAG SEQADV 8IUB VAL A 25 UNP A5FBI2 EXPRESSION TAG SEQADV 8IUB PRO A 26 UNP A5FBI2 EXPRESSION TAG SEQADV 8IUB ARG A 27 UNP A5FBI2 EXPRESSION TAG SEQADV 8IUB GLY A 28 UNP A5FBI2 EXPRESSION TAG SEQADV 8IUB SER A 29 UNP A5FBI2 EXPRESSION TAG SEQADV 8IUB HIS A 30 UNP A5FBI2 EXPRESSION TAG SEQADV 8IUB MET A 31 UNP A5FBI2 EXPRESSION TAG SEQADV 8IUB ALA A 32 UNP A5FBI2 EXPRESSION TAG SEQADV 8IUB SER A 33 UNP A5FBI2 EXPRESSION TAG SEQRES 1 A 576 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 576 LEU VAL PRO ARG GLY SER HIS MET ALA SER ALA GLU ASP SEQRES 3 A 576 ALA VAL THR ALA LYS ILE THR LEU LYS THR ASP LYS ALA SEQRES 4 A 576 SER TYR LYS PRO GLY GLU THR VAL ASN PHE THR ALA ASP SEQRES 5 A 576 LYS VAL PHE ASN SER SER LEU ILE ARG TYR THR HIS LEU SEQRES 6 A 576 GLY LYS VAL ILE LYS GLU GLU THR PHE SER GLY THR SER SEQRES 7 A 576 TRP SER TRP LEU PRO PRO SER ASP ASP PHE GLN GLY TYR SEQRES 8 A 576 MET VAL ALA ILE TYR GLN THR ASN THR ASP GLY THR GLN SEQRES 9 A 576 THR ILE LEU GLY THR VAL GLY ILE ASP VAL SER SER ASP SEQRES 10 A 576 TRP ALA LYS PHE PRO ARG TYR GLY PHE LEU SER GLU PHE SEQRES 11 A 576 GLY ASN ILE SER GLU SER ASP ARG ALA ALA VAL ILE ASP SEQRES 12 A 576 ASN LEU LYS ASP TYR HIS ILE ASN GLY ILE GLN PHE TYR SEQRES 13 A 576 ASP TRP GLN TYR ARG GLN HIS GLN PRO LEU ALA GLY THR SEQRES 14 A 576 VAL SER ASN PRO MET PRO VAL TRP ASN ASP ILE ILE ASN SEQRES 15 A 576 ARG GLU VAL TYR GLY SER THR VAL SER GLY TYR ILE ALA SEQRES 16 A 576 GLN ALA HIS SER LYS ASN MET LYS ALA MET PHE TYR ASN SEQRES 17 A 576 LEU ALA TYR GLY VAL LEU ASN ASP TYR ASP PRO ASN LEU SEQRES 18 A 576 ILE LYS GLN GLN GLN PHE VAL TYR LYS ASP ALA ASN HIS SEQRES 19 A 576 ASN ASP LYS ASP LYS HIS GLU LEU GLY TRP PRO PHE ILE SEQRES 20 A 576 SER ASN ILE TYR ILE THR ASP PRO ALA ASN THR ALA TRP SEQRES 21 A 576 GLN ASN TYR LEU ALA GLN LYS ASN ASP ASP VAL TYR LYS SEQRES 22 A 576 VAL TYR ASP PHE ASP GLY PHE HIS ILE ASP GLN LEU GLY SEQRES 23 A 576 ASP ARG GLY ASN VAL PHE ARG TYR ASP GLY THR ASN ALA SEQRES 24 A 576 ASP LEU LYS ASN ALA PHE PRO SER PHE ILE SER ALA MET SEQRES 25 A 576 LYS SER ALA ASN THR ASN LYS LYS LEU VAL MET ASN ALA SEQRES 26 A 576 VAL ASN GLN TYR GLY GLN LYS GLU ILE ALA GLY LYS GLU SEQRES 27 A 576 LEU ASP PHE LEU TYR THR GLU VAL TRP SER PRO ASN GLU SEQRES 28 A 576 GLY PHE LYS ASP LEU THR GLN VAL LEU THR ASP ASN ALA SEQRES 29 A 576 ALA TYR SER ASN ASN SER LYS ASN THR VAL LEU ALA ALA SEQRES 30 A 576 TYR MET ASN TYR ASN LYS ALA ASN ASN GLN GLY MET PHE SEQRES 31 A 576 ASN THR PRO GLY VAL LEU LEU THR ASP ALA VAL ILE PHE SEQRES 32 A 576 ALA PHE GLY GLY SER HIS LEU GLU LEU GLY GLU HIS MET SEQRES 33 A 576 LEU GLY LYS GLU TYR PHE PRO ASN LYS ASN LEU SER MET SEQRES 34 A 576 SER ALA GLU LEU LYS SER SER LEU LEU GLU TYR TYR ASP SEQRES 35 A 576 PHE MET THR ALA TYR GLN ASN LEU LEU ARG ASP GLY GLY SEQRES 36 A 576 THR TYR THR ASN PRO THR ILE ALA THR GLY ASP GLY LYS SEQRES 37 A 576 LEU ASN LEU GLY SER TRP PRO PRO THR MET GLY LYS VAL SEQRES 38 A 576 ALA ALA VAL GLY LYS GLN VAL GLY SER ARG GLU ILE ILE SEQRES 39 A 576 HIS LEU LEU ASN PHE THR ASN ALA ASN SER LEU ASN TRP SEQRES 40 A 576 ARG ASP THR ASP GLY THR GLN ASN VAL PRO ASP LEU ILE SEQRES 41 A 576 LYS GLN ALA MET LEU ASN LEU ASN HIS SER GLY LYS VAL SEQRES 42 A 576 THR LYS ILE TRP TYR ALA SER PRO ASP TYR ASN GLY GLY SEQRES 43 A 576 ALA ALA VAL GLU LEU SER PHE SER GLN ASN GLY GLU LYS SEQRES 44 A 576 VAL ASN PHE LYS VAL PRO VAL LEU GLN TYR TRP ALA MET SEQRES 45 A 576 ILE VAL VAL GLU HET GLC B 1 24 HET GLC B 2 22 HET GLC B 3 22 HET SO4 A 601 5 HET NA A 602 1 HET NA A 603 1 HET NA A 604 1 HETNAM GLC ALPHA-D-GLUCOPYRANOSE HETNAM SO4 SULFATE ION HETNAM NA SODIUM ION HETSYN GLC ALPHA-D-GLUCOSE; D-GLUCOSE; GLUCOSE FORMUL 2 GLC 3(C6 H12 O6) FORMUL 3 SO4 O4 S 2- FORMUL 4 NA 3(NA 1+) FORMUL 7 HOH *540(H2 O) HELIX 1 AA1 SER A 144 TYR A 158 1 15 HELIX 2 AA2 GLY A 197 LYS A 210 1 14 HELIX 3 AA3 LYS A 233 PHE A 237 5 5 HELIX 4 AA4 ASN A 267 TYR A 285 1 19 HELIX 5 AA5 ASP A 310 ASN A 313 5 4 HELIX 6 AA6 ALA A 314 ASN A 326 1 13 HELIX 7 AA7 GLY A 340 ALA A 345 1 6 HELIX 8 AA8 GLY A 362 SER A 377 1 16 HELIX 9 AA9 ASN A 392 ASN A 396 5 5 HELIX 10 AB1 ASN A 401 PHE A 415 1 15 HELIX 11 AB2 SER A 440 TYR A 457 1 18 HELIX 12 AB3 TYR A 457 ARG A 462 1 6 HELIX 13 AB4 TYR A 553 ALA A 557 5 5 SHEET 1 AA1 3 LEU A 44 THR A 46 0 SHEET 2 AA1 3 VAL A 57 ALA A 61 -1 O THR A 60 N LYS A 45 SHEET 3 AA1 3 SER A 88 TRP A 91 -1 O TRP A 91 N VAL A 57 SHEET 1 AA2 4 LYS A 77 THR A 83 0 SHEET 2 AA2 4 SER A 68 HIS A 74 -1 N ILE A 70 O GLU A 82 SHEET 3 AA2 4 GLN A 99 THR A 108 -1 O MET A 102 N THR A 73 SHEET 4 AA2 4 GLN A 114 VAL A 124 -1 O LEU A 117 N ILE A 105 SHEET 1 AA3 8 TYR A 134 LEU A 137 0 SHEET 2 AA3 8 GLY A 162 PHE A 165 1 O GLN A 164 N GLY A 135 SHEET 3 AA3 8 LYS A 213 LEU A 219 1 O MET A 215 N ILE A 163 SHEET 4 AA3 8 GLY A 289 ASP A 293 1 O ASP A 293 N ASN A 218 SHEET 5 AA3 8 LYS A 330 VAL A 336 1 O VAL A 332 N ILE A 292 SHEET 6 AA3 8 LEU A 352 GLU A 355 1 O TYR A 353 N ALA A 335 SHEET 7 AA3 8 THR A 383 ALA A 386 1 O VAL A 384 N LEU A 352 SHEET 8 AA3 8 SER A 418 HIS A 419 1 O SER A 418 N LEU A 385 SHEET 1 AA4 2 VAL A 186 ASN A 188 0 SHEET 2 AA4 2 GLU A 194 TYR A 196 -1 O VAL A 195 N TRP A 187 SHEET 1 AA5 3 GLY A 222 VAL A 223 0 SHEET 2 AA5 3 ILE A 260 ILE A 262 -1 O TYR A 261 N VAL A 223 SHEET 3 AA5 3 LYS A 249 HIS A 250 -1 N HIS A 250 O ILE A 260 SHEET 1 AA6 2 GLY A 398 MET A 399 0 SHEET 2 AA6 2 LEU A 437 SER A 438 1 O SER A 438 N GLY A 398 SHEET 1 AA7 3 THR A 466 THR A 468 0 SHEET 2 AA7 3 VAL A 491 VAL A 498 -1 O GLN A 497 N THR A 466 SHEET 3 AA7 3 LEU A 481 GLY A 482 1 N GLY A 482 O VAL A 491 SHEET 1 AA8 6 THR A 466 THR A 468 0 SHEET 2 AA8 6 VAL A 491 VAL A 498 -1 O GLN A 497 N THR A 466 SHEET 3 AA8 6 ARG A 501 ASN A 508 -1 O LEU A 507 N ALA A 492 SHEET 4 AA8 6 TRP A 580 GLU A 586 -1 O ILE A 583 N ILE A 504 SHEET 5 AA8 6 LYS A 545 ALA A 549 -1 N TRP A 547 O VAL A 584 SHEET 6 AA8 6 VAL A 559 LEU A 561 -1 O LEU A 561 N ILE A 546 SHEET 1 AA9 4 ILE A 472 THR A 474 0 SHEET 2 AA9 4 ILE A 530 ASN A 538 -1 O ASN A 536 N ALA A 473 SHEET 3 AA9 4 LYS A 569 LEU A 577 -1 O VAL A 570 N LEU A 537 SHEET 4 AA9 4 SER A 564 ASN A 566 -1 N ASN A 566 O LYS A 569 LINK O6 GLC B 1 C1 GLC B 2 1555 1555 1.47 LINK O6 GLC B 2 C1 GLC B 3 1555 1555 1.46 LINK O THR A 119 NA NA A 602 1555 1555 2.59 LINK OG1 THR A 119 NA NA A 602 1555 1555 2.34 LINK O GLU A 139 NA NA A 604 1555 1555 2.76 LINK OH TYR A 203 NA NA A 604 1555 1555 2.66 LINK OD1 ASP A 293 NA NA A 603 1555 1555 2.40 LINK OD2 ASP A 293 NA NA A 603 1555 1555 2.41 LINK O GLN A 294 NA NA A 603 1555 1555 2.44 LINK OE1 GLU A 424 NA NA A 604 1555 1555 2.68 LINK OE1 GLU A 449 NA NA A 602 1555 1555 2.29 LINK OD2 ASP A 452 NA NA A 602 1555 1555 2.30 LINK NA NA A 602 O HOH A 805 1555 1555 2.77 LINK NA NA A 602 O HOH A1145 1555 1555 2.42 LINK NA NA A 603 O HOH A 933 1555 1555 2.34 LINK NA NA A 603 O HOH A 986 1555 1555 2.34 LINK NA NA A 604 O HOH A 889 1555 1555 2.79 CISPEP 1 TRP A 254 PRO A 255 0 1.77 CISPEP 2 SER A 358 PRO A 359 0 6.00 CISPEP 3 TRP A 484 PRO A 485 0 -0.48 CRYST1 41.911 91.058 137.354 90.00 90.00 90.00 P 21 21 21 4 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 0.023860 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010982 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007280 0.00000