HEADER HYDROLASE 25-JUN-12 4AZB TITLE DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE TITLE 2 PNEUMOCOCCAL EXO-BETA-D-N-ACETYLGLUCOSAMINIDASE, STRH COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-N-ACETYLHEXOSAMINIDASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC MODULE, RESIDUES 181-614; COMPND 5 SYNONYM: GLYCOSIDE HYDROLASE 20; COMPND 6 EC: 3.2.1.52; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 170187; SOURCE 4 STRAIN: TIGR4; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PET28A KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR B.PLUVINAGE,K.A.STUBBS,D.J.VOCADLO,A.B.BORASTON REVDAT 4 20-DEC-23 4AZB 1 REMARK SHEET REVDAT 3 13-NOV-13 4AZB 1 JRNL REVDAT 2 30-OCT-13 4AZB 1 JRNL REVDAT 1 10-JUL-13 4AZB 0 JRNL AUTH B.PLUVINAGE,K.A.STUBBS,D.J.VOCADLO,A.B.BORASTON JRNL TITL INHIBITION OF THE FAMILY 20 GLYCOSIDE HYDROLASE CATALYTIC JRNL TITL 2 MODULES IN THE STREPTOCOCCUS PNEUMONIAE JRNL TITL 3 EXO-BETA-D-N-ACETYLGLUCOSAMINIDASE, STRH. JRNL REF ORG.BIOMOL.CHEM. V. 11 7907 2013 JRNL REFN ISSN 1477-0520 JRNL PMID 24132305 JRNL DOI 10.1039/C3OB41579A REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0102 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 41.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 26882 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) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1428 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1968 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.1820 REMARK 3 BIN FREE R VALUE SET COUNT : 113 REMARK 3 BIN FREE R VALUE : 0.2340 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3180 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 65 REMARK 3 SOLVENT ATOMS : 298 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.10000 REMARK 3 B22 (A**2) : 0.10000 REMARK 3 B33 (A**2) : -0.15000 REMARK 3 B12 (A**2) : 0.05000 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): 0.202 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.164 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.102 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.711 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.937 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3419 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4629 ; 1.109 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 425 ; 5.870 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 164 ;37.514 ;25.488 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 562 ;14.319 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;14.321 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 484 ; 0.073 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2650 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2077 ; 0.498 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3321 ; 0.918 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1342 ; 1.252 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1308 ; 2.017 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL 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): 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 : 1.40 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. U VALUES REFINED INDIVIDUALLY REMARK 4 REMARK 4 4AZB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 25-JUN-12. REMARK 100 THE DEPOSITION ID IS D_1290053032. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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 : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97884 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28340 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 45.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 10.70 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.10 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 2YL6 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 33.86667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 67.73333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 67.73333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 33.86667 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 6750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31510 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -94.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -33.86667 REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, TRP 449 TO GLY REMARK 400 ENGINEERED RESIDUE IN CHAIN A, TYR 450 TO GLY 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 LEU A 563 REMARK 465 ASN A 564 REMARK 465 ARG A 565 REMARK 465 TYR A 566 REMARK 465 THR A 567 REMARK 465 ALA A 568 REMARK 465 GLU A 569 REMARK 465 SER A 570 REMARK 465 VAL A 571 REMARK 465 THR A 572 REMARK 465 ALA A 573 REMARK 465 VAL A 574 REMARK 465 LYS A 575 REMARK 465 GLU A 576 REMARK 465 ALA A 577 REMARK 465 GLU A 578 REMARK 465 LYS A 579 REMARK 465 THR A 606 REMARK 465 VAL A 607 REMARK 465 ASN A 608 REMARK 465 ASN A 609 REMARK 465 LEU A 610 REMARK 465 THR A 611 REMARK 465 LEU A 612 REMARK 465 THR A 613 REMARK 465 PRO A 614 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 320 NZ REMARK 480 LYS A 350 CE NZ REMARK 480 SER A 551 OG REMARK 480 GLU A 553 OE1 OE2 REMARK 480 LYS A 602 CG CD CE NZ 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 OD1 ASN A 364 O HOH A 2165 2.08 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 LYS A 320 CE LYS A 320 NZ -0.881 REMARK 500 LYS A 350 CD LYS A 350 CE 0.711 REMARK 500 SER A 551 CB SER A 551 OG 1.196 REMARK 500 GLU A 553 CD GLU A 553 OE1 -0.336 REMARK 500 GLU A 553 CD GLU A 553 OE2 0.212 REMARK 500 LYS A 602 CB LYS A 602 CG 0.315 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 LYS A 320 CD - CE - NZ ANGL. DEV. = 48.5 DEGREES REMARK 500 LYS A 350 CG - CD - CE ANGL. DEV. = -58.5 DEGREES REMARK 500 SER A 551 CA - CB - OG ANGL. DEV. = -45.8 DEGREES REMARK 500 GLU A 553 OE1 - CD - OE2 ANGL. DEV. = 8.2 DEGREES REMARK 500 GLU A 553 CG - CD - OE2 ANGL. DEV. = -14.9 DEGREES REMARK 500 LYS A 602 CA - CB - CG ANGL. DEV. = 17.9 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 ASN A 225 99.50 -167.23 REMARK 500 ASP A 226 -74.64 60.86 REMARK 500 LYS A 350 -12.03 70.09 REMARK 500 PRO A 560 125.76 -39.70 REMARK 500 SER A 586 32.55 -76.43 REMARK 500 LEU A 603 -56.03 55.28 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 GLU A 553 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN -2-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 19-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE OAN A 1606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1608 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1609 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1610 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1611 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1612 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1613 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1614 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 1615 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2YL5 RELATED DB: PDB REMARK 900 INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR REMARK 900 INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS REMARK 900 RELATED ID: 2YL6 RELATED DB: PDB REMARK 900 INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR REMARK 900 INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS REMARK 900 RELATED ID: 2YL8 RELATED DB: PDB REMARK 900 INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR REMARK 900 INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS REMARK 900 RELATED ID: 2YL9 RELATED DB: PDB REMARK 900 INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR REMARK 900 INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS REMARK 900 RELATED ID: 2YLA RELATED DB: PDB REMARK 900 INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR REMARK 900 INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS REMARK 900 RELATED ID: 2YLL RELATED DB: PDB REMARK 900 INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR REMARK 900 INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS REMARK 900 RELATED ID: 4AZ5 RELATED DB: PDB REMARK 900 DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE REMARK 900 PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH REMARK 900 RELATED ID: 4AZ6 RELATED DB: PDB REMARK 900 DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE REMARK 900 PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH REMARK 900 RELATED ID: 4AZ7 RELATED DB: PDB REMARK 900 DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE REMARK 900 PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH REMARK 900 RELATED ID: 4AZI RELATED DB: PDB REMARK 900 DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE REMARK 900 PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH REMARK 900 RELATED ID: 4AZH RELATED DB: PDB REMARK 900 DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE REMARK 900 PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH REMARK 900 RELATED ID: 4AZG RELATED DB: PDB REMARK 900 DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE REMARK 900 PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH REMARK 900 RELATED ID: 4AZC RELATED DB: PDB REMARK 900 DIFFERENTIAL INHIBITION OF THE TANDEM GH20 CATALYTIC MODULES IN THE REMARK 900 PNEUMOCOCCAL EXO-BETA-D-N- ACETYLGLUCOSAMINIDASE, STRH DBREF 4AZB A 181 614 UNP P49610 STRH_STRPN 181 614 SEQADV 4AZB GLY A 481 UNP B2DIT9 TRP 449 ENGINEERED MUTATION SEQADV 4AZB GLY A 482 UNP B2DIT9 TYR 450 ENGINEERED MUTATION SEQRES 1 A 434 ASN GLU LYS LEU ALA LYS LYS LYS ILE VAL SER ILE ASP SEQRES 2 A 434 ALA GLY ARG LYS TYR PHE SER PRO GLU GLN LEU LYS GLU SEQRES 3 A 434 ILE ILE ASP LYS ALA LYS HIS TYR GLY TYR THR ASP LEU SEQRES 4 A 434 HIS LEU LEU VAL GLY ASN ASP GLY LEU ARG PHE MET LEU SEQRES 5 A 434 ASP ASP MET SER ILE THR ALA ASN GLY LYS THR TYR ALA SEQRES 6 A 434 SER ASP ASP VAL LYS ARG ALA ILE GLU LYS GLY THR ASN SEQRES 7 A 434 ASP TYR TYR ASN ASP PRO ASN GLY ASN HIS LEU THR GLU SEQRES 8 A 434 SER GLN MET THR ASP LEU ILE ASN TYR ALA LYS ASP LYS SEQRES 9 A 434 GLY ILE GLY LEU ILE PRO THR VAL ASN SER PRO GLY HIS SEQRES 10 A 434 MET ASP ALA ILE LEU ASN ALA MET LYS GLU LEU GLY ILE SEQRES 11 A 434 GLN ASN PRO ASN PHE SER TYR PHE GLY LYS LYS SER ALA SEQRES 12 A 434 ARG THR VAL ASP LEU ASP ASN GLU GLN ALA VAL ALA PHE SEQRES 13 A 434 THR LYS ALA LEU ILE ASP LYS TYR ALA ALA TYR PHE ALA SEQRES 14 A 434 LYS LYS THR GLU ILE PHE ASN ILE GLY LEU ASP GLU TYR SEQRES 15 A 434 ALA ASN ASP ALA THR ASP ALA LYS GLY TRP SER VAL LEU SEQRES 16 A 434 GLN ALA ASP LYS TYR TYR PRO ASN GLU GLY TYR PRO VAL SEQRES 17 A 434 LYS GLY TYR GLU LYS PHE ILE ALA TYR ALA ASN ASP LEU SEQRES 18 A 434 ALA ARG ILE VAL LYS SER HIS GLY LEU LYS PRO MET ALA SEQRES 19 A 434 PHE ASN ASP GLY ILE TYR TYR ASN SER ASP THR SER PHE SEQRES 20 A 434 GLY SER PHE ASP LYS ASP ILE ILE VAL SER MET TRP THR SEQRES 21 A 434 GLY GLY TRP GLY GLY TYR ASP VAL ALA SER SER LYS LEU SEQRES 22 A 434 LEU ALA GLU LYS GLY HIS GLN ILE LEU ASN THR ASN ASP SEQRES 23 A 434 ALA TRP TYR TYR VAL LEU GLY ARG ASN ALA ASP GLY GLN SEQRES 24 A 434 GLY GLY GLY ASN LEU ASP GLN GLY LEU ASN GLY ILE LYS SEQRES 25 A 434 ASN THR PRO ILE THR SER VAL PRO LYS THR GLU GLY ALA SEQRES 26 A 434 ASP ILE PRO ILE ILE GLY GLY MET VAL ALA ALA TRP ALA SEQRES 27 A 434 ASP THR PRO SER ALA ARG TYR SER PRO SER ARG LEU PHE SEQRES 28 A 434 LYS LEU MET ARG HIS PHE ALA ASN ALA ASN ALA GLU TYR SEQRES 29 A 434 PHE ALA ALA ASP TYR GLU SER ALA GLU GLN ALA LEU ASN SEQRES 30 A 434 GLU VAL PRO LYS ASP LEU ASN ARG TYR THR ALA GLU SER SEQRES 31 A 434 VAL THR ALA VAL LYS GLU ALA GLU LYS ALA ILE ARG SER SEQRES 32 A 434 LEU ASP SER ASN LEU SER ARG ALA GLN GLN ASP THR ILE SEQRES 33 A 434 ASP GLN ALA ILE ALA LYS LEU GLN GLU THR VAL ASN ASN SEQRES 34 A 434 LEU THR LEU THR PRO HET OAN A1606 50 HET EDO A1607 4 HET EDO A1608 4 HET EDO A1609 4 HET EDO A1610 4 HET EDO A1611 4 HET SO4 A1612 5 HET SO4 A1613 5 HET SO4 A1614 5 HET SO4 A1615 5 HETNAM OAN O-(2-ACETAMIDO-2-DEOXY D-GLUCOPYRANOSYLIDENE) AMINO-N- HETNAM 2 OAN PHENYLCARBAMATE HETNAM EDO 1,2-ETHANEDIOL HETNAM SO4 SULFATE ION HETSYN OAN PUGNAC HETSYN EDO ETHYLENE GLYCOL FORMUL 2 OAN C15 H19 N3 O7 FORMUL 3 EDO 5(C2 H6 O2) FORMUL 8 SO4 4(O4 S 2-) FORMUL 12 HOH *298(H2 O) HELIX 1 1 SER A 200 GLY A 215 1 16 HELIX 2 2 ALA A 245 TYR A 261 1 17 HELIX 3 3 GLU A 271 LYS A 284 1 14 HELIX 4 4 MET A 298 LEU A 308 1 11 HELIX 5 5 ASN A 330 ALA A 349 1 20 HELIX 6 6 LYS A 370 TYR A 381 1 12 HELIX 7 7 LYS A 389 SER A 407 1 19 HELIX 8 8 TYR A 420 ASP A 424 5 5 HELIX 9 9 SER A 450 GLY A 458 1 9 HELIX 10 10 ASN A 465 TYR A 469 5 5 HELIX 11 11 ASN A 483 THR A 494 1 12 HELIX 12 12 SER A 526 ASN A 541 1 16 HELIX 13 13 TYR A 549 GLU A 558 1 10 HELIX 14 14 GLN A 592 ILE A 600 1 9 SHEET 1 AA10 LYS A 187 ASP A 193 0 SHEET 2 AA10 GLY A 511 TRP A 517 1 O GLY A 512 N ILE A 189 SHEET 3 AA10 TYR A 470 VAL A 471 1 O TYR A 470 N TRP A 517 SHEET 4 AA10 ASP A 218 GLY A 224 0 SHEET 5 AA10 GLY A 287 SER A 294 0 SHEET 6 AA10 ILE A 354 GLY A 358 0 SHEET 7 AA10 LYS A 411 PHE A 415 0 SHEET 8 AA10 ILE A 435 MET A 438 0 SHEET 9 AA10 ILE A 461 ASN A 463 0 SHEET 10 AA10 LYS A 187 ASP A 193 1 O LYS A 187 N GLY A 512 SHEET 1 AB 2 PHE A 230 MET A 231 0 SHEET 2 AB 2 LEU A 269 THR A 270 1 O LEU A 269 N MET A 231 SHEET 1 AC 2 ILE A 237 ALA A 239 0 SHEET 2 AC 2 LYS A 242 TYR A 244 -1 O LYS A 242 N ALA A 239 SHEET 1 AD 2 ASN A 314 TYR A 317 0 SHEET 2 AD 2 LYS A 320 VAL A 326 -1 O LYS A 320 N TYR A 317 CISPEP 1 SER A 294 PRO A 295 0 -5.71 SITE 1 AC1 16 ARG A 196 HIS A 297 ASP A 360 GLU A 361 SITE 2 AC1 16 TRP A 439 TRP A 443 ASP A 466 TYR A 469 SITE 3 AC1 16 TRP A 517 ASP A 519 EDO A1608 HOH A2038 SITE 4 AC1 16 HOH A2165 HOH A2244 HOH A2274 HOH A2296 SITE 1 AC2 1 ASN A 422 SITE 1 AC3 4 TRP A 443 GLU A 503 OAN A1606 HOH A2224 SITE 1 AC4 5 TYR A 317 TYR A 386 HOH A2127 HOH A2297 SITE 2 AC4 5 HOH A2298 SITE 1 AC5 1 TYR A 317 SITE 1 AC6 4 LYS A 452 GLU A 456 GLU A 503 HOH A2230 SITE 1 AC7 7 GLY A 441 PRO A 500 LYS A 501 THR A 502 SITE 2 AC7 7 HOH A2226 HOH A2228 HOH A2243 SITE 1 AC8 4 ARG A 524 SER A 526 PRO A 527 SER A 528 SITE 1 AC9 3 LYS A 532 ARG A 535 HIS A 536 SITE 1 BC1 3 HIS A 213 TYR A 214 ARG A 535 CRYST1 90.070 90.070 101.600 90.00 90.00 120.00 P 31 2 1 6 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 0.011102 0.006410 0.000000 0.00000 SCALE2 0.000000 0.012820 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009843 0.00000