HEADER HYDROLASE 31-MAY-11 2YL8 TITLE INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND MOLECULAR TITLE 2 INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-N-ACETYLHEXOSAMINIDASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 181-614; COMPND 5 SYNONYM: GLYCOSIDE HYDROLASE GH20; 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,M.A.HIGGINS,D.W.ABBOTT,C.ROBB,A.B.DALIA,L.DENG, AUTHOR 2 J.N.WEISER,T.B.PARSONS,A.J.FAIRBANKS,D.J.VOCADLO,A.B.BORASTON REVDAT 4 08-MAY-24 2YL8 1 HETSYN REVDAT 3 29-JUL-20 2YL8 1 COMPND REMARK HETNAM LINK REVDAT 3 2 1 SITE ATOM REVDAT 2 23-NOV-11 2YL8 1 AUTHOR JRNL REMARK REVDAT 1 07-SEP-11 2YL8 0 JRNL AUTH B.PLUVINAGE,M.A.HIGGINS,D.W.ABBOTT,C.ROBB,A.B.DALIA,L.DENG, JRNL AUTH 2 J.N.WEISER,T.B.PARSONS,A.J.FAIRBANKS,D.J.VOCADLO, JRNL AUTH 3 A.B.BORASTON JRNL TITL INHIBITION OF THE PNEUMOCOCCAL VIRULENCE FACTOR STRH AND JRNL TITL 2 MOLECULAR INSIGHTS INTO N-GLYCAN RECOGNITION AND HYDROLYSIS. JRNL REF STRUCTURE V. 19 1603 2011 JRNL REFN ISSN 0969-2126 JRNL PMID 22078560 JRNL DOI 10.1016/J.STR.2011.08.011 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 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) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.60 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 46762 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) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.164 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2491 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) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.80 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3397 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2110 REMARK 3 BIN FREE R VALUE SET COUNT : 215 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3397 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 72 REMARK 3 SOLVENT ATOMS : 623 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.13000 REMARK 3 B22 (A**2) : -0.16000 REMARK 3 B33 (A**2) : 0.03000 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): 0.112 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.111 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.067 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.032 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.931 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3729 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5073 ; 1.425 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 483 ; 5.820 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 182 ;36.988 ;25.549 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 634 ;12.641 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 14 ;16.347 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 543 ; 0.094 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2883 ; 0.007 ; 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): 2264 ; 0.733 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3654 ; 1.290 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1465 ; 2.361 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1406 ; 3.903 ; 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 2YL8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-MAY-11. REMARK 100 THE DEPOSITION ID IS D_1290048501. 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 : NULL 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) : 0.97915 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 : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49280 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.750 REMARK 200 RESOLUTION RANGE LOW (A) : 35.600 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.75 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : 0.40000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.400 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: NULL REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.51 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL 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 39.28500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 54.64500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 56.46500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 39.28500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 54.64500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 56.46500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 39.28500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 54.64500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 56.46500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 39.28500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 54.64500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 56.46500 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 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 MN MN A1620 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2382 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2384 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, GLU 361 TO GLN REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 370 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 2314 2.08 REMARK 500 OD1 ASP A 400 O HOH A 2374 2.11 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 93.40 -161.16 REMARK 500 ASP A 226 -75.12 69.95 REMARK 500 TYR A 261 117.07 -162.81 REMARK 500 LYS A 350 -23.62 71.73 REMARK 500 LYS A 350 -25.05 72.82 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 A2001 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH A2156 DISTANCE = 6.55 ANGSTROMS REMARK 525 HOH A2287 DISTANCE = 6.85 ANGSTROMS REMARK 525 HOH A2303 DISTANCE = 6.44 ANGSTROMS REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 POLYETHYLENE GLYCOL (15P): (N=34) REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 15P A 1624 REMARK 610 15P A 1625 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 MN A1619 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 247 OD2 REMARK 620 2 HOH A2089 O 83.5 REMARK 620 3 HOH A2642 O 177.0 98.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A1618 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 259 OD2 REMARK 620 2 HOH A2124 O 87.9 REMARK 620 3 HOH A2126 O 92.1 92.3 REMARK 620 4 HOH A2127 O 86.5 174.2 89.4 REMARK 620 5 HOH A2128 O 85.1 86.5 177.0 91.6 REMARK 620 6 HOH A2641 O 177.7 93.6 86.0 92.0 96.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A1615 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 329 OD2 REMARK 620 2 HOH A2257 O 84.3 REMARK 620 3 HOH A2258 O 91.7 85.5 REMARK 620 4 HOH A2259 O 87.0 169.0 88.2 REMARK 620 5 HOH A2260 O 86.1 94.0 177.8 92.0 REMARK 620 6 HOH A2359 O 178.3 96.6 89.8 92.3 92.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A1617 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 422 OD1 REMARK 620 2 HOH A2393 O 96.4 REMARK 620 3 HOH A2394 O 89.0 132.1 REMARK 620 4 HOH A2640 O 144.7 66.8 81.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A1616 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 477 OD1 REMARK 620 2 ASP A 485 OD2 96.2 REMARK 620 3 HOH A2455 O 96.8 88.4 REMARK 620 4 HOH A2466 O 173.0 90.8 84.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A1621 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 550 OE1 REMARK 620 2 GLU A 553 OE1 94.1 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A1622 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 550 OE2 REMARK 620 2 HOH A2051 O 74.0 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A1620 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 585 OD2 REMARK 620 2 ASP A 585 OD2 157.2 REMARK 620 N 1 REMARK 900 REMARK 900 RELATED ENTRIES 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: 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: 2YL5 RELATED DB: PDB REMARK 900 INHIBITION OF THE PNEUMOCCOCAL 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 DBREF 2YL8 A 181 614 UNP P49610 STRH_STRPN 181 614 SEQADV 2YL8 GLN A 361 UNP P49610 GLU 361 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 GLN 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 TRP TYR 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 MAN B 1 12 HET NAG B 2 14 HET MN A1615 1 HET MN A1616 1 HET MN A1617 1 HET MN A1618 1 HET MN A1619 1 HET MN A1620 1 HET MN A1621 1 HET MN A1622 1 HET MN A1623 1 HET 15P A1624 24 HET 15P A1625 9 HET EDO A1628 4 HETNAM MAN ALPHA-D-MANNOPYRANOSE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM MN MANGANESE (II) ION HETNAM 15P POLYETHYLENE GLYCOL (N=34) HETNAM EDO 1,2-ETHANEDIOL HETSYN MAN ALPHA-D-MANNOSE; D-MANNOSE; MANNOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN 15P PEG 1500 HETSYN EDO ETHYLENE GLYCOL FORMUL 2 MAN C6 H12 O6 FORMUL 2 NAG C8 H15 N O6 FORMUL 3 MN 9(MN 2+) FORMUL 12 15P 2(C69 H140 O35) FORMUL 14 EDO C2 H6 O2 FORMUL 15 HOH *623(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 GLY A 309 1 12 HELIX 5 5 ASN A 330 ALA A 349 1 20 HELIX 6 6 ALA A 363 ASP A 368 1 6 HELIX 7 7 LYS A 370 TYR A 381 1 12 HELIX 8 8 LYS A 389 HIS A 408 1 20 HELIX 9 9 TYR A 420 ASP A 424 5 5 HELIX 10 10 SER A 450 LYS A 457 1 8 HELIX 11 11 ASN A 465 TYR A 469 5 5 HELIX 12 12 ASN A 483 THR A 494 1 12 HELIX 13 13 SER A 526 ASN A 541 1 16 HELIX 14 14 TYR A 549 GLU A 558 1 10 HELIX 15 15 THR A 567 SER A 583 1 17 HELIX 16 16 GLN A 592 ASN A 609 1 18 SHEET 1 1 1 LYS A 187 ASP A 193 0 SHEET 1 2 1 ASP A 218 GLY A 224 0 SHEET 1 3 1 PHE A 230 MET A 231 0 SHEET 1 4 1 ILE A 237 ALA A 239 0 SHEET 1 5 1 LYS A 242 TYR A 244 0 SHEET 1 6 1 LEU A 269 THR A 270 0 SHEET 1 7 1 GLY A 287 SER A 294 0 SHEET 1 8 1 ASN A 314 TYR A 317 0 SHEET 1 9 1 LYS A 320 VAL A 326 0 SHEET 1 10 1 ILE A 354 GLY A 358 0 SHEET 1 11 1 LYS A 411 PHE A 415 0 SHEET 1 12 1 ILE A 435 MET A 438 0 SHEET 1 13 1 ILE A 461 ASN A 463 0 SHEET 1 14 1 TYR A 470 VAL A 471 0 SHEET 1 15 1 GLY A 511 TRP A 517 0 LINK O2 MAN B 1 C1 NAG B 2 1555 1555 1.44 LINK OD2AASP A 247 MN MN A1619 1555 1555 2.27 LINK OD2 ASP A 259 MN MN A1618 1555 1555 2.13 LINK OD2 ASP A 329 MN MN A1615 1555 1555 2.20 LINK OD1 ASN A 422 MN MN A1617 1555 1555 2.11 LINK OD1 ASP A 477 MN MN A1616 1555 1555 2.29 LINK OD2 ASP A 485 MN MN A1616 1555 1555 2.20 LINK OE1 GLU A 550 MN MN A1621 1555 1555 2.24 LINK OE2 GLU A 550 MN MN A1622 1555 1555 2.29 LINK OE1 GLU A 553 MN MN A1621 1555 1555 2.15 LINK OD2 ASP A 585 MN MN A1620 4565 1555 2.18 LINK OD2 ASP A 585 MN MN A1620 1555 1555 2.19 LINK MN MN A1615 O HOH A2257 1555 1555 2.24 LINK MN MN A1615 O HOH A2258 1555 1555 2.17 LINK MN MN A1615 O HOH A2259 1555 1555 2.27 LINK MN MN A1615 O HOH A2260 1555 1555 2.14 LINK MN MN A1615 O HOH A2359 1555 1555 2.26 LINK MN MN A1616 O HOH A2455 1555 1555 2.21 LINK MN MN A1616 O HOH A2466 1555 1555 2.09 LINK MN MN A1617 O HOH A2393 1555 1555 2.18 LINK MN MN A1617 O HOH A2394 1555 1555 2.38 LINK MN MN A1617 O HOH A2640 1555 1555 2.62 LINK MN MN A1618 O HOH A2124 1555 1555 2.17 LINK MN MN A1618 O HOH A2126 1555 1555 2.24 LINK MN MN A1618 O HOH A2127 1555 1555 2.12 LINK MN MN A1618 O HOH A2128 1555 1555 2.26 LINK MN MN A1618 O HOH A2641 1555 1555 2.15 LINK MN MN A1619 O HOH A2089 1555 1555 2.42 LINK MN MN A1619 O HOH A2642 1555 1555 2.34 LINK MN MN A1622 O HOH A2051 1555 1555 2.27 LINK MN MN A1623 O HOH A2645 1555 1555 2.36 CISPEP 1 SER A 294 PRO A 295 0 -5.63 CRYST1 78.570 109.290 112.930 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 0.012728 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009150 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008855 0.00000