HEADER LYASE 11-JUL-03 1OJO TITLE SPECIFICITY AND MECHANISM OF STREPTOCOCCUS PNEUMONIAE HYALURONATE TITLE 2 LYASE: COMPLEX OF THE TYR408PHE MUTANT WITH 4-SULPHATED CHONDROITIN TITLE 3 DISACCHARIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYALURONATE LYASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: HYALURONATE LYASE, RESIDUES 285-1009; COMPND 5 SYNONYM: HYALURONIDASE, HYASE; COMPND 6 EC: 4.2.2.1; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 1313; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS LYASE, PROTEIN-CARBOHYDRATE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR D.J.RIGDEN,M.J.JEDRZEJAS REVDAT 6 13-DEC-23 1OJO 1 HETSYN REVDAT 5 29-JUL-20 1OJO 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE ATOM REVDAT 4 23-JAN-13 1OJO 1 COMPND REMARK VERSN HET REVDAT 4 2 1 HETNAM FORMUL LINK SITE REVDAT 4 3 1 SCALE1 SCALE2 SCALE3 TER REVDAT 4 4 1 HETATM CONECT REVDAT 3 24-FEB-09 1OJO 1 VERSN REVDAT 2 11-DEC-03 1OJO 1 JRNL REVDAT 1 30-OCT-03 1OJO 0 JRNL AUTH D.J.RIGDEN,M.J.JEDRZEJAS JRNL TITL STRUCTURES OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE IN JRNL TITL 2 COMPLEX WITH CHONDROITIN AND CHONDROITIN SULFATE JRNL TITL 3 DISACCHARIDES: INSIGHTS INTO SPECIFICITY AND MECHANISM OF JRNL TITL 4 ACTION JRNL REF J.BIOL.CHEM. V. 278 50596 2003 JRNL REFN ISSN 0021-9258 JRNL PMID 14523022 JRNL DOI 10.1074/JBC.M307596200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.LI,S.J.KELLY,E.LAMANI,M.FERRARONI,M.J.JEDRZEJAS REMARK 1 TITL STRUCTURAL BASIS OF HYALURONAN DEGRADATION BY STREPTOCOCCUS REMARK 1 TITL 2 PNEUMONIAE HYALURONATE LYASE REMARK 1 REF EMBO J. V. 19 1228 2000 REMARK 1 REFN ISSN 0261-4189 REMARK 1 PMID 10716923 REMARK 1 DOI 10.1093/EMBOJ/19.6.1228 REMARK 2 REMARK 2 RESOLUTION. 1.75 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.75 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 2256586.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 893555 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 SET) : 0.202 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4429 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.003 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.75 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 8413 REMARK 3 BIN R VALUE (WORKING SET) : 0.3100 REMARK 3 BIN FREE R VALUE : 0.2890 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 394 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.015 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5798 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 50 REMARK 3 SOLVENT ATOMS : 536 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -8.30000 REMARK 3 B22 (A**2) : 1.19000 REMARK 3 B33 (A**2) : 7.11000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.19 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.23 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.770 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.120 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.630 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.530 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.530 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 49.76 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1OJO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-JUL-03. REMARK 100 THE DEPOSITION ID IS D_1290013055. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-JUN-02 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : OXFORD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 63869 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 39.960 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.7 REMARK 200 DATA REDUNDANCY : 7.900 REMARK 200 R MERGE (I) : 0.08900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 25.0000 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) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.40 REMARK 200 R MERGE FOR SHELL (I) : 0.75700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS 1.0 REMARK 200 STARTING MODEL: PDB ENTRY 1C82 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.5M AMMONIUM SULFATE, 200MM SODIUM REMARK 280 CACODYLATE, PH 6.0, PH 6.00 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 41.86950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 50.57550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 51.88950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 50.57550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 41.86950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 51.88950 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: PQS 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 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED MUTATION TYR 525 PHE 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 ALA A 168 REMARK 465 SER A 169 REMARK 465 GLN A 892 REMARK 465 HIS A 893 REMARK 465 HIS A 894 REMARK 465 HIS A 895 REMARK 465 HIS A 896 REMARK 465 HIS A 897 REMARK 465 HIS A 898 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 ARG A 790 CB CG CD NE CZ NH1 NH2 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 ALA A 186 -54.61 -137.11 REMARK 500 VAL A 280 -44.46 -138.56 REMARK 500 ILE A 296 -63.41 -126.07 REMARK 500 ASN A 341 66.55 -163.76 REMARK 500 ASN A 341 66.55 -164.05 REMARK 500 VAL A 356 -60.92 -100.05 REMARK 500 THR A 400 -56.04 74.44 REMARK 500 ASN A 401 35.10 -154.33 REMARK 500 TYR A 404 22.09 -144.12 REMARK 500 ALA A 407 -65.72 -139.69 REMARK 500 ASP A 591 45.67 -87.10 REMARK 500 ASN A 598 -155.67 -124.15 REMARK 500 SER A 605 -165.91 -117.08 REMARK 500 ALA A 666 135.00 -176.20 REMARK 500 LYS A 674 -65.27 64.95 REMARK 500 ASN A 705 79.17 -119.84 REMARK 500 ASN A 705 79.17 -118.36 REMARK 500 ARG A 790 9.84 89.29 REMARK 500 ASN A 820 72.83 -155.27 REMARK 500 ASN A 821 -169.65 -127.38 REMARK 500 ASP A 866 -6.94 48.63 REMARK 500 SER A 880 -155.21 -93.46 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 A2080 DISTANCE = 5.98 ANGSTROMS REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1C82 RELATED DB: PDB REMARK 900 MECHANISM OF HYALURONAN BINDING AND DEGRADATION: STRUCTURE OF REMARK 900 STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE IN COMPLEX WITH REMARK 900 HYALURONIC ACID DISACCHARIDE AT 1.7 A RESOLUTION REMARK 900 RELATED ID: 1EGU RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE AT REMARK 900 1.56 A RESOLUTION REMARK 900 RELATED ID: 1F9G RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE HYALURONATELYASE REMARK 900 COCRYSTALLIZED WITH ASCORBIC ACID REMARK 900 RELATED ID: 1LOH RELATED DB: PDB REMARK 900 STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE IN COMPLEX REMARK 900 WITHHEXASACCHARIDE HYALURONAN SUBSTRATE REMARK 900 RELATED ID: 1LXK RELATED DB: PDB REMARK 900 STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE IN COMPLEX REMARK 900 WITHTETRASACCHARIDE HYALURONAN SUBSTRATE REMARK 900 RELATED ID: 1N7N RELATED DB: PDB REMARK 900 STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE W292A MUTANT REMARK 900 RELATED ID: 1N7O RELATED DB: PDB REMARK 900 STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE F343V MUTANT REMARK 900 RELATED ID: 1N7P RELATED DB: PDB REMARK 900 STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE W292A /F343VDOUBLE MUTANT REMARK 900 RELATED ID: 1N7Q RELATED DB: PDB REMARK 900 STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE W291A /W292ADOUBLE REMARK 900 MUTANT COMPLEX WITH HYALURONAN HEXASACCHRIDE REMARK 900 RELATED ID: 1N7R RELATED DB: PDB REMARK 900 STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASEW291A/ W292A/F343V MUTANT REMARK 900 COMPLEX WITH HEXASACCHARIDE HYALURONAN REMARK 900 RELATED ID: 1OJM RELATED DB: PDB REMARK 900 SPECIFICITY AND MECHANISM OF STREPTOCOCCUS PNEUMONIAE HYALURONATE REMARK 900 LYASE: COMPLEX WITH UNSULPHATED CHONDROITIN DISACCHARIDE REMARK 900 RELATED ID: 1OJN RELATED DB: PDB REMARK 900 SPECIFICITY AND MECHANISM OF STREPTOCOCCUS PNEUMONIAE HYALURONATE REMARK 900 LYASE: COMPLEX OF THE TYR408PHE MUTANT WITH 6-SULPHATED CHONDROITIN REMARK 900 DISACCHARIDE REMARK 900 RELATED ID: 1OJP RELATED DB: PDB REMARK 900 SPECIFICITY AND MECHANISM OF STREPTOCOCCUS PNEUMONIAE HYALURONATE REMARK 900 LYASE: COMPLEX WITH 6-SULPHATED CHONDROITIN DISACCHARIDE REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE PROTEIN USED WAS THE Y408F MUTANT. THE SIX RESIDUE REMARK 999 HIS TAG, ALONG WITH RESIDUES 168-169 AND 892, WERE NOT REMARK 999 SEEN IN THE DENSITY. THE ELECTRON DENSITY OF RESIDUE 731 REMARK 999 SUGGESTS IT IS A VALINE REMARK 999 THE SEQUENCE CONFLICT AT RESIDUE A196 (SWS RESIDUE 313) REMARK 999 IS MARKED AS A KNOWN SEQUENCE CONFLICT IN THE SWS ENTRY. DBREF 1OJO A 168 892 UNP Q54873 HYSA_STRPN 285 1009 DBREF 1OJO A 893 898 PDB 1OJO 1OJO 893 898 SEQADV 1OJO THR A 173 UNP Q54873 ALA 290 CONFLICT SEQADV 1OJO ASP A 196 UNP Q54873 GLU 313 SEE REMARK 999 SEQADV 1OJO ILE A 223 UNP Q54873 THR 340 CONFLICT SEQADV 1OJO PHE A 408 UNP Q54873 TYR 525 ENGINEERED MUTATION SEQADV 1OJO ARG A 496 UNP Q54873 CYS 613 CONFLICT SEQADV 1OJO THR A 541 UNP Q54873 PRO 613 CONFLICT SEQADV 1OJO SER A 704 UNP Q54873 GLY 821 CONFLICT SEQADV 1OJO SER A 736 UNP Q54873 PHE 853 CONFLICT SEQRES 1 A 731 ALA SER VAL LYS ASP THR TYR THR ASP ARG LEU ASP ASP SEQRES 2 A 731 TRP ASN GLY ILE ILE ALA GLY ASN GLN TYR TYR ASP SER SEQRES 3 A 731 LYS ASN ASP GLN MET ALA LYS LEU ASN GLN GLU LEU GLU SEQRES 4 A 731 GLY LYS VAL ALA ASP SER LEU SER SER ILE SER SER GLN SEQRES 5 A 731 ALA ASP ARG ILE TYR LEU TRP GLU LYS PHE SER ASN TYR SEQRES 6 A 731 LYS THR SER ALA ASN LEU THR ALA THR TYR ARG LYS LEU SEQRES 7 A 731 GLU GLU MET ALA LYS GLN VAL THR ASN PRO SER SER ARG SEQRES 8 A 731 TYR TYR GLN ASP GLU THR VAL VAL ARG THR VAL ARG ASP SEQRES 9 A 731 SER MET GLU TRP MET HIS LYS HIS VAL TYR ASN SER GLU SEQRES 10 A 731 LYS SER ILE VAL GLY ASN TRP TRP ASP TYR GLU ILE GLY SEQRES 11 A 731 THR PRO ARG ALA ILE ASN ASN THR LEU SER LEU MET LYS SEQRES 12 A 731 GLU TYR PHE SER ASP GLU GLU ILE LYS LYS TYR THR ASP SEQRES 13 A 731 VAL ILE GLU LYS PHE VAL PRO ASP PRO GLU HIS PHE ARG SEQRES 14 A 731 LYS THR THR ASP ASN PRO PHE LYS ALA LEU GLY GLY ASN SEQRES 15 A 731 LEU VAL ASP MET GLY ARG VAL LYS VAL ILE ALA GLY LEU SEQRES 16 A 731 LEU ARG LYS ASP ASP GLN GLU ILE SER SER THR ILE ARG SEQRES 17 A 731 SER ILE GLU GLN VAL PHE LYS LEU VAL ASP GLN GLY GLU SEQRES 18 A 731 GLY PHE TYR GLN ASP GLY SER TYR ILE ASP HIS THR ASN SEQRES 19 A 731 VAL ALA TYR THR GLY ALA PHE GLY ASN VAL LEU ILE ASP SEQRES 20 A 731 GLY LEU SER GLN LEU LEU PRO VAL ILE GLN LYS THR LYS SEQRES 21 A 731 ASN PRO ILE ASP LYS ASP LYS MET GLN THR MET TYR HIS SEQRES 22 A 731 TRP ILE ASP LYS SER PHE ALA PRO LEU LEU VAL ASN GLY SEQRES 23 A 731 GLU LEU MET ASP MET SER ARG GLY ARG SER ILE SER ARG SEQRES 24 A 731 ALA ASN SER GLU GLY HIS VAL ALA ALA VAL GLU VAL LEU SEQRES 25 A 731 ARG GLY ILE HIS ARG ILE ALA ASP MET SER GLU GLY GLU SEQRES 26 A 731 THR LYS GLN ARG LEU GLN SER LEU VAL LYS THR ILE VAL SEQRES 27 A 731 GLN SER ASP SER TYR TYR ASP VAL PHE LYS ASN LEU LYS SEQRES 28 A 731 THR TYR LYS ASP ILE SER LEU MET GLN SER LEU LEU SER SEQRES 29 A 731 ASP ALA GLY VAL ALA SER VAL PRO ARG THR SER TYR LEU SEQRES 30 A 731 SER ALA PHE ASN LYS MET ASP LYS THR ALA MET TYR ASN SEQRES 31 A 731 ALA GLU LYS GLY PHE GLY PHE GLY LEU SER LEU PHE SER SEQRES 32 A 731 SER ARG THR LEU ASN TYR GLU HIS MET ASN LYS GLU ASN SEQRES 33 A 731 LYS ARG GLY TRP TYR THR SER ASP GLY MET PHE TYR LEU SEQRES 34 A 731 TYR ASN GLY ASP LEU SER HIS TYR SER ASP GLY TYR TRP SEQRES 35 A 731 PRO THR VAL ASN PRO TYR LYS MET PRO GLY THR THR GLU SEQRES 36 A 731 THR ASP ALA LYS ARG ALA ASP SER ASP THR GLY LYS VAL SEQRES 37 A 731 LEU PRO SER ALA PHE VAL GLY THR SER LYS LEU ASP ASP SEQRES 38 A 731 ALA ASN ALA THR ALA THR MET ASP PHE THR ASN TRP ASN SEQRES 39 A 731 GLN THR LEU THR ALA HIS LYS SER TRP PHE MET LEU LYS SEQRES 40 A 731 ASP LYS ILE ALA PHE LEU GLY SER ASN ILE GLN ASN THR SEQRES 41 A 731 SER THR ASP THR ALA ALA THR THR ILE ASP GLN ARG LYS SEQRES 42 A 731 LEU GLU SER SER ASN PRO TYR LYS VAL TYR VAL ASN ASP SEQRES 43 A 731 LYS GLU ALA SER LEU THR GLU GLN GLU LYS ASP TYR PRO SEQRES 44 A 731 GLU THR GLN SER VAL PHE LEU GLU SER SER ASP SER LYS SEQRES 45 A 731 LYS ASN ILE GLY TYR PHE PHE PHE LYS LYS SER SER ILE SEQRES 46 A 731 SER MET SER LYS ALA LEU GLN LYS GLY ALA TRP LYS ASP SEQRES 47 A 731 ILE ASN GLU GLY GLN SER ASP LYS GLU VAL GLU ASN GLU SEQRES 48 A 731 PHE LEU THR ILE SER GLN ALA HIS LYS GLN ASN ARG ASP SEQRES 49 A 731 SER TYR GLY TYR MET LEU ILE PRO ASN VAL ASP ARG ALA SEQRES 50 A 731 THR PHE ASN GLN MET ILE LYS GLU LEU GLU SER SER LEU SEQRES 51 A 731 ILE GLU ASN ASN GLU THR LEU GLN SER VAL TYR ASP ALA SEQRES 52 A 731 LYS GLN GLY VAL TRP GLY ILE VAL LYS TYR ASP ASP SER SEQRES 53 A 731 VAL SER THR ILE SER ASN GLN PHE GLN VAL LEU LYS ARG SEQRES 54 A 731 GLY VAL TYR THR ILE ARG LYS GLU GLY ASP GLU TYR LYS SEQRES 55 A 731 ILE ALA TYR TYR ASN PRO GLU THR GLN GLU SER ALA PRO SEQRES 56 A 731 ASP GLN GLU VAL PHE LYS LYS LEU GLU GLN HIS HIS HIS SEQRES 57 A 731 HIS HIS HIS HET ASG B 1 19 HET GCD B 2 11 HET SO4 A1200 5 HET SO4 A1201 5 HET SO4 A1202 5 HET SO4 A1203 5 HETNAM ASG 2-ACETAMIDO-2-DEOXY-4-O-SULFO-BETA-D-GALACTOPYRANOSE HETNAM GCD 4-DEOXY-ALPHA-L-THREO-HEX-4-ENOPYRANURONIC ACID HETNAM SO4 SULFATE ION HETSYN ASG 2-DEOXY-2-ACETAMIDO-BETA-D-GALACTOSE-4-SULFATE; N- HETSYN 2 ASG ACETYL-4-O-SULFO-BETA-D-GALACTOSAMINE; 2-ACETAMIDO-2- HETSYN 3 ASG DEOXY-4-O-SULFO-BETA-D-GALACTOSE; 2-ACETAMIDO-2-DEOXY- HETSYN 4 ASG 4-O-SULFO-D-GALACTOSE; 2-ACETAMIDO-2-DEOXY-4-O-SULFO- HETSYN 5 ASG GALACTOSE HETSYN GCD 4,5-DEHYDRO-D-GLUCURONIC ACID; 4-DEOXY-ALPHA-L-THREO- HETSYN 2 GCD HEX-4-ENURONIC ACID; 4-DEOXY-L-THREO-HEX-4-ENURONIC HETSYN 3 GCD ACID; 4-DEOXY-THREO-HEX-4-ENURONIC ACID FORMUL 2 ASG C8 H15 N O9 S FORMUL 2 GCD C6 H8 O6 FORMUL 3 SO4 4(O4 S 2-) FORMUL 7 HOH *536(H2 O) HELIX 1 1 ASP A 172 ALA A 186 1 15 HELIX 2 2 GLY A 187 TYR A 191 5 5 HELIX 3 3 ASN A 195 ILE A 216 1 22 HELIX 4 4 TRP A 226 SER A 230 5 5 HELIX 5 5 SER A 235 THR A 253 1 19 HELIX 6 6 ASP A 262 VAL A 280 1 19 HELIX 7 7 ASN A 290 ILE A 296 1 7 HELIX 8 8 ILE A 296 MET A 309 1 14 HELIX 9 9 SER A 314 VAL A 329 1 16 HELIX 10 10 LEU A 346 ARG A 364 1 19 HELIX 11 11 ASP A 366 GLU A 378 1 13 HELIX 12 12 GLN A 379 LYS A 382 5 4 HELIX 13 13 ALA A 407 GLN A 424 1 18 HELIX 14 14 ASP A 431 GLN A 436 1 6 HELIX 15 15 GLN A 436 SER A 445 1 10 HELIX 16 16 PHE A 446 PRO A 448 5 3 HELIX 17 17 ASP A 457 SER A 469 5 13 HELIX 18 18 GLU A 470 MET A 488 1 19 HELIX 19 19 GLU A 490 ASP A 508 1 19 HELIX 20 20 ASP A 512 LEU A 517 5 6 HELIX 21 21 THR A 519 ASP A 532 1 14 HELIX 22 22 ASN A 548 MET A 550 5 3 HELIX 23 23 GLY A 607 VAL A 612 1 6 HELIX 24 24 ASN A 613 MET A 617 5 5 HELIX 25 25 ASP A 737 LYS A 740 5 4 HELIX 26 26 ALA A 762 ASN A 767 1 6 HELIX 27 27 ASP A 802 LEU A 813 1 12 HELIX 28 28 PRO A 882 VAL A 886 1 5 SHEET 1 AA 2 HIS A 334 PHE A 335 0 SHEET 2 AA 2 PHE A 343 LYS A 344 -1 O PHE A 343 N PHE A 335 SHEET 1 AB 3 GLY A 389 PHE A 390 0 SHEET 2 AB 3 TYR A 396 ASP A 398 -1 O ILE A 397 N GLY A 389 SHEET 3 AB 3 VAL A 402 ALA A 403 -1 O VAL A 402 N ASP A 398 SHEET 1 AC 2 LEU A 450 VAL A 451 0 SHEET 2 AC 2 GLU A 454 LEU A 455 -1 O GLU A 454 N VAL A 451 SHEET 1 AD 4 TYR A 543 PHE A 547 0 SHEET 2 AD 4 LYS A 552 ASN A 557 -1 O LYS A 552 N PHE A 547 SHEET 3 AD 4 PHE A 562 SER A 567 -1 O PHE A 562 N ASN A 557 SHEET 4 AD 4 MET A 593 TYR A 597 -1 O MET A 593 N SER A 567 SHEET 1 AE 7 THR A 621 THR A 623 0 SHEET 2 AE 7 ALA A 692 LYS A 700 -1 O ALA A 693 N GLU A 622 SHEET 3 AE 7 VAL A 775 ALA A 785 -1 O LEU A 780 N ARG A 699 SHEET 4 AE 7 ILE A 742 GLY A 761 -1 O SER A 753 N SER A 783 SHEET 5 AE 7 LYS A 723 GLU A 734 -1 O LYS A 723 N MET A 754 SHEET 6 AE 7 LYS A 708 VAL A 711 -1 O LYS A 708 N GLU A 734 SHEET 7 AE 7 LYS A 714 ALA A 716 -1 O LYS A 714 N VAL A 711 SHEET 1 AF 9 THR A 621 THR A 623 0 SHEET 2 AF 9 ALA A 692 LYS A 700 -1 O ALA A 693 N GLU A 622 SHEET 3 AF 9 VAL A 775 ALA A 785 -1 O LEU A 780 N ARG A 699 SHEET 4 AF 9 ILE A 742 GLY A 761 -1 O SER A 753 N SER A 783 SHEET 5 AF 9 ASP A 791 PRO A 799 -1 O GLY A 794 N PHE A 747 SHEET 6 AF 9 ILE A 677 ASN A 686 -1 O ILE A 677 N LEU A 797 SHEET 7 AF 9 LEU A 664 LEU A 673 -1 O THR A 665 N GLN A 685 SHEET 8 AF 9 ASN A 650 THR A 658 -1 O ALA A 651 N MET A 672 SHEET 9 AF 9 VAL A 641 LYS A 645 -1 O GLY A 642 N THR A 654 SHEET 1 AG 5 LEU A 817 ASN A 820 0 SHEET 2 AG 5 LEU A 824 ASP A 829 -1 O SER A 826 N ILE A 818 SHEET 3 AG 5 VAL A 834 LYS A 839 -1 O VAL A 834 N ASP A 829 SHEET 4 AG 5 GLY A 857 GLU A 864 -1 O GLY A 857 N LYS A 839 SHEET 5 AG 5 GLU A 867 TYR A 873 -1 O GLU A 867 N GLU A 864 SHEET 1 AH 3 SER A 845 ILE A 847 0 SHEET 2 AH 3 PHE A 851 VAL A 853 -1 O PHE A 851 N ILE A 847 SHEET 3 AH 3 PHE A 887 LYS A 889 -1 O LYS A 888 N GLN A 852 LINK O3 ASG B 1 C1 GCD B 2 1555 1555 1.39 CRYST1 83.739 103.779 101.151 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 0.011942 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009636 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009886 0.00000