HEADER HYDROLASE 21-JAN-09 2W91 TITLE STRUCTURE OF A STREPTOCOCCUS PNEUMONIAE FAMILY 85 GLYCOSIDE HYDROLASE, TITLE 2 ENDO-D. COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDO-BETA-N-ACETYLGLUCOSAMINIDASE D; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CATALYTIC MODULE, RESIDUES 159-807; COMPND 5 SYNONYM: ENDO-D CATALYTIC MODULE; COMPND 6 ENGINEERED: 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: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS HYDROLASE, N-GLYCAN, SECRETED, OXAZOLINE, NAG-THIAZOLINE, SUBSTRATE- KEYWDS 2 PARTICIPATION, ENZYME MECHANISM, ANCHIMERIC ASSISTANCE EXPDTA X-RAY DIFFRACTION AUTHOR D.W.ABBOTT,M.S.MACAULEY,D.J.VOCADLO,A.B.BORASTON REVDAT 4 08-MAY-24 2W91 1 REMARK REVDAT 3 28-APR-09 2W91 1 JRNL REMARK REVDAT 2 10-FEB-09 2W91 1 JRNL REVDAT 1 27-JAN-09 2W91 0 JRNL AUTH D.W.ABBOTT,M.S.MACAULEY,D.J.VOCADLO,A.B.BORASTON JRNL TITL STREPTOCOCCUS PNEUMONIAE ENDOHEXOSAMINIDASE D, STRUCTURAL JRNL TITL 2 AND MECHANISTIC INSIGHT INTO SUBSTRATE-ASSISTED CATALYSIS IN JRNL TITL 3 FAMILY 85 GLYCOSIDE HYDROLASES. JRNL REF J.BIOL.CHEM. V. 284 11676 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 19181667 JRNL DOI 10.1074/JBC.M809663200 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 129975 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.129 REMARK 3 R VALUE (WORKING SET) : 0.127 REMARK 3 FREE R VALUE : 0.162 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 6871 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 7804 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2120 REMARK 3 BIN FREE R VALUE SET COUNT : 395 REMARK 3 BIN FREE R VALUE : 0.2760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5072 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 8 REMARK 3 SOLVENT ATOMS : 978 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.20000 REMARK 3 B22 (A**2) : 0.08000 REMARK 3 B33 (A**2) : -0.04000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.23000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.052 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.050 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.028 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.527 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.977 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.967 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5244 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3547 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7105 ; 1.590 ; 1.932 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8614 ; 0.902 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 644 ; 6.709 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 261 ;36.400 ;24.866 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 872 ;11.717 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 19 ;13.122 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 730 ; 0.109 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5929 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1111 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 944 ; 0.220 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3712 ; 0.201 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2537 ; 0.189 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2622 ; 0.089 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 743 ; 0.168 ; 0.200 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): 13 ; 0.578 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 30 ; 0.197 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 32 ; 0.213 ; 0.200 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): 3333 ; 1.854 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1308 ; 0.748 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5060 ; 2.345 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2412 ; 3.502 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2040 ; 4.601 ; 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): 10392 ; 1.945 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 978 ; 8.989 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 8653 ; 3.491 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 2W91 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1290038607. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 113 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X8C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 129975 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.41000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: OTHER REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.73 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.44 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 67.53000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.42500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 67.53000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.42500 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 REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A2207 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2417 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2436 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2778 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2825 LIES ON A SPECIAL POSITION. REMARK 375 HOH A2826 LIES ON A SPECIAL POSITION. 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 GLY A 168 REMARK 465 SER A 169 REMARK 465 HIS A 170 REMARK 465 MET A 171 REMARK 465 LYS A 172 REMARK 465 SER A 809 REMARK 465 LEU A 810 REMARK 465 PRO A 811 REMARK 465 LYS A 812 REMARK 465 PRO A 813 REMARK 465 LEU A 814 REMARK 465 ALA A 815 REMARK 465 GLU A 816 REMARK 465 ASN A 817 REMARK 465 ILE A 818 REMARK 465 VAL A 819 REMARK 465 PRO A 820 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 THR A 808 CA C O CB OG1 CG2 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 O HOH A 2189 O HOH A 2231 2.01 REMARK 500 O HOH A 2870 O HOH A 2871 2.07 REMARK 500 OE1 GLU A 685 O HOH A 2822 2.07 REMARK 500 O HOH A 2563 O HOH A 2564 2.08 REMARK 500 ND2 ASN A 527 O HOH A 2617 2.14 REMARK 500 O HOH A 2003 O HOH A 2864 2.15 REMARK 500 O HOH A 2126 O HOH A 2130 2.16 REMARK 500 O HOH A 2043 O HOH A 2864 2.17 REMARK 500 O HOH A 2131 O HOH A 2214 2.18 REMARK 500 O HOH A 2227 O HOH A 2393 2.18 REMARK 500 O HOH A 2367 O HOH A 2641 2.18 REMARK 500 O HOH A 2046 O HOH A 2863 2.19 REMARK 500 CG2 THR A 173 O HOH A 2005 2.19 REMARK 500 O HOH A 2090 O HOH A 2091 2.19 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 C22 1PE A 1809 C22 1PE A 1809 2555 1.60 REMARK 500 O HOH A 2171 O HOH A 2519 4444 2.09 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 ASP A 259 CB ASP A 259 CG 0.126 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 ASP A 259 CB - CG - OD1 ANGL. DEV. = -6.6 DEGREES REMARK 500 ASP A 259 CB - CG - OD2 ANGL. DEV. = 8.3 DEGREES REMARK 500 ARG A 382 NE - CZ - NH1 ANGL. DEV. = 4.0 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 ASP A 253 16.75 -142.44 REMARK 500 ASP A 374 86.86 -64.15 REMARK 500 ALA A 375 -78.78 -146.26 REMARK 500 TYR A 383 116.31 -162.71 REMARK 500 PRO A 404 -76.49 -76.80 REMARK 500 ASN A 413 38.38 -94.61 REMARK 500 SER A 447 -130.05 61.10 REMARK 500 LYS A 612 83.30 -151.39 REMARK 500 PHE A 645 54.44 -112.55 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 A2213 DISTANCE = 6.01 ANGSTROMS 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 1PE A 1809 REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1PE A 1809 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2W92 RELATED DB: PDB REMARK 900 STRUCTURE OF A STREPTOCOCCUS PNEUMONIAE FAMILY 85 GLYCOSIDE REMARK 900 HYDROLASE, ENDO-D, IN COMPLEX WITH NAG-THIAZOLINE. DBREF 2W91 A 168 171 PDB 2W91 2W91 168 171 DBREF 2W91 A 172 820 UNP Q93HW0 Q93HW0_STRPN 159 807 SEQRES 1 A 653 GLY SER HIS MET LYS THR LEU LYS PRO LYS GLU ILE LYS SEQRES 2 A 653 PHE ASN SER TRP GLU GLU LEU LEU LYS TRP GLU PRO GLY SEQRES 3 A 653 ALA ARG GLU ASP ASP ALA ILE ASN ARG GLY SER VAL VAL SEQRES 4 A 653 LEU ALA SER ARG ARG THR GLY HIS LEU VAL ASN GLU LYS SEQRES 5 A 653 ALA SER LYS GLU ALA LYS VAL GLN ALA LEU SER ASN THR SEQRES 6 A 653 ASN SER LYS ALA LYS ASP HIS ALA SER VAL GLY GLY GLU SEQRES 7 A 653 GLU PHE LYS ALA TYR ALA PHE ASP TYR TRP GLN TYR LEU SEQRES 8 A 653 ASP SER MET VAL PHE TRP GLU GLY LEU VAL PRO THR PRO SEQRES 9 A 653 ASP VAL ILE ASP ALA GLY HIS ARG ASN GLY VAL PRO VAL SEQRES 10 A 653 TYR GLY THR LEU PHE PHE ASN TRP SER ASN SER ILE ALA SEQRES 11 A 653 ASP GLN GLU ARG PHE ALA GLU ALA LEU LYS GLN ASP ALA SEQRES 12 A 653 ASP GLY SER PHE PRO ILE ALA ARG LYS LEU VAL ASP MET SEQRES 13 A 653 ALA LYS TYR TYR GLY TYR ASP GLY TYR PHE ILE ASN GLN SEQRES 14 A 653 GLU THR THR GLY ASP LEU VAL LYS PRO LEU GLY GLU LYS SEQRES 15 A 653 MET ARG GLN PHE MET LEU TYR SER LYS GLU TYR ALA ALA SEQRES 16 A 653 LYS VAL ASN HIS PRO ILE LYS TYR SER TRP TYR ASP ALA SEQRES 17 A 653 MET THR TYR ASN TYR GLY ARG TYR HIS GLN ASP GLY LEU SEQRES 18 A 653 GLY GLU TYR ASN TYR GLN PHE MET GLN PRO GLU GLY ASP SEQRES 19 A 653 LYS VAL PRO ALA ASP ASN PHE PHE ALA ASN PHE ASN TRP SEQRES 20 A 653 ASP LYS ALA LYS ASN ASP TYR THR ILE ALA THR ALA ASN SEQRES 21 A 653 TRP ILE GLY ARG ASN PRO TYR ASP VAL PHE ALA GLY LEU SEQRES 22 A 653 GLU LEU GLN GLN GLY GLY SER TYR LYS THR LYS VAL LYS SEQRES 23 A 653 TRP ASN ASP ILE LEU ASP GLU ASN GLY LYS LEU ARG LEU SEQRES 24 A 653 SER LEU GLY LEU PHE ALA PRO ASP THR ILE THR SER LEU SEQRES 25 A 653 GLY LYS THR GLY GLU ASP TYR HIS LYS ASN GLU ASP ILE SEQRES 26 A 653 PHE PHE THR GLY TYR GLN GLY ASP PRO THR GLY GLN LYS SEQRES 27 A 653 PRO GLY ASP LYS ASP TRP TYR GLY ILE ALA ASN LEU VAL SEQRES 28 A 653 ALA ASP ARG THR PRO ALA VAL GLY ASN THR PHE THR THR SEQRES 29 A 653 SER PHE ASN THR GLY HIS GLY LYS LYS TRP PHE VAL ASP SEQRES 30 A 653 GLY LYS VAL SER LYS ASP SER GLU TRP ASN TYR ARG SER SEQRES 31 A 653 VAL SER GLY VAL LEU PRO THR TRP ARG TRP TRP GLN THR SEQRES 32 A 653 SER THR GLY GLU LYS LEU ARG ALA GLU TYR ASP PHE THR SEQRES 33 A 653 ASP ALA TYR ASN GLY GLY ASN SER LEU LYS PHE SER GLY SEQRES 34 A 653 ASP VAL ALA GLY LYS THR ASP GLN ASP VAL ARG LEU TYR SEQRES 35 A 653 SER THR LYS LEU GLU VAL THR GLU LYS THR LYS LEU ARG SEQRES 36 A 653 VAL ALA HIS LYS GLY GLY LYS GLY SER LYS VAL TYR MET SEQRES 37 A 653 ALA PHE SER THR THR PRO ASP TYR LYS PHE ASP ASP ALA SEQRES 38 A 653 ASP ALA TRP LYS GLU LEU THR LEU SER ASP ASN TRP THR SEQRES 39 A 653 ASN GLU GLU PHE ASP LEU SER SER LEU ALA GLY LYS THR SEQRES 40 A 653 ILE TYR ALA VAL LYS LEU PHE PHE GLU HIS GLU GLY ALA SEQRES 41 A 653 VAL LYS ASP TYR GLN PHE ASN LEU GLY GLN LEU THR ILE SEQRES 42 A 653 SER ASP ASN HIS GLN GLU PRO GLN SER PRO THR SER PHE SEQRES 43 A 653 SER VAL VAL LYS GLN SER LEU LYS ASN ALA GLN GLU ALA SEQRES 44 A 653 GLU ALA VAL VAL GLN PHE LYS GLY ASN LYS ASP ALA ASP SEQRES 45 A 653 PHE TYR GLU VAL TYR GLU LYS ASP GLY ASP SER TRP LYS SEQRES 46 A 653 LEU LEU THR GLY SER SER SER THR THR ILE TYR LEU PRO SEQRES 47 A 653 LYS VAL SER ARG SER ALA SER ALA GLN GLY THR THR GLN SEQRES 48 A 653 GLU LEU LYS VAL VAL ALA VAL GLY LYS ASN GLY VAL ARG SEQRES 49 A 653 SER GLU ALA ALA THR THR THR PHE ASP TRP GLY MET THR SEQRES 50 A 653 VAL LYS ASP THR SER LEU PRO LYS PRO LEU ALA GLU ASN SEQRES 51 A 653 ILE VAL PRO HET 1PE A1809 8 HETNAM 1PE PENTAETHYLENE GLYCOL HETSYN 1PE PEG400 FORMUL 2 1PE C10 H22 O6 FORMUL 3 HOH *978(H2 O) HELIX 1 1 SER A 183 LYS A 189 1 7 HELIX 2 2 ASP A 197 ARG A 202 1 6 HELIX 3 3 TYR A 254 LEU A 258 5 5 HELIX 4 4 THR A 270 ASN A 280 1 11 HELIX 5 5 SER A 295 LEU A 306 1 12 HELIX 6 6 PHE A 314 GLY A 328 1 15 HELIX 7 7 VAL A 343 PRO A 345 5 3 HELIX 8 8 LEU A 346 VAL A 364 1 19 HELIX 9 9 ASN A 392 MET A 396 5 5 HELIX 10 10 ASP A 415 GLY A 430 1 16 HELIX 11 11 ASN A 432 TYR A 434 5 3 HELIX 12 12 LEU A 442 GLY A 446 1 5 HELIX 13 13 SER A 447 THR A 450 5 4 HELIX 14 14 LYS A 453 LEU A 458 1 6 HELIX 15 15 PRO A 473 GLY A 480 5 8 HELIX 16 16 THR A 482 THR A 495 1 14 HELIX 17 17 GLY A 513 VAL A 518 1 6 HELIX 18 18 ARG A 556 SER A 559 5 4 HELIX 19 19 ASP A 647 ASP A 649 5 3 HELIX 20 20 SER A 668 ALA A 671 5 4 SHEET 1 AA 2 ARG A 211 THR A 212 0 SHEET 2 AA 2 ARG A 521 THR A 522 -1 O THR A 522 N ARG A 211 SHEET 1 AB 9 VAL A 226 SER A 230 0 SHEET 2 AB 9 SER A 467 PHE A 471 1 O LEU A 468 N GLN A 227 SHEET 3 AB 9 VAL A 436 GLU A 441 1 O VAL A 436 N SER A 467 SHEET 4 AB 9 ASN A 407 ALA A 410 1 O PHE A 408 N PHE A 437 SHEET 5 AB 9 LYS A 369 TYR A 373 1 O TRP A 372 N PHE A 409 SHEET 6 AB 9 GLY A 331 THR A 338 1 O TYR A 332 N SER A 371 SHEET 7 AB 9 VAL A 284 SER A 293 1 O GLY A 286 N PHE A 333 SHEET 8 AB 9 SER A 260 PHE A 263 1 O MET A 261 N TYR A 285 SHEET 9 AB 9 VAL A 226 SER A 230 1 O ALA A 228 N VAL A 262 SHEET 1 AC 8 VAL A 525 GLY A 526 0 SHEET 2 AC 8 THR A 602 GLU A 614 1 O LYS A 612 N GLY A 526 SHEET 3 AC 8 TRP A 568 SER A 571 -1 O TRP A 568 N ARG A 607 SHEET 4 AC 8 THR A 602 GLU A 614 -1 O ASP A 605 N THR A 570 SHEET 5 AC 8 TRP A 651 GLU A 653 0 SHEET 6 AC 8 LYS A 632 SER A 638 -1 O MET A 635 N LYS A 652 SHEET 7 AC 8 THR A 674 HIS A 684 -1 N TYR A 676 O SER A 638 SHEET 8 AC 8 THR A 602 GLU A 614 -1 O THR A 602 N HIS A 684 SHEET 1 AD 8 THR A 528 THR A 531 0 SHEET 2 AD 8 VAL A 688 SER A 701 -1 O LEU A 698 N THR A 531 SHEET 3 AD 8 ARG A 577 ASP A 581 0 SHEET 4 AD 8 SER A 591 VAL A 598 -1 O SER A 591 N ASP A 581 SHEET 5 AD 8 VAL A 688 SER A 701 -1 O VAL A 688 N VAL A 598 SHEET 6 AD 8 SER A 657 ASP A 666 0 SHEET 7 AD 8 LYS A 620 GLY A 627 -1 O LEU A 621 N PHE A 665 SHEET 8 AD 8 VAL A 688 SER A 701 -1 O ASN A 694 N LYS A 626 SHEET 1 AE 2 HIS A 537 GLY A 538 0 SHEET 2 AE 2 TRP A 553 ASN A 554 -1 O TRP A 553 N GLY A 538 SHEET 1 AF 2 TRP A 541 VAL A 543 0 SHEET 2 AF 2 LYS A 546 LYS A 549 -1 O LYS A 546 N VAL A 543 SHEET 1 AG 3 THR A 711 ASN A 722 0 SHEET 2 AG 3 GLU A 725 LYS A 733 -1 O GLU A 725 N LYS A 721 SHEET 3 AG 3 THR A 761 SER A 768 -1 O ILE A 762 N VAL A 730 SHEET 1 AH 4 SER A 750 SER A 757 0 SHEET 2 AH 4 ALA A 738 ASP A 747 -1 O TYR A 741 N SER A 757 SHEET 3 AH 4 THR A 777 GLY A 786 -1 O GLU A 779 N LYS A 746 SHEET 4 AH 4 ALA A 795 ASP A 800 -1 O ALA A 795 N VAL A 782 CISPEP 1 ARG A 566 TRP A 567 0 12.63 SITE 1 AC1 4 ALA A 424 THR A 425 TRP A 428 HOH A2978 CRYST1 135.060 58.850 96.670 90.00 110.37 90.00 C 1 2 1 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 0.007404 0.000000 0.002749 0.00000 SCALE2 0.000000 0.016992 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011035 0.00000