HEADER HYDROLASE 21-OCT-09 2WW5 TITLE 3D-STRUCTURE OF THE MODULAR AUTOLYSIN LYTC FROM STREPTOCOCCUS TITLE 2 PNEUMONIAE AT 1.6 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: 1,4-BETA-N-ACETYLMURAMIDASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LYTC AUTOLYSIN; COMPND 5 EC: 3.2.1.17; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS PNEUMONIAE; SOURCE 3 ORGANISM_TAXID: 171101; SOURCE 4 STRAIN: R6; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PLCC14 KEYWDS HYDROLASE, GLYCOSIDASE, CHOLINE-BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR I.PEREZ-DORADO,R.SANLES,J.A.HERMOSO,A.GONZALEZ,A.GARCIA,P.GARCIA, AUTHOR 2 J.L.GARCIA,M.MENENDEZ REVDAT 5 08-MAY-24 2WW5 1 REMARK SHEET REVDAT 4 21-SEP-11 2WW5 1 JRNL REVDAT 3 13-JUL-11 2WW5 1 VERSN REVDAT 2 28-APR-10 2WW5 1 KEYWDS JRNL REVDAT 1 21-APR-10 2WW5 0 JRNL AUTH I.PEREZ-DORADO,A.GONZALEZ,M.MORALES,R.SANLES,W.STRIKER, JRNL AUTH 2 W.VOLLMER,S.MOBASHERY,J.L.GARCIA,A.GARCIA,M.MARTINEZ-RIPOLL, JRNL AUTH 3 P.GARCIA,J.A.HERMOSO JRNL TITL INSIGHTS INTO PNEUMOCOCCAL FRATRICIDE FROM THE CRYSTAL JRNL TITL 2 STRUCTURES OF THE MODULAR KILLING FACTOR LYTC. JRNL REF NAT.STRUCT.MOL.BIOL. V. 17 576 2010 JRNL REFN ISSN 1545-9993 JRNL PMID 20400948 JRNL DOI 10.1038/NSMB.1817 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.MONTERROSO,J.L.SAIZ,P.GARCIA,J.L.GARCIA,M.MENENDEZ REMARK 1 TITL INSIGHTS INTO THE STRUCTURE-FUNCTION RELATIONSHIPS OF REMARK 1 TITL 2 PNEUMOCOCCAL CELL WALL LYSOZYMES, LYTC AND CPL- 1. REMARK 1 REF J.BIOL.CHEM. V. 283 28618 2008 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 18667432 REMARK 1 DOI 10.1074/JBC.M802808200 REMARK 1 REFERENCE 2 REMARK 1 AUTH B.MONTERROSO,C.LOPEZ-ZUMEL,J.L.GARCIA,J.L.SAIZ,P.GARCIA, REMARK 1 AUTH 2 N.E.CAMPILLO,M.MENENDEZ REMARK 1 TITL UNRAVELLING THE STRUCTURE OF THE PNEUMOCOCCAL AUTOLYTIC REMARK 1 TITL 2 LYSOZYME. REMARK 1 REF BIOCHEM.J. V. 391 41 2005 REMARK 1 REFN ISSN 0264-6021 REMARK 1 PMID 15943581 REMARK 1 DOI 10.1042/BJ20050612 REMARK 1 REFERENCE 3 REMARK 1 AUTH P.GARCIA,M.PAZ GONZALEZ,E.GARCIA,J.L.GARCIA,R.LOPEZ REMARK 1 TITL THE MOLECULAR CHARACTERIZATION OF THE FIRST AUTOLYTIC REMARK 1 TITL 2 LYSOZYME OF STREPTOCOCCUS PNEUMONIAE REVEALS EVOLUTIONARY REMARK 1 TITL 3 MOBILE DOMAINS. REMARK 1 REF MOL.MICROBIOL. V. 33 128 1999 REMARK 1 REFN ISSN 0950-382X REMARK 1 PMID 10411730 REMARK 2 REMARK 2 RESOLUTION. 1.61 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) : 1.61 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 72.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 70725 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.100 REMARK 3 FREE R VALUE TEST SET COUNT : 5410 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) : 1.61 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.65 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4762 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.67 REMARK 3 BIN R VALUE (WORKING SET) : 0.3370 REMARK 3 BIN FREE R VALUE SET COUNT : 336 REMARK 3 BIN FREE R VALUE : 0.3910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3645 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 93 REMARK 3 SOLVENT ATOMS : 565 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.28000 REMARK 3 B22 (A**2) : 0.09000 REMARK 3 B33 (A**2) : -0.45000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.13000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.086 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.084 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.056 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.081 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.964 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3852 ; 0.009 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5204 ; 1.077 ; 1.923 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 430 ; 5.093 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 211 ;37.443 ;24.408 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 622 ;10.166 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;18.124 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 480 ; 0.077 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2993 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1686 ; 0.194 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2614 ; 0.310 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 405 ; 0.101 ; 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): 53 ; 0.163 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 34 ; 0.108 ; 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): 2179 ; 0.731 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3391 ; 1.153 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2056 ; 1.800 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1813 ; 2.629 ; 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 : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 38 A 76 REMARK 3 ORIGIN FOR THE GROUP (A): 31.2979 -53.4587 4.1636 REMARK 3 T TENSOR REMARK 3 T11: -0.0048 T22: 0.0069 REMARK 3 T33: -0.0549 T12: 0.0117 REMARK 3 T13: 0.0036 T23: -0.0074 REMARK 3 L TENSOR REMARK 3 L11: 1.2478 L22: 2.1182 REMARK 3 L33: 1.7996 L12: 0.2129 REMARK 3 L13: 0.5885 L23: -0.0918 REMARK 3 S TENSOR REMARK 3 S11: 0.1072 S12: 0.1542 S13: -0.0595 REMARK 3 S21: 0.0131 S22: -0.0713 S23: -0.0021 REMARK 3 S31: 0.0811 S32: 0.2177 S33: -0.0359 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 77 A 217 REMARK 3 ORIGIN FOR THE GROUP (A): 31.7130 -16.3112 17.8517 REMARK 3 T TENSOR REMARK 3 T11: 0.0093 T22: -0.0118 REMARK 3 T33: -0.0235 T12: -0.0277 REMARK 3 T13: -0.0113 T23: 0.0312 REMARK 3 L TENSOR REMARK 3 L11: 0.1559 L22: 1.7378 REMARK 3 L33: 0.2008 L12: 0.3566 REMARK 3 L13: 0.1237 L23: 0.5906 REMARK 3 S TENSOR REMARK 3 S11: -0.0411 S12: 0.0510 S13: 0.0484 REMARK 3 S21: -0.0449 S22: 0.0320 S23: 0.0742 REMARK 3 S31: 0.0180 S32: 0.0352 S33: 0.0091 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 218 A 242 REMARK 3 ORIGIN FOR THE GROUP (A): 33.7893 22.0514 26.5375 REMARK 3 T TENSOR REMARK 3 T11: -0.0583 T22: -0.0601 REMARK 3 T33: 0.0720 T12: -0.0194 REMARK 3 T13: -0.0052 T23: 0.0311 REMARK 3 L TENSOR REMARK 3 L11: 2.5215 L22: 2.3221 REMARK 3 L33: 1.5071 L12: -1.7823 REMARK 3 L13: -0.3907 L23: 1.5158 REMARK 3 S TENSOR REMARK 3 S11: -0.0854 S12: -0.0513 S13: 0.1424 REMARK 3 S21: -0.0316 S22: -0.0012 S23: 0.0732 REMARK 3 S31: -0.0290 S32: 0.0630 S33: 0.0866 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 243 A 267 REMARK 3 ORIGIN FOR THE GROUP (A): 14.7426 31.9006 30.3787 REMARK 3 T TENSOR REMARK 3 T11: 0.0167 T22: -0.0363 REMARK 3 T33: 0.0025 T12: -0.0264 REMARK 3 T13: 0.0326 T23: -0.0194 REMARK 3 L TENSOR REMARK 3 L11: 1.7590 L22: 0.1705 REMARK 3 L33: 0.6863 L12: 0.5231 REMARK 3 L13: -0.5235 L23: -0.2448 REMARK 3 S TENSOR REMARK 3 S11: 0.1025 S12: -0.0453 S13: 0.1300 REMARK 3 S21: 0.0529 S22: -0.0828 S23: 0.0126 REMARK 3 S31: -0.0882 S32: 0.0547 S33: -0.0197 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 268 A 365 REMARK 3 RESIDUE RANGE : A 381 A 468 REMARK 3 ORIGIN FOR THE GROUP (A): 1.9062 14.6935 21.3525 REMARK 3 T TENSOR REMARK 3 T11: -0.0231 T22: -0.0085 REMARK 3 T33: -0.0111 T12: -0.0084 REMARK 3 T13: 0.0046 T23: -0.0049 REMARK 3 L TENSOR REMARK 3 L11: 0.6237 L22: 0.1326 REMARK 3 L33: 0.5758 L12: 0.2572 REMARK 3 L13: 0.0733 L23: -0.0925 REMARK 3 S TENSOR REMARK 3 S11: -0.0295 S12: 0.0706 S13: -0.0435 REMARK 3 S21: 0.0044 S22: 0.0684 S23: -0.0245 REMARK 3 S31: -0.0058 S32: -0.0447 S33: -0.0390 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 366 A 380 REMARK 3 ORIGIN FOR THE GROUP (A): 8.9205 1.3223 8.0283 REMARK 3 T TENSOR REMARK 3 T11: 0.0062 T22: 0.0266 REMARK 3 T33: 0.0089 T12: -0.0099 REMARK 3 T13: 0.0021 T23: -0.0491 REMARK 3 L TENSOR REMARK 3 L11: 1.3565 L22: 3.3874 REMARK 3 L33: 1.0541 L12: -0.5100 REMARK 3 L13: 1.1807 L23: -0.7348 REMARK 3 S TENSOR REMARK 3 S11: 0.1545 S12: 0.1138 S13: -0.3516 REMARK 3 S21: -0.3365 S22: 0.1170 S23: -0.2766 REMARK 3 S31: 0.4306 S32: 0.0735 S33: -0.2715 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. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. MODEL REMARK 3 WAS SUBJECTED TO A FINAL CYCLE OF REFINEMENT USING REFMAC5 WITH REMARK 3 TLS. THE FIRST 37 AMINO-ACIDS OF THE POLYPEPTIDE CHAIN WERE NOT REMARK 3 MODELLED DUE TO THEY WERE NOT VISIBLE IN THE ELECTRON DENSITY REMARK 3 MAP. REMARK 4 REMARK 4 2WW5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1290038960. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-08 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 : ESRF REMARK 200 BEAMLINE : ID14-4 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9800 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 76161 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.610 REMARK 200 RESOLUTION RANGE LOW (A) : 72.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.61 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.42000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELX, SHARP REMARK 200 STARTING MODEL: NONE REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 34.69000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 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 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 ASN A 1 REMARK 465 GLU A 2 REMARK 465 THR A 3 REMARK 465 GLU A 4 REMARK 465 VAL A 5 REMARK 465 ALA A 6 REMARK 465 LYS A 7 REMARK 465 THR A 8 REMARK 465 SER A 9 REMARK 465 GLN A 10 REMARK 465 ASP A 11 REMARK 465 THR A 12 REMARK 465 THR A 13 REMARK 465 THR A 14 REMARK 465 ALA A 15 REMARK 465 SER A 16 REMARK 465 SER A 17 REMARK 465 SER A 18 REMARK 465 SER A 19 REMARK 465 GLU A 20 REMARK 465 GLN A 21 REMARK 465 ASN A 22 REMARK 465 GLN A 23 REMARK 465 SER A 24 REMARK 465 SER A 25 REMARK 465 ASN A 26 REMARK 465 LYS A 27 REMARK 465 THR A 28 REMARK 465 GLN A 29 REMARK 465 THR A 30 REMARK 465 SER A 31 REMARK 465 ALA A 32 REMARK 465 GLU A 33 REMARK 465 VAL A 34 REMARK 465 GLN A 35 REMARK 465 THR A 36 REMARK 465 ASN A 37 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 39 -65.07 -128.27 REMARK 500 ASP A 51 -171.20 -69.80 REMARK 500 ASP A 219 -103.91 -136.74 REMARK 500 THR A 265 -169.59 -117.32 REMARK 500 ASN A 401 75.52 -109.86 REMARK 500 THR A 413 -98.97 -129.25 REMARK 500 GLU A 435 57.58 39.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AL" 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 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CHT A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CHT A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CHT A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CHT A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CHT A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CHT A 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CHT A 707 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 802 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WWD RELATED DB: PDB REMARK 900 3D-STRUCTURE OF THE MODULAR AUTOLYSIN LYTC FROM STREPTOCOCCUS REMARK 900 PNEUMONIAE IN COMPLEX WITH PNEUMMOCOCCAL PEPTIDOGLYCAN FRAGMENT REMARK 900 RELATED ID: 2WWC RELATED DB: PDB REMARK 900 3D-STRUCTURE OF THE MODULAR AUTOLYSIN LYTC FROM STREPTOCOCCUS REMARK 900 PNEUMONIAE IN COMPLEX WITH SYNTHETIC PEPTIDOGLYCAN LIGAND REMARK 999 REMARK 999 SEQUENCE REMARK 999 ENTRY ACCESSION CODE CORRESPONDS TO THE IMMATURE PROTEIN REMARK 999 WHICH POSSESSES A SIGNAL PEPTIDE OF 33 AMINO-ACIDS BUT THE REMARK 999 STRUCTURE HERE REPORTED CORRESPONDS TO THE MATURE FORM. REMARK 999 THE FIRST AMINO-ACID OF THE MATURE PROTEIN IS REFERED AS REMARK 999 TO RESIDUE 1. DBREF 2WW5 A 1 468 UNP Q9Z4J8 Q9Z4J8_STRPN 34 501 SEQRES 1 A 468 ASN GLU THR GLU VAL ALA LYS THR SER GLN ASP THR THR SEQRES 2 A 468 THR ALA SER SER SER SER GLU GLN ASN GLN SER SER ASN SEQRES 3 A 468 LYS THR GLN THR SER ALA GLU VAL GLN THR ASN ALA ALA SEQRES 4 A 468 ALA TYR TRP ASP GLY ASP TYR TYR VAL LYS ASP ASP GLY SEQRES 5 A 468 SER LYS ALA GLN SER GLU TRP ILE PHE ASP ASN TYR TYR SEQRES 6 A 468 LYS ALA TRP PHE TYR ILE ASN SER ASP GLY ARG TYR SER SEQRES 7 A 468 GLN ASN GLU TRP HIS GLY ASN TYR TYR LEU LYS SER GLY SEQRES 8 A 468 GLY TYR MET ALA GLN ASN GLU TRP ILE TYR ASP SER ASN SEQRES 9 A 468 TYR LYS SER TRP PHE TYR LEU LYS SER ASP GLY ALA TYR SEQRES 10 A 468 ALA HIS GLN GLU TRP GLN LEU ILE GLY ASN LYS TRP TYR SEQRES 11 A 468 TYR PHE LYS LYS TRP GLY TYR MET ALA LYS SER GLN TRP SEQRES 12 A 468 GLN GLY SER TYR PHE LEU ASN GLY GLN GLY ALA MET ILE SEQRES 13 A 468 GLN ASN GLU TRP LEU TYR ASP PRO ALA TYR SER ALA TYR SEQRES 14 A 468 PHE TYR LEU LYS SER ASP GLY THR TYR ALA ASN GLN GLU SEQRES 15 A 468 TRP GLN LYS VAL GLY GLY LYS TRP TYR TYR PHE LYS LYS SEQRES 16 A 468 TRP GLY TYR MET ALA ARG ASN GLU TRP GLN GLY ASN TYR SEQRES 17 A 468 TYR LEU THR GLY SER GLY ALA MET ALA THR ASP GLU VAL SEQRES 18 A 468 ILE MET ASP GLY ALA ARG TYR ILE PHE ALA ALA SER GLY SEQRES 19 A 468 GLU LEU LYS GLU LYS LYS ASP LEU ASN VAL GLY TRP VAL SEQRES 20 A 468 HIS ARG ASP GLY LYS ARG TYR PHE PHE ASN ASN ARG GLU SEQRES 21 A 468 GLU GLN VAL GLY THR GLU HIS ALA LYS LYS ILE ILE ASP SEQRES 22 A 468 ILE SER GLU HIS ASN GLY ARG ILE ASN ASP TRP LYS LYS SEQRES 23 A 468 VAL ILE ASP GLU ASN GLU VAL ASP GLY VAL ILE VAL ARG SEQRES 24 A 468 LEU GLY TYR SER GLY LYS GLU ASP LYS GLU LEU ALA HIS SEQRES 25 A 468 ASN ILE LYS GLU LEU ASN ARG LEU GLY ILE PRO TYR GLY SEQRES 26 A 468 VAL TYR LEU TYR THR TYR ALA GLU ASN GLU THR ASP ALA SEQRES 27 A 468 GLU ASN ASP ALA LYS GLN THR ILE GLU LEU ILE LYS LYS SEQRES 28 A 468 TYR ASN MET ASN LEU SER TYR PRO ILE TYR TYR ASP VAL SEQRES 29 A 468 GLU ASN TRP GLU TYR VAL ASN LYS SER LYS ARG ALA PRO SEQRES 30 A 468 SER ASP THR ASP THR TRP VAL LYS ILE ILE ASN LYS TYR SEQRES 31 A 468 MET ASP THR MET LYS GLN ALA GLY TYR GLN ASN VAL TYR SEQRES 32 A 468 VAL TYR SER TYR ARG SER LEU LEU GLN THR ARG LEU LYS SEQRES 33 A 468 HIS PRO ASP ILE LEU LYS HIS VAL ASN TRP VAL ALA ALA SEQRES 34 A 468 TYR THR ASN ALA LEU GLU TRP GLU ASN PRO TYR TYR SER SEQRES 35 A 468 GLY GLU LYS GLY TRP GLN TYR THR SER SER GLU TYR MET SEQRES 36 A 468 LYS GLY ILE GLN GLY ARG VAL ASP VAL SER VAL TRP TYR HET GOL A 601 6 HET GOL A 602 6 HET GOL A 603 6 HET GOL A 604 6 HET GOL A 605 6 HET GOL A 606 6 HET GOL A 607 6 HET CHT A 701 7 HET CHT A 702 7 HET CHT A 703 7 HET CHT A 704 7 HET CHT A 705 7 HET CHT A 706 7 HET CHT A 707 7 HET CL A 801 1 HET CL A 802 1 HETNAM GOL GLYCEROL HETNAM CHT CHOLINE ION HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 7(C3 H8 O3) FORMUL 9 CHT 7(C5 H14 N O 1+) FORMUL 16 CL 2(CL 1-) FORMUL 18 HOH *565(H2 O) HELIX 1 1 LYS A 89 TYR A 93 5 5 HELIX 2 2 LYS A 133 TYR A 137 5 5 HELIX 3 3 LYS A 194 TYR A 198 5 5 HELIX 4 4 SER A 275 GLY A 279 5 5 HELIX 5 5 ASP A 283 GLU A 292 1 10 HELIX 6 6 GLU A 309 GLY A 321 1 13 HELIX 7 7 ASN A 334 TYR A 352 1 19 HELIX 8 8 ASP A 379 ALA A 397 1 19 HELIX 9 9 ARG A 408 GLN A 412 1 5 HELIX 10 10 HIS A 417 LYS A 422 1 6 SHEET 1 AA 2 TYR A 41 ASP A 43 0 SHEET 2 AA 2 TYR A 46 VAL A 48 -1 O TYR A 46 N ASP A 43 SHEET 1 AB 2 GLU A 58 ASP A 62 0 SHEET 2 AB 2 ALA A 67 ILE A 71 -1 O ALA A 67 N ASP A 62 SHEET 1 AC 2 GLU A 81 HIS A 83 0 SHEET 2 AC 2 TYR A 86 LEU A 88 -1 O TYR A 86 N HIS A 83 SHEET 1 AD 2 GLU A 98 ASP A 102 0 SHEET 2 AD 2 SER A 107 LEU A 111 -1 O SER A 107 N ASP A 102 SHEET 1 AE 2 GLU A 121 ILE A 125 0 SHEET 2 AE 2 LYS A 128 PHE A 132 -1 O LYS A 128 N ILE A 125 SHEET 1 AF 2 GLN A 142 GLN A 144 0 SHEET 2 AF 2 TYR A 147 LEU A 149 -1 O TYR A 147 N GLN A 144 SHEET 1 AG 2 GLU A 159 TYR A 162 0 SHEET 2 AG 2 TYR A 169 LEU A 172 -1 O PHE A 170 N LEU A 161 SHEET 1 AH 2 GLU A 182 VAL A 186 0 SHEET 2 AH 2 LYS A 189 PHE A 193 -1 O LYS A 189 N VAL A 186 SHEET 1 AI 2 GLU A 203 GLN A 205 0 SHEET 2 AI 2 TYR A 208 LEU A 210 -1 O TYR A 208 N GLN A 205 SHEET 1 AJ 3 GLU A 220 MET A 223 0 SHEET 2 AJ 3 ALA A 226 PHE A 230 -1 O ALA A 226 N MET A 223 SHEET 3 AJ 3 LEU A 236 ASP A 241 -1 N LYS A 237 O ILE A 229 SHEET 1 AK 3 GLY A 245 ARG A 249 0 SHEET 2 AK 3 LYS A 252 PHE A 256 -1 O LYS A 252 N ARG A 249 SHEET 3 AK 3 GLN A 262 VAL A 263 -1 O VAL A 263 N PHE A 255 SHEET 1 AL 9 LYS A 269 ILE A 274 0 SHEET 2 AL 9 VAL A 462 TYR A 468 -1 O ASP A 463 N ASP A 273 SHEET 3 AL 9 LYS A 445 GLU A 453 -1 O LYS A 445 N TYR A 468 SHEET 4 AL 9 VAL A 424 ALA A 428 1 O ASN A 425 N GLY A 446 SHEET 5 AL 9 VAL A 402 TYR A 407 1 O VAL A 404 N ASN A 425 SHEET 6 AL 9 ILE A 360 ASP A 363 1 O ILE A 360 N TYR A 403 SHEET 7 AL 9 TYR A 324 TYR A 329 1 O VAL A 326 N TYR A 361 SHEET 8 AL 9 GLY A 295 TYR A 302 1 O VAL A 296 N GLY A 325 SHEET 9 AL 9 LYS A 269 ILE A 274 0 SITE 1 AC1 7 ASN A 72 ARG A 76 TYR A 77 SER A 78 SITE 2 AC1 7 GLU A 81 ARG A 408 GLN A 412 SITE 1 AC2 5 TRP A 135 TYR A 137 GLU A 260 HOH A2331 SITE 2 AC2 5 HOH A2558 SITE 1 AC3 4 ASN A 127 TRP A 129 GLN A 157 HOH A2560 SITE 1 AC4 4 TRP A 122 GLN A 144 TYR A 147 CHT A 705 SITE 1 AC5 7 GLN A 142 TRP A 143 ASP A 163 ALA A 165 SITE 2 AC5 7 TYR A 166 HOH A2181 HOH A2561 SITE 1 AC6 6 ARG A 253 GLU A 266 ASP A 294 HOH A2562 SITE 2 AC6 6 HOH A2563 HOH A2564 SITE 1 AC7 3 TYR A 302 TYR A 369 VAL A 370 SITE 1 AC8 6 TRP A 42 TYR A 65 PHE A 69 TYR A 77 SITE 2 AC8 6 GLY A 91 TYR A 93 SITE 1 AC9 6 TRP A 59 TRP A 68 TYR A 86 MET A 94 SITE 2 AC9 6 ASP A 114 HOH A2071 SITE 1 BC1 6 TRP A 82 GLY A 84 TYR A 105 PHE A 109 SITE 2 BC1 6 TYR A 117 TRP A 135 SITE 1 BC2 5 TRP A 99 TRP A 108 TYR A 130 MET A 138 SITE 2 BC2 5 GLN A 152 SITE 1 BC3 4 TRP A 122 TRP A 129 ASP A 175 GOL A 604 SITE 1 BC4 6 TRP A 143 GLY A 145 TYR A 166 PHE A 170 SITE 2 BC4 6 TYR A 178 TRP A 196 SITE 1 BC5 4 TYR A 191 MET A 199 ARG A 201 SER A 213 SITE 1 BC6 4 ASN A 85 ALA A 116 TYR A 117 HIS A 119 SITE 1 BC7 3 ARG A 408 SER A 409 HOH A2483 CRYST1 59.800 69.380 75.870 90.00 106.03 90.00 P 1 21 1 2 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 0.016722 0.000000 0.004805 0.00000 SCALE2 0.000000 0.014413 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013714 0.00000