10 20 30 40 50 60 70 80 2WWD - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER HYDROLASE 22-OCT-09 2WWD
TITLE 3D-STRUCTURE OF THE MODULAR AUTOLYSIN LYTC FROM TITLE 2 STREPTOCOCCUS PNEUMONIAE IN COMPLEX WITH PNEUMMOCOCCAL TITLE 3 PEPTIDOGLYCAN FRAGMENT
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 PROTEINS
EXPDTA X-RAY DIFFRACTION
AUTHOR I.PEREZ-DORADO,R.SANLES,J.A.HERMOSO,A.GONZALEZ,A.GARCIA,P.GARCIA, AUTHOR 2 J.L.GARCIA
REVDAT 4 03-APR-13 2WWD 1 JRNL REMARK HETSYN REVDAT 3 13-JUL-11 2WWD 1 VERSN REVDAT 2 28-APR-10 2WWD 1 KEYWDS JRNL REVDAT 1 21-APR-10 2WWD 0
JRNL AUTH I.PEREZ-DORADO,A.GONZALEZ,M.MORALES,R.SANLES,W.STRIKER, JRNL AUTH 2 W.VOLLMER,S.MOBASHERY,J.L.GARCIA,M.MARTINEZ-RIPOLL,P.GARCIA, JRNL AUTH 3 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. 2.25 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 57.17 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 25982 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) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1925 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.25 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.31 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1897 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.76 REMARK 3 BIN R VALUE (WORKING SET) : 0.2750 REMARK 3 BIN FREE R VALUE SET COUNT : 152 REMARK 3 BIN FREE R VALUE : 0.3210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3654 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 96 REMARK 3 SOLVENT ATOMS : 136 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) : 38.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.58000 REMARK 3 B22 (A**2) : -0.42000 REMARK 3 B33 (A**2) : 0.24000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.73000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.291 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.208 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.153 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.134 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.947 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): 3899 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5273 ; 1.097 ; 1.936 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 431 ; 5.465 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 212 ;37.205 ;24.434 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 614 ;14.444 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;23.612 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 494 ; 0.079 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3025 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1690 ; 0.196 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2589 ; 0.308 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 192 ; 0.133 ; 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): 72 ; 0.211 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.148 ; 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): 2181 ; 0.542 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3395 ; 0.981 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2098 ; 1.158 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1878 ; 1.802 ; 4.500 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 37 A 76 REMARK 3 ORIGIN FOR THE GROUP (A): 31.3182 -53.4008 3.5460 REMARK 3 T TENSOR REMARK 3 T11: 0.0382 T22: -0.0326 REMARK 3 T33: -0.0848 T12: -0.0273 REMARK 3 T13: -0.0006 T23: -0.0479 REMARK 3 L TENSOR REMARK 3 L11: 1.4282 L22: 4.0716 REMARK 3 L33: 3.7297 L12: -1.2355 REMARK 3 L13: -0.7335 L23: 0.1858 REMARK 3 S TENSOR REMARK 3 S11: -0.0663 S12: 0.1623 S13: -0.0304 REMARK 3 S21: 0.3172 S22: 0.1602 S23: -0.0195 REMARK 3 S31: 0.2591 S32: 0.1184 S33: -0.0938 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): 31.5136 -16.2703 18.3963 REMARK 3 T TENSOR REMARK 3 T11: 0.0209 T22: -0.0374 REMARK 3 T33: -0.0175 T12: -0.0344 REMARK 3 T13: -0.0320 T23: -0.0020 REMARK 3 L TENSOR REMARK 3 L11: 0.2619 L22: 2.3662 REMARK 3 L33: 0.4722 L12: 0.6412 REMARK 3 L13: 0.1485 L23: 0.9195 REMARK 3 S TENSOR REMARK 3 S11: -0.0588 S12: -0.0331 S13: 0.0435 REMARK 3 S21: -0.1201 S22: 0.0700 S23: 0.0609 REMARK 3 S31: 0.0182 S32: 0.0197 S33: -0.0112 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): 33.7124 21.7035 28.5084 REMARK 3 T TENSOR REMARK 3 T11: -0.1437 T22: -0.0625 REMARK 3 T33: 0.2304 T12: -0.0589 REMARK 3 T13: -0.0350 T23: -0.1624 REMARK 3 L TENSOR REMARK 3 L11: 5.9565 L22: 11.4282 REMARK 3 L33: 10.3428 L12: -5.6482 REMARK 3 L13: -5.2786 L23: 8.5951 REMARK 3 S TENSOR REMARK 3 S11: -0.0234 S12: -0.0059 S13: 0.3414 REMARK 3 S21: -0.1347 S22: -0.6668 S23: 0.9701 REMARK 3 S31: -0.1516 S32: -0.0861 S33: 0.6903 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): 14.8410 31.1129 33.0489 REMARK 3 T TENSOR REMARK 3 T11: -0.0329 T22: -0.1221 REMARK 3 T33: 0.1414 T12: -0.0632 REMARK 3 T13: 0.1402 T23: -0.0332 REMARK 3 L TENSOR REMARK 3 L11: 7.4975 L22: 2.7944 REMARK 3 L33: 3.1545 L12: 0.4970 REMARK 3 L13: -1.4500 L23: -0.0155 REMARK 3 S TENSOR REMARK 3 S11: 0.5791 S12: -0.3526 S13: 0.8101 REMARK 3 S21: 0.2118 S22: -0.2556 S23: -0.0134 REMARK 3 S31: -0.4455 S32: 0.2864 S33: -0.3234 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): 1.9399 14.5061 22.6326 REMARK 3 T TENSOR REMARK 3 T11: -0.0341 T22: -0.0207 REMARK 3 T33: -0.0245 T12: 0.0059 REMARK 3 T13: 0.0262 T23: -0.0032 REMARK 3 L TENSOR REMARK 3 L11: 1.8615 L22: 0.4488 REMARK 3 L33: 0.8365 L12: 0.3784 REMARK 3 L13: 0.2693 L23: 0.1732 REMARK 3 S TENSOR REMARK 3 S11: 0.0254 S12: 0.1954 S13: -0.1032 REMARK 3 S21: -0.0244 S22: 0.0215 S23: -0.0593 REMARK 3 S31: 0.0023 S32: -0.0229 S33: -0.0469 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): 9.0133 1.9002 8.7140 REMARK 3 T TENSOR REMARK 3 T11: 0.0198 T22: 0.0465 REMARK 3 T33: 0.0308 T12: 0.0599 REMARK 3 T13: -0.0775 T23: -0.1525 REMARK 3 L TENSOR REMARK 3 L11: 1.7998 L22: 0.2358 REMARK 3 L33: 6.0100 L12: -0.4356 REMARK 3 L13: -2.6028 L23: 1.1710 REMARK 3 S TENSOR REMARK 3 S11: 0.1679 S12: 0.5722 S13: -0.8409 REMARK 3 S21: -0.4009 S22: 0.2757 S23: -0.3135 REMARK 3 S31: 0.4192 S32: 0.6253 S33: -0.4436 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: THE FIRST 37 AA OF THE POLYPEPTIDE REMARK 3 CHAIN WERE NOT MODELLED DUE TO POOR ELECTRON DENSITY. ATOM REMARK 3 RECORD CONTAINS RESIDUAL B FACTORS ONLY.
REMARK 4 REMARK 4 2WWD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-OCT-09. REMARK 100 THE PDBE ID CODE IS EBI-41457.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-JUL-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) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27909 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.25 REMARK 200 RESOLUTION RANGE LOW (A) : 75.00 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.0 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.5 REMARK 200 R MERGE (I) : 0.08 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.70 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.37 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.6 REMARK 200 R MERGE FOR SHELL (I) : 0.50 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.60 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2WW5 REMARK 200 REMARK 200 REMARK: NONE
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.1 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 33.43500 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 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 38 96.37 -173.43 REMARK 500 ASP A 43 79.85 -113.52 REMARK 500 ASP A 51 -93.81 -58.41 REMARK 500 ASP A 219 -83.56 -140.69 REMARK 500 ARG A 259 30.40 -93.51 REMARK 500 THR A 265 -162.02 -119.02 REMARK 500 SER A 303 104.91 -42.70 REMARK 500 GLU A 333 -12.84 -142.33 REMARK 500 THR A 413 -105.68 -111.70 REMARK 500 ARG A 414 4.32 -67.85 REMARK 500 REMARK 500 REMARK: NULL
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 MU2 A 470
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 NAG A 469 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MU2 A 470 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 607 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CHT A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CHT A 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CHT A 703 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CHT A 704 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CHT A 705 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CHT A 706 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CHT A 707
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2WW5 RELATED DB: PDB REMARK 900 3D-STRUCTURE OF THE MODULAR AUTOLYSIN LYTC REMARK 900 FROM STREPTOCOCCUS PNEUMONIAE AT 1.6 A REMARK 900 RESOLUTION REMARK 900 RELATED ID: 2WWC RELATED DB: PDB REMARK 900 3D-STRUCTURE OF THE MODULAR AUTOLYSIN LYTC REMARK 900 FROM STREPTOCOCCUS PNEUMONIAE IN COMPLEX WITH REMARK 900 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 2WWD 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 NAG A 469 14 HET MU2 A 470 33 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
HETNAM CHT CHOLINE ION HETNAM GOL GLYCEROL HETNAM MU2 N-ACETYLMURAMYL-L-ALANYL-D-ISOGLUTAMINE HETNAM NAG N-ACETYL-D-GLUCOSAMINE
HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL
FORMUL 2 CHT 7(C5 H14 N O 1+) FORMUL 3 GOL 7(C3 H8 O3) FORMUL 4 MU2 C19 H32 N4 O11 FORMUL 5 NAG C8 H15 N O6 FORMUL 6 HOH *136(H2 O)
HELIX 1 1 LYS A 133 TYR A 137 5 5 HELIX 2 2 LYS A 194 TYR A 198 5 5 HELIX 3 3 SER A 275 GLY A 279 5 5 HELIX 4 4 ASP A 283 ASN A 291 1 9 HELIX 5 5 GLU A 309 GLY A 321 1 13 HELIX 6 6 ASN A 334 TYR A 352 1 19 HELIX 7 7 ASP A 379 ALA A 397 1 19 HELIX 8 8 ARG A 408 THR A 413 1 6 HELIX 9 9 HIS A 417 LYS A 422 1 6
SHEET 1 AA 1 TYR A 41 ASP A 43 0 SHEET 2 AA 1 TYR A 46 VAL A 48 -1 O TYR A 46 N ASP A 43 SHEET 1 AB 1 GLU A 58 ASP A 62 0 SHEET 2 AB 1 ALA A 67 ILE A 71 -1 O ALA A 67 N ASP A 62 SHEET 1 AC 1 GLU A 81 HIS A 83 0 SHEET 2 AC 1 TYR A 86 LEU A 88 -1 O TYR A 86 N HIS A 83 SHEET 1 AD 1 GLU A 98 ASP A 102 0 SHEET 2 AD 1 SER A 107 LEU A 111 -1 O SER A 107 N ASP A 102 SHEET 1 AE 1 GLU A 121 ILE A 125 0 SHEET 2 AE 1 LYS A 128 PHE A 132 -1 O LYS A 128 N ILE A 125 SHEET 1 AF 1 GLN A 142 GLN A 144 0 SHEET 2 AF 1 TYR A 147 LEU A 149 -1 O TYR A 147 N GLN A 144 SHEET 1 AG 1 GLU A 159 ASP A 163 0 SHEET 2 AG 1 ALA A 168 LEU A 172 -1 O ALA A 168 N ASP A 163 SHEET 1 AH 1 GLU A 182 VAL A 186 0 SHEET 2 AH 1 LYS A 189 PHE A 193 -1 O LYS A 189 N VAL A 186 SHEET 1 AI 1 GLU A 203 GLN A 205 0 SHEET 2 AI 1 TYR A 208 LEU A 210 -1 O TYR A 208 N GLN A 205 SHEET 1 AJ 2 GLU A 220 MET A 223 0 SHEET 2 AJ 2 ALA A 226 PHE A 230 -1 O ALA A 226 N MET A 223 SHEET 3 AJ 2 LEU A 236 ASP A 241 -1 N LYS A 237 O ILE A 229 SHEET 1 AK 2 GLY A 245 ARG A 249 0 SHEET 2 AK 2 LYS A 252 PHE A 256 -1 O LYS A 252 N ARG A 249 SHEET 3 AK 2 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 28 O VAL A 296 N GLY A 325 SHEET 9 AL 9 LYS A 269 ILE A 274
LINK C1 NAG A 469 O4 MU2 A 470 1555 1555 1.43
SITE 1 AC1 6 GLU A 365 TYR A 405 TYR A 407 ALA A 428 SITE 2 AC1 6 TYR A 430 MU2 A 470 SITE 1 AC2 9 SER A 73 ASP A 74 TYR A 407 ARG A 408 SITE 2 AC2 9 SER A 409 ALA A 429 TYR A 430 THR A 431 SITE 3 AC2 9 NAG A 469 SITE 1 AC3 3 LYS A 89 MET A 94 GLU A 98 SITE 1 AC4 3 TYR A 105 LYS A 106 LYS A 133 SITE 1 AC5 5 TRP A 122 GLN A 144 GLY A 145 SER A 146 SITE 2 AC5 5 TYR A 147 SITE 1 AC6 3 GLN A 142 TRP A 143 ASP A 163 SITE 1 AC7 5 TYR A 178 ASN A 180 GLN A 181 LYS A 195 SITE 2 AC7 5 TRP A 196 SITE 1 AC8 4 LYS A 173 ASN A 180 GLN A 181 GLU A 182 SITE 1 AC9 4 ARG A 253 GLU A 266 ALA A 268 ASP A 294 SITE 1 BC1 6 TRP A 42 GLY A 44 TYR A 65 PHE A 69 SITE 2 BC1 6 GLY A 91 TYR A 93 SITE 1 BC2 5 TRP A 59 TRP A 68 TYR A 86 MET A 94 SITE 2 BC2 5 ASP A 114 SITE 1 BC3 6 TRP A 82 GLY A 84 PHE A 109 TYR A 117 SITE 2 BC3 6 TRP A 135 ARG A 259 SITE 1 BC4 5 TRP A 99 TRP A 108 TYR A 130 MET A 138 SITE 2 BC4 5 GLN A 152 SITE 1 BC5 3 TRP A 122 TRP A 129 TYR A 147 SITE 1 BC6 5 GLY A 145 TYR A 166 PHE A 170 TYR A 178 SITE 2 BC6 5 TRP A 196 SITE 1 BC7 4 TRP A 160 TYR A 169 TYR A 191 SER A 213
CRYST1 59.400 66.870 77.920 90.00 105.77 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 0.016835 0.000000 0.004754 0.00000
SCALE2 0.000000 0.014954 0.000000 0.00000
SCALE3 0.000000 0.000000 0.013336 0.00000