HEADER HYDROLASE 17-FEB-26 23TZ TITLE CRYSTAL STRUCTURE OF CLEAVED DL-ENDOPEPTIDASE CWLO FROM BACILLUS TITLE 2 SUBTILIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PEPTIDOGLYCAN DL-ENDOPEPTIDASE CWLO; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: D-GAMMA-GLUTAMYL-MESO-DIAMINOPIMELYL DL-ENDOPEPTIDASE,PSPA2; COMPND 5 EC: 3.4.-.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168; SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 GENE: CWLO, YVCE, YZKA, BSU34800; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI B; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 37762 KEYWDS BACILLUS SUBTILIS, AUTOLYSIN, DL-ENDOPEPTIDASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.NAKANE,B.MIKAMI,K.OGURA,W.HASHIMOTO REVDAT 1 11-MAR-26 23TZ 0 JRNL AUTH M.NAKANE,B.MIKAMI,K.OGURA,W.HASHIMOTO JRNL TITL CRYSTAL STRUCTURE OF CLEAVED DL-ENDOPEPTIDASE CWLO FROM JRNL TITL 2 BACILLUS SUBTILIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.21.2_5419: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 11902 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 596 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 38.8100 - 3.3300 1.00 2987 158 0.1636 0.1782 REMARK 3 2 3.3300 - 2.6500 1.00 2807 147 0.2191 0.2166 REMARK 3 3 2.6400 - 2.3100 1.00 2777 147 0.2463 0.2965 REMARK 3 4 2.3100 - 2.1000 1.00 2735 144 0.2768 0.3084 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.47 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1035 REMARK 3 ANGLE : 0.819 1399 REMARK 3 CHIRALITY : 0.056 150 REMARK 3 PLANARITY : 0.006 185 REMARK 3 DIHEDRAL : 14.338 362 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 339 THROUGH 376 ) REMARK 3 ORIGIN FOR THE GROUP (A): 16.3504 -4.3966 -5.7654 REMARK 3 T TENSOR REMARK 3 T11: 0.3995 T22: 0.2791 REMARK 3 T33: 0.3284 T12: -0.1085 REMARK 3 T13: 0.0762 T23: -0.1126 REMARK 3 L TENSOR REMARK 3 L11: 5.4581 L22: 2.8776 REMARK 3 L33: 7.2869 L12: -2.3951 REMARK 3 L13: -2.6948 L23: 3.1857 REMARK 3 S TENSOR REMARK 3 S11: -0.0013 S12: -0.2267 S13: 0.0153 REMARK 3 S21: 0.1524 S22: 0.1322 S23: -0.0342 REMARK 3 S31: -0.0460 S32: -0.2036 S33: -0.0980 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 377 THROUGH 430 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.0180 -3.2807 -19.0310 REMARK 3 T TENSOR REMARK 3 T11: 0.4617 T22: 0.3575 REMARK 3 T33: 0.3634 T12: 0.1038 REMARK 3 T13: 0.1146 T23: 0.0446 REMARK 3 L TENSOR REMARK 3 L11: 1.3768 L22: 3.6329 REMARK 3 L33: 6.1633 L12: -2.1130 REMARK 3 L13: -2.2787 L23: 3.2983 REMARK 3 S TENSOR REMARK 3 S11: 0.7590 S12: 0.4954 S13: 0.3611 REMARK 3 S21: -0.7838 S22: -0.4914 S23: -0.3699 REMARK 3 S31: -1.2501 S32: -0.8776 S33: -0.1902 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 431 THROUGH 473 ) REMARK 3 ORIGIN FOR THE GROUP (A): 26.1522 -7.1850 -17.6140 REMARK 3 T TENSOR REMARK 3 T11: 0.3399 T22: 0.3682 REMARK 3 T33: 0.4301 T12: -0.0537 REMARK 3 T13: 0.1021 T23: -0.0451 REMARK 3 L TENSOR REMARK 3 L11: 2.6864 L22: 2.2208 REMARK 3 L33: 5.8605 L12: -1.6052 REMARK 3 L13: -3.3324 L23: 3.4891 REMARK 3 S TENSOR REMARK 3 S11: 0.4779 S12: -0.2701 S13: 0.6786 REMARK 3 S21: -0.1024 S22: 0.2189 S23: -0.4608 REMARK 3 S31: -0.5407 S32: 0.7453 S33: -0.3897 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 23TZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-FEB-26. REMARK 100 THE DEPOSITION ID IS D_1300070415. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-OCT-25 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER R 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11908 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 41.400 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.67 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.5200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.34 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M 2-(N-MORPHOLINO)ETHANESULFONIC REMARK 280 ACID (MES) MONOHYDRATE, PH 6.5, 12% (W/V) POLYETHYLENE GLYCOL 20, REMARK 280 000, VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 55.73400 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.27400 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.27400 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 83.60100 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.27400 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.27400 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 27.86700 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.27400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.27400 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 83.60100 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.27400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.27400 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 27.86700 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 55.73400 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 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 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 THR A 425 -98.94 -112.89 REMARK 500 REMARK 500 REMARK: NULL DBREF 23TZ A 339 473 UNP P40767 CWLO_BACSU 339 473 SEQRES 1 A 135 ASN SER GLY GLY ILE GLU GLY ALA ILE SER VAL GLY SER SEQRES 2 A 135 SER ILE VAL GLY GLN SER PRO TYR LYS PHE GLY GLY GLY SEQRES 3 A 135 ARG THR GLN SER ASP ILE ASN ASN ARG ILE PHE ASP CYS SEQRES 4 A 135 SER SER PHE VAL ARG TRP ALA TYR ALA SER ALA GLY VAL SEQRES 5 A 135 ASN LEU GLY PRO VAL GLY GLY THR THR THR ASP THR LEU SEQRES 6 A 135 VAL GLY ARG GLY GLN ALA VAL SER ALA SER GLU MET LYS SEQRES 7 A 135 ARG GLY ASP LEU VAL PHE PHE ASP THR TYR LYS THR ASN SEQRES 8 A 135 GLY HIS VAL GLY ILE TYR LEU GLY ASN GLY THR PHE LEU SEQRES 9 A 135 ASN ASP ASN THR SER HIS GLY VAL SER VAL ASP SER MET SEQRES 10 A 135 SER ASN PRO TYR TRP LYS ALA ALA PHE LYS GLY VAL VAL SEQRES 11 A 135 ARG ARG VAL VAL GLN HET EDO A 501 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 2 EDO C2 H6 O2 FORMUL 3 HOH *25(H2 O) HELIX 1 AA1 GLY A 341 SER A 352 1 12 HELIX 2 AA2 THR A 366 ASN A 372 1 7 HELIX 3 AA3 ASP A 376 SER A 387 1 12 HELIX 4 AA4 THR A 399 GLY A 405 1 7 HELIX 5 AA5 SER A 411 MET A 415 5 5 HELIX 6 AA6 ASN A 457 ALA A 463 1 7 SHEET 1 AA1 6 GLN A 408 ALA A 409 0 SHEET 2 AA1 6 PHE A 464 ARG A 470 -1 O ARG A 470 N GLN A 408 SHEET 3 AA1 6 LEU A 420 PHE A 423 -1 N LEU A 420 O ARG A 469 SHEET 4 AA1 6 HIS A 431 TYR A 435 -1 O GLY A 433 N VAL A 421 SHEET 5 AA1 6 THR A 440 ASN A 445 -1 O LEU A 442 N ILE A 434 SHEET 6 AA1 6 GLY A 449 SER A 454 -1 O SER A 451 N ASN A 443 CRYST1 58.548 58.548 111.468 90.00 90.00 90.00 P 43 21 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.017080 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017080 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008971 0.00000 CONECT 1013 1014 1015 CONECT 1014 1013 CONECT 1015 1013 1016 CONECT 1016 1015 MASTER 270 0 1 6 6 0 0 6 1032 1 4 11 END