HEADER ANTIMICROBIAL PROTEIN 14-JAN-23 8I2D TITLE CRYSTAL STRUCTURE OF BACILLUS SUBTILIS LYTE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE PEPTIDOGLYCAN ENDOPEPTIDASE LYTE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: GAMMA-D-GLUTAMATE-MESO-DIAMINOPIMELATE MUROPEPTIDASE LYTE, COMPND 5 MINOR AUTOLYSIN LYTE,VEGETATIVE CELL WALL HYDROLASE LYTE; COMPND 6 EC: 3.4.-.-; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168; SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: LYTE; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI B; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 37762 KEYWDS DL-ENDOPEPTIDASE, ANTIMICROBIAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.TANDUKAR,E.KWON,D.Y.KIM REVDAT 2 17-MAY-23 8I2D 1 JRNL REVDAT 1 19-APR-23 8I2D 0 JRNL AUTH S.TANDUKAR,E.KWON,D.Y.KIM JRNL TITL STRUCTURAL INSIGHTS INTO THE REGULATION OF PEPTIDOGLYCAN JRNL TITL 2 DL-ENDOPEPTIDASES BY INHIBITORY PROTEIN ISEA. JRNL REF STRUCTURE V. 31 619 2023 JRNL REFN ISSN 0969-2126 JRNL PMID 36963396 JRNL DOI 10.1016/J.STR.2023.02.013 REMARK 2 REMARK 2 RESOLUTION. 1.31 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19 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) : 1.31 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 26032 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 1268 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 42.9000 - 2.7200 1.00 2952 151 0.1777 0.1621 REMARK 3 2 2.7200 - 2.1600 1.00 2793 147 0.1742 0.1755 REMARK 3 3 2.1600 - 1.8900 1.00 2774 127 0.1597 0.1877 REMARK 3 4 1.8900 - 1.7200 1.00 2750 123 0.1637 0.1898 REMARK 3 5 1.7200 - 1.5900 1.00 2687 173 0.1698 0.2015 REMARK 3 6 1.5900 - 1.5000 1.00 2723 129 0.1739 0.2075 REMARK 3 7 1.5000 - 1.4200 1.00 2712 127 0.1765 0.2162 REMARK 3 8 1.4200 - 1.3600 1.00 2701 145 0.1887 0.2187 REMARK 3 9 1.3600 - 1.3100 1.00 2672 146 0.2048 0.2260 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.110 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 : 0.005 927 REMARK 3 ANGLE : 0.754 1257 REMARK 3 CHIRALITY : 0.077 132 REMARK 3 PLANARITY : 0.008 156 REMARK 3 DIHEDRAL : 6.177 127 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 16.3055 42.0716 33.2787 REMARK 3 T TENSOR REMARK 3 T11: 0.0548 T22: 0.0659 REMARK 3 T33: 0.0680 T12: -0.0067 REMARK 3 T13: 0.0047 T23: -0.0056 REMARK 3 L TENSOR REMARK 3 L11: 0.6974 L22: 0.9586 REMARK 3 L33: 0.9589 L12: -0.3526 REMARK 3 L13: 0.0193 L23: 0.2536 REMARK 3 S TENSOR REMARK 3 S11: -0.0191 S12: -0.0626 S13: 0.0048 REMARK 3 S21: 0.0649 S22: 0.0016 S23: 0.0125 REMARK 3 S31: 0.0352 S32: -0.0411 S33: 0.0110 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 8I2D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-JAN-23. REMARK 100 THE DEPOSITION ID IS D_1300033899. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-19 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 : PAL/PLS REMARK 200 BEAMLINE : 7A (6B, 6C1) 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 QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26096 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.310 REMARK 200 RESOLUTION RANGE LOW (A) : 68.070 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 11.50 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.31 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.33 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.80 REMARK 200 R MERGE FOR SHELL (I) : 0.44600 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: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.03 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG3350, 200 MM SODIUM REMARK 280 THIOCYANATE, MICROBATCH, 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 34.03500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.62500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.62500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 51.05250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.62500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.62500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 17.01750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.62500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.62500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 51.05250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.62500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.62500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 17.01750 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 34.03500 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 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 A 406 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 430 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 559 LIES ON A SPECIAL POSITION. 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 531 O HOH A 542 2.12 REMARK 500 O HOH A 507 O HOH A 530 2.13 REMARK 500 O HOH A 451 O HOH A 515 2.17 REMARK 500 O HOH A 540 O HOH A 565 2.18 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 O HOH A 447 O HOH A 470 4465 2.13 REMARK 500 O HOH A 420 O HOH A 568 5555 2.14 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 THR A 289 -84.54 -114.18 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 A 572 DISTANCE = 5.81 ANGSTROMS REMARK 525 HOH A 573 DISTANCE = 5.84 ANGSTROMS REMARK 525 HOH A 574 DISTANCE = 6.06 ANGSTROMS REMARK 525 HOH A 575 DISTANCE = 6.38 ANGSTROMS DBREF 8I2D A 218 334 UNP P54421 LYTE_BACSU 218 334 SEQRES 1 A 117 LEU ASN VAL SER LYS LEU VAL SER ASP ALA LYS ALA LEU SEQRES 2 A 117 VAL GLY THR PRO TYR LYS TRP GLY GLY THR THR THR SER SEQRES 3 A 117 GLY PHE ASP CYS SER GLY PHE ILE TRP TYR VAL LEU ASN SEQRES 4 A 117 LYS GLN THR SER VAL GLY ARG THR SER THR ALA GLY TYR SEQRES 5 A 117 TRP SER SER MSE LYS SER ILE ALA SER PRO SER VAL GLY SEQRES 6 A 117 ASP PHE VAL PHE PHE THR THR TYR LYS SER GLY PRO SER SEQRES 7 A 117 HIS MSE GLY ILE TYR ILE GLY ASN ASN SER PHE ILE HIS SEQRES 8 A 117 ALA GLY SER ASP GLY VAL GLN ILE SER SER LEU ASN ASN SEQRES 9 A 117 SER TYR TRP LYS PRO ARG TYR LEU GLY ALA LYS ARG PHE MODRES 8I2D MSE A 273 MET MODIFIED RESIDUE MODRES 8I2D MSE A 297 MET MODIFIED RESIDUE HET MSE A 273 8 HET MSE A 297 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 HOH *175(H2 O) HELIX 1 AA1 ASN A 219 LEU A 230 1 12 HELIX 2 AA2 ASP A 246 LYS A 257 1 12 HELIX 3 AA3 SER A 265 MSE A 273 1 9 HELIX 4 AA4 TRP A 324 PRO A 326 5 3 SHEET 1 AA1 2 THR A 240 THR A 241 0 SHEET 2 AA1 2 GLY A 244 PHE A 245 -1 O GLY A 244 N THR A 241 SHEET 1 AA2 6 LYS A 274 SER A 275 0 SHEET 2 AA2 6 TYR A 328 ARG A 333 -1 O ARG A 333 N LYS A 274 SHEET 3 AA2 6 PHE A 284 PHE A 287 -1 N PHE A 286 O LEU A 329 SHEET 4 AA2 6 HIS A 296 GLY A 302 -1 O HIS A 296 N PHE A 287 SHEET 5 AA2 6 SER A 305 GLY A 310 -1 O ILE A 307 N ILE A 299 SHEET 6 AA2 6 GLY A 313 SER A 318 -1 O SER A 317 N PHE A 306 LINK C SER A 272 N MSE A 273 1555 1555 1.33 LINK C MSE A 273 N LYS A 274 1555 1555 1.34 LINK C HIS A 296 N MSE A 297 1555 1555 1.33 LINK C MSE A 297 N GLY A 298 1555 1555 1.33 CRYST1 55.250 55.250 68.070 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 0.018100 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018100 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014691 0.00000