HEADER HYDROLASE 12-DEC-24 9HP7 TITLE CRYSTAL STRUCTURE OF GH19 E228Q DOMAIN OF D29-LYSA IN COMPLEX WITH TITLE 2 (GLCNAC)4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDOLYSIN A; COMPND 3 CHAIN: B; COMPND 4 SYNONYM: GENE 10 PROTEIN,GP10,LYSIS PROTEIN,LYSOZYME; COMPND 5 EC: 3.-.-.-; COMPND 6 ENGINEERED: YES; COMPND 7 OTHER_DETAILS: N-TERMINAL GP RESIDUES CORRESPOND TO PRESCISSION COMPND 8 CLEAVEGE SITE. RESIDUES FROM 179 TO 370 CORRESPOND TO GH19 DOMAIN OF COMPND 9 D29-LYSA WITH THE MUTATION E228Q SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM PHAGE D29; SOURCE 3 ORGANISM_TAXID: 2905674; SOURCE 4 GENE: 10; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PEPTIDOGLYCAN HYDROLASE, D29-LYSA, GH19, (GLCNAC)4, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR F.CEBALLOS-ZUNIGA,I.PEREZ-DORADO REVDAT 1 22-APR-26 9HP7 0 JRNL AUTH F.CEBALLOS-ZUNIGA,L.GALVEZ-LARROSA,I.G.MUNOZ,L.INFANTES, JRNL AUTH 2 J.FERNANDEZ-CARRILLO,I.PEREZ-DORADO JRNL TITL DISSECTING THE MOLECULAR BASIS UNDERLYING MYCOBACTERIAL JRNL TITL 2 CELL-WALL HYDROLYSIS BY THE CATALYTIC DOMAINS OF D29LYSA AND JRNL TITL 3 DS6ALYSA PHAGE ENDOLYSINS. JRNL REF INT.J.BIOL.MACROMOL. V. 334 48896 2025 JRNL REFN ISSN 0141-8130 JRNL PMID 41207583 JRNL DOI 10.1016/J.IJBIOMAC.2025.148896 REMARK 2 REMARK 2 RESOLUTION. 1.83 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.1_5286 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.83 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 19225 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.201 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 977 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 1.9200 - 1.8300 1.00 2706 136 0.2774 0.3311 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) : 0.177 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.902 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.55 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.69 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 : 0.004 1609 REMARK 3 ANGLE : 0.660 2193 REMARK 3 CHIRALITY : 0.042 250 REMARK 3 PLANARITY : 0.006 284 REMARK 3 DIHEDRAL : 13.962 652 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 9HP7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-DEC-24. REMARK 100 THE DEPOSITION ID IS D_1292143915. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-24 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 : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19241 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.826 REMARK 200 RESOLUTION RANGE LOW (A) : 38.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.83 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.75800 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CONDITION E1 FROM MORPHEUS CRYSTAL REMARK 280 SCREENING: - 0.12M ETHYLENE GLYCOLS - 0.1M BUFFER SYSTEM 1 PH REMARK 280 6.5 - 30% PRECIPITANT MIX 1, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 45.53100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.42250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 45.53100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.42250 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 APPLY THE FOLLOWING TO CHAINS: B, 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 GLY B 177 REMARK 465 PRO B 178 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 OD2 ASP B 323 O HOH B 501 2.17 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 SER B 267 174.24 73.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 401 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 245 O REMARK 620 2 ASP B 245 OD1 74.0 REMARK 620 3 THR B 253 O 67.8 139.3 REMARK 620 4 THR B 253 OG1 138.0 147.5 72.8 REMARK 620 5 GLU B 255 O 97.9 82.0 89.5 95.9 REMARK 620 6 ASP B 257 OD1 152.1 78.2 139.8 69.4 81.2 REMARK 620 7 ASP B 259 OD1 91.1 83.3 110.5 89.2 159.9 82.5 REMARK 620 N 1 2 3 4 5 6 DBREF 9HP7 B 179 370 UNP O64203 ENLYS_BPMD2 179 370 SEQADV 9HP7 GLY B 177 UNP O64203 EXPRESSION TAG SEQADV 9HP7 PRO B 178 UNP O64203 EXPRESSION TAG SEQADV 9HP7 GLN B 228 UNP O64203 GLU 228 ENGINEERED MUTATION SEQRES 1 B 194 GLY PRO VAL ASP ALA ALA GLU ILE LEU ALA ARG ALA THR SEQRES 2 B 194 GLY LEU ALA TYR ASN ARG ALA VAL ALA LEU LEU PRO ALA SEQRES 3 B 194 VAL ARG ASP GLY LEU ILE GLN ALA ASP CYS THR ASN PRO SEQRES 4 B 194 ASN ARG ILE ALA MET TRP LEU ALA GLN ILE GLY HIS GLN SEQRES 5 B 194 SER ASP ASP PHE LYS ALA THR ALA GLU TYR ALA SER GLY SEQRES 6 B 194 ASP ALA TYR ASP THR ARG THR ASP LEU GLY ASN THR PRO SEQRES 7 B 194 GLU VAL ASP GLY ASP GLY ARG LEU TYR LYS GLY ARG SER SEQRES 8 B 194 TRP ILE MET ILE THR GLY LYS ASP ASN TYR ARG ASP PHE SEQRES 9 B 194 SER ARG TRP ALA HIS GLY ARG GLY LEU VAL PRO THR PRO SEQRES 10 B 194 ASP TYR PHE VAL VAL HIS PRO LEU GLU LEU SER GLU LEU SEQRES 11 B 194 ARG TRP ALA GLY ILE GLY ALA ALA TRP TYR TRP THR VAL SEQRES 12 B 194 GLU ARG PRO ASP ILE ASN ALA LEU SER ASP ARG ARG ASP SEQRES 13 B 194 LEU GLU THR VAL THR ARG ARG ILE ASN GLY GLY LEU THR SEQRES 14 B 194 ASN LEU ASP ASP ARG ARG ARG ARG TYR ASN LEU ALA LEU SEQRES 15 B 194 ALA VAL GLY ASP GLN LEU LEU THR LEU ILE GLY ASP HET NAG A 1 15 HET NAG A 2 14 HET NAG A 3 14 HET NAG A 4 14 HET CA B 401 1 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM CA CALCIUM ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 2 NAG 4(C8 H15 N O6) FORMUL 3 CA CA 2+ FORMUL 4 HOH *111(H2 O) HELIX 1 AA1 ASP B 180 GLY B 190 1 11 HELIX 2 AA2 ALA B 192 ALA B 210 1 19 HELIX 3 AA3 ASN B 214 SER B 229 1 16 HELIX 4 AA4 GLY B 241 ASP B 245 5 5 HELIX 5 AA5 ARG B 247 GLY B 251 5 5 HELIX 6 AA6 GLY B 258 TYR B 263 1 6 HELIX 7 AA7 GLY B 273 ARG B 287 1 15 HELIX 8 AA8 ASP B 294 HIS B 299 1 6 HELIX 9 AA9 PRO B 300 ARG B 307 5 8 HELIX 10 AB1 TRP B 308 VAL B 319 1 12 HELIX 11 AB2 ASP B 323 ARG B 330 1 8 HELIX 12 AB3 ASP B 332 GLY B 342 1 11 HELIX 13 AB4 ASN B 346 ALA B 359 1 14 HELIX 14 AB5 VAL B 360 GLY B 369 5 10 LINK O4 NAG A 1 C1 NAG A 2 1555 1555 1.44 LINK O4 NAG A 2 C1 NAG A 3 1555 1555 1.44 LINK O4 NAG A 3 C1 NAG A 4 1555 1555 1.44 LINK O ASP B 245 CA CA B 401 1555 1555 2.27 LINK OD1 ASP B 245 CA CA B 401 1555 1555 2.36 LINK O THR B 253 CA CA B 401 1555 1555 2.54 LINK OG1 THR B 253 CA CA B 401 1555 1555 2.50 LINK O GLU B 255 CA CA B 401 1555 1555 2.29 LINK OD1 ASP B 257 CA CA B 401 1555 1555 2.44 LINK OD1 ASP B 259 CA CA B 401 1555 1555 2.35 CRYST1 91.062 44.845 69.530 90.00 126.42 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 0.010982 0.000000 0.008102 0.00000 SCALE2 0.000000 0.022299 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017873 0.00000 CONECT 498 1578 CONECT 501 1578 CONECT 559 1578 CONECT 561 1578 CONECT 573 1578 CONECT 592 1578 CONECT 604 1578 CONECT 1521 1522 1530 1533 CONECT 1522 1521 1523 1529 CONECT 1523 1522 1524 1531 CONECT 1524 1523 1525 1532 CONECT 1525 1524 1526 1533 CONECT 1526 1525 1534 CONECT 1527 1528 1529 1535 CONECT 1528 1527 CONECT 1529 1522 1527 CONECT 1530 1521 CONECT 1531 1523 CONECT 1532 1524 1536 CONECT 1533 1521 1525 CONECT 1534 1526 CONECT 1535 1527 CONECT 1536 1532 1537 1547 CONECT 1537 1536 1538 1544 CONECT 1538 1537 1539 1545 CONECT 1539 1538 1540 1546 CONECT 1540 1539 1541 1547 CONECT 1541 1540 1548 CONECT 1542 1543 1544 1549 CONECT 1543 1542 CONECT 1544 1537 1542 CONECT 1545 1538 CONECT 1546 1539 1550 CONECT 1547 1536 1540 CONECT 1548 1541 CONECT 1549 1542 CONECT 1550 1546 1551 1561 CONECT 1551 1550 1552 1558 CONECT 1552 1551 1553 1559 CONECT 1553 1552 1554 1560 CONECT 1554 1553 1555 1561 CONECT 1555 1554 1562 CONECT 1556 1557 1558 1563 CONECT 1557 1556 CONECT 1558 1551 1556 CONECT 1559 1552 CONECT 1560 1553 1564 CONECT 1561 1550 1554 CONECT 1562 1555 CONECT 1563 1556 CONECT 1564 1560 1565 1575 CONECT 1565 1564 1566 1572 CONECT 1566 1565 1567 1573 CONECT 1567 1566 1568 1574 CONECT 1568 1567 1569 1575 CONECT 1569 1568 1576 CONECT 1570 1571 1572 1577 CONECT 1571 1570 CONECT 1572 1565 1570 CONECT 1573 1566 CONECT 1574 1567 CONECT 1575 1564 1568 CONECT 1576 1569 CONECT 1577 1570 CONECT 1578 498 501 559 561 CONECT 1578 573 592 604 MASTER 242 0 5 14 0 0 0 6 1685 1 66 15 END