HEADER HYDROLASE 30-MAR-22 7XE5 TITLE T4 LYSOZYME MUTANT-S44C/C54T/N68C/A93C/C97A/T115C, PH4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENDOLYSIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LYSIS PROTEIN,LYSOZYME,MURAMIDASE; COMPND 5 EC: 3.2.1.17; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA VIRUS T4; SOURCE 3 ORGANISM_TAXID: 10665; SOURCE 4 GENE: E, T4TP126; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INTERMOLECULAR DISULFIDE SYMMETRY CROSS-LINKED CRYSTAL, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR T.TAMADA,T.HIROMOTO REVDAT 2 29-NOV-23 7XE5 1 REMARK REVDAT 1 22-MAR-23 7XE5 0 JRNL AUTH T.HIROMOTO,T.IKURA,E.HONJO,M.BLABER,R.KUROKI,T.TAMADA JRNL TITL CREATION OF CROSS-LINKED CRYSTALS WITH INTERMOLECULAR JRNL TITL 2 DISULFIDE BONDS CONNECTING SYMMETRY-RELATED MOLECULES ALLOWS JRNL TITL 3 RETENTION OF TERTIARY STRUCTURE IN DIFFERENT SOLVENT JRNL TITL 4 CONDITIONS. JRNL REF FRONT MOL BIOSCI V. 9 08394 2022 JRNL REFN ESSN 2296-889X JRNL PMID 35755825 JRNL DOI 10.3389/FMOLB.2022.908394 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 50487 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.154 REMARK 3 R VALUE (WORKING SET) : 0.153 REMARK 3 FREE R VALUE : 0.171 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.940 REMARK 3 FREE R VALUE TEST SET COUNT : 1989 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 32.2900 - 3.1300 1.00 3701 150 0.1590 0.1825 REMARK 3 2 3.1300 - 2.4900 1.00 3541 146 0.1678 0.1641 REMARK 3 3 2.4900 - 2.1700 1.00 3518 147 0.1512 0.1726 REMARK 3 4 2.1700 - 1.9700 1.00 3487 146 0.1515 0.1569 REMARK 3 5 1.9700 - 1.8300 1.00 3457 138 0.1372 0.1571 REMARK 3 6 1.8300 - 1.7200 1.00 3484 145 0.1427 0.1675 REMARK 3 7 1.7200 - 1.6400 1.00 3462 142 0.1199 0.1504 REMARK 3 8 1.6400 - 1.5700 1.00 3458 140 0.1318 0.1411 REMARK 3 9 1.5700 - 1.5100 1.00 3423 143 0.1233 0.1573 REMARK 3 10 1.5100 - 1.4500 1.00 3466 142 0.1344 0.1760 REMARK 3 11 1.4500 - 1.4100 1.00 3408 138 0.1426 0.1643 REMARK 3 12 1.4100 - 1.3700 1.00 3440 141 0.1577 0.1941 REMARK 3 13 1.3700 - 1.3300 1.00 3418 140 0.1893 0.2325 REMARK 3 14 1.3300 - 1.3000 0.94 3235 131 0.2308 0.2581 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) : 0.118 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.872 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.16 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.70 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 1433 REMARK 3 ANGLE : 0.977 1933 REMARK 3 CHIRALITY : 0.070 212 REMARK 3 PLANARITY : 0.007 245 REMARK 3 DIHEDRAL : 8.533 222 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 7XE5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-MAR-22. REMARK 100 THE DEPOSITION ID IS D_1300028645. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JAN-06 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 : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50560 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 32.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 10.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : 6.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 5VNR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.72 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: A CRYSTAL WAS SOAKED INTO PRECIPITANT REMARK 280 -FREE SOLUTION (PH4), VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.58133 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 32.29067 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 32.29067 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 64.58133 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 TOTAL BURIED SURFACE AREA: 170 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8800 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 KCAL/MOL 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: 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 487 O HOH A 488 1.89 REMARK 500 O HOH A 323 O HOH A 474 1.91 REMARK 500 O HOH A 514 O HOH A 525 2.00 REMARK 500 O2 GOL A 201 O HOH A 301 2.03 REMARK 500 O HOH A 346 O HOH A 464 2.03 REMARK 500 O HOH A 485 O HOH A 516 2.06 REMARK 500 O HOH A 325 O HOH A 485 2.08 REMARK 500 O HOH A 362 O HOH A 542 2.09 REMARK 500 O HOH A 330 O HOH A 494 2.11 REMARK 500 O HOH A 320 O HOH A 486 2.13 REMARK 500 ND2 ASN A 55 O HOH A 302 2.14 REMARK 500 OE2 GLU A 108 O HOH A 303 2.16 REMARK 500 O3 GOL A 201 O HOH A 304 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 CYS A 115 CA - CB - SG ANGL. DEV. = 7.4 DEGREES 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 545 DISTANCE = 5.99 ANGSTROMS DBREF 7XE5 A 1 164 UNP D9IEF7 D9IEF7_BPT4 1 164 SEQADV 7XE5 CYS A 44 UNP D9IEF7 SER 44 ENGINEERED MUTATION SEQADV 7XE5 THR A 54 UNP D9IEF7 CYS 54 ENGINEERED MUTATION SEQADV 7XE5 CYS A 68 UNP D9IEF7 ASN 68 ENGINEERED MUTATION SEQADV 7XE5 CYS A 93 UNP D9IEF7 ALA 93 ENGINEERED MUTATION SEQADV 7XE5 ALA A 97 UNP D9IEF7 CYS 97 ENGINEERED MUTATION SEQADV 7XE5 CYS A 115 UNP D9IEF7 THR 115 ENGINEERED MUTATION SEQRES 1 A 164 MET ASN ILE PHE GLU MET LEU ARG ILE ASP GLU GLY LEU SEQRES 2 A 164 ARG LEU LYS ILE TYR LYS ASP THR GLU GLY TYR TYR THR SEQRES 3 A 164 ILE GLY ILE GLY HIS LEU LEU THR LYS SER PRO SER LEU SEQRES 4 A 164 ASN ALA ALA LYS CYS GLU LEU ASP LYS ALA ILE GLY ARG SEQRES 5 A 164 ASN THR ASN GLY VAL ILE THR LYS ASP GLU ALA GLU LYS SEQRES 6 A 164 LEU PHE CYS GLN ASP VAL ASP ALA ALA VAL ARG GLY ILE SEQRES 7 A 164 LEU ARG ASN ALA LYS LEU LYS PRO VAL TYR ASP SER LEU SEQRES 8 A 164 ASP CYS VAL ARG ARG ALA ALA LEU ILE ASN MET VAL PHE SEQRES 9 A 164 GLN MET GLY GLU THR GLY VAL ALA GLY PHE CYS ASN SER SEQRES 10 A 164 LEU ARG MET LEU GLN GLN LYS ARG TRP ASP GLU ALA ALA SEQRES 11 A 164 VAL ASN LEU ALA LYS SER ARG TRP TYR ASN GLN THR PRO SEQRES 12 A 164 ASN ARG ALA LYS ARG VAL ILE THR THR PHE ARG THR GLY SEQRES 13 A 164 THR TRP ASP ALA TYR LYS ASN LEU HET GOL A 201 6 HET GOL A 202 6 HET HEZ A 203 8 HET GOL A 204 6 HET HEZ A 205 8 HET PO4 A 206 5 HET NA A 207 1 HETNAM GOL GLYCEROL HETNAM HEZ HEXANE-1,6-DIOL HETNAM PO4 PHOSPHATE ION HETNAM NA SODIUM ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 3(C3 H8 O3) FORMUL 4 HEZ 2(C6 H14 O2) FORMUL 7 PO4 O4 P 3- FORMUL 8 NA NA 1+ FORMUL 9 HOH *245(H2 O) HELIX 1 AA1 ASN A 2 GLY A 12 1 11 HELIX 2 AA2 SER A 38 GLY A 51 1 14 HELIX 3 AA3 THR A 59 ARG A 80 1 22 HELIX 4 AA4 LYS A 83 LEU A 91 1 9 HELIX 5 AA5 ASP A 92 GLY A 107 1 16 HELIX 6 AA6 GLY A 107 GLY A 113 1 7 HELIX 7 AA7 PHE A 114 GLN A 123 1 10 HELIX 8 AA8 ARG A 125 ALA A 134 1 10 HELIX 9 AA9 SER A 136 THR A 142 1 7 HELIX 10 AB1 THR A 142 GLY A 156 1 15 HELIX 11 AB2 TRP A 158 LYS A 162 5 5 SHEET 1 AA1 3 ARG A 14 LYS A 19 0 SHEET 2 AA1 3 TYR A 25 GLY A 28 -1 O THR A 26 N TYR A 18 SHEET 3 AA1 3 HIS A 31 LEU A 32 -1 O HIS A 31 N ILE A 27 SSBOND 1 CYS A 44 CYS A 115 1555 3655 2.04 SSBOND 2 CYS A 68 CYS A 93 1555 5555 2.02 CRYST1 60.295 60.295 96.872 90.00 90.00 120.00 P 32 2 1 6 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 0.016585 0.009575 0.000000 0.00000 SCALE2 0.000000 0.019151 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010323 0.00000