HEADER HYDROLASE 17-DEC-20 7L3D TITLE T4 LYSOZYME L99A - 3-IODOTOLUENE - RT 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; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE T4; SOURCE 3 ORGANISM_TAXID: 10665; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RT, 3-IODOTOLUENE, L99A, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.FISCHER,S.Y.C.BRADFORD REVDAT 2 18-OCT-23 7L3D 1 REMARK REVDAT 1 27-OCT-21 7L3D 0 JRNL AUTH S.Y.C.BRADFORD,L.EL KHOURY,Y.GE,M.OSATO,D.L.MOBLEY,M.FISCHER JRNL TITL TEMPERATURE ARTIFACTS IN PROTEIN STRUCTURES BIAS JRNL TITL 2 LIGAND-BINDING PREDICTIONS. JRNL REF CHEM SCI V. 12 11275 2021 JRNL REFN ISSN 2041-6520 JRNL PMID 34667539 JRNL DOI 10.1039/D1SC02751D REMARK 2 REMARK 2 RESOLUTION. 1.35 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14-3260 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) : 1.35 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.55 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 46007 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.144 REMARK 3 FREE R VALUE : 0.162 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 2349 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 46.5520 - 3.4706 0.97 2765 136 0.1512 0.1430 REMARK 3 2 3.4706 - 2.7548 0.99 2639 159 0.1373 0.1480 REMARK 3 3 2.7548 - 2.4066 1.00 2646 148 0.1359 0.1599 REMARK 3 4 2.4066 - 2.1866 1.00 2611 152 0.1182 0.1338 REMARK 3 5 2.1866 - 2.0299 0.99 2619 131 0.1077 0.1371 REMARK 3 6 2.0299 - 1.9102 0.96 2539 124 0.1118 0.1565 REMARK 3 7 1.9102 - 1.8145 0.99 2622 130 0.1142 0.1440 REMARK 3 8 1.8145 - 1.7355 0.99 2524 166 0.1207 0.1558 REMARK 3 9 1.7355 - 1.6687 0.99 2615 128 0.1260 0.1574 REMARK 3 10 1.6687 - 1.6111 0.98 2518 156 0.1373 0.1673 REMARK 3 11 1.6111 - 1.5607 0.98 2596 122 0.1497 0.2014 REMARK 3 12 1.5607 - 1.5161 0.98 2526 140 0.1718 0.2169 REMARK 3 13 1.5161 - 1.4762 0.97 2526 142 0.2033 0.2496 REMARK 3 14 1.4762 - 1.4402 0.96 2456 143 0.2467 0.2975 REMARK 3 15 1.4402 - 1.4074 0.95 2479 140 0.2781 0.2837 REMARK 3 16 1.4074 - 1.3775 0.96 2488 121 0.2995 0.3458 REMARK 3 17 1.3775 - 1.3500 0.95 2489 111 0.3105 0.3170 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) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.660 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.77 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 1501 REMARK 3 ANGLE : 0.712 2035 REMARK 3 CHIRALITY : 0.061 218 REMARK 3 PLANARITY : 0.004 268 REMARK 3 DIHEDRAL : 19.172 583 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 7L3D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-JAN-21. REMARK 100 THE DEPOSITION ID IS D_1000253643. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-18 REMARK 200 TEMPERATURE (KELVIN) : 278 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID 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 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46564 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.350 REMARK 200 RESOLUTION RANGE LOW (A) : 52.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.35 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.70 REMARK 200 R MERGE FOR SHELL (I) : 0.91500 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 2.8.2 REMARK 200 STARTING MODEL: 4W51 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.83 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE GROWN FROM A 10 MG/ML REMARK 280 FROZEN PROTEIN SOLUTION BY THE HANGING DROP METHOD AT 291-293K, REMARK 280 WITH A 1:1 DROP RATIO OF PROTEIN TO SOLUTION AND OVER A WELL REMARK 280 SOLUTION OF 0.1 M TRIS-HYDROCHLORIDE (PH 8), 20%-26% (W/V) PEG REMARK 280 4000, 70-170 MM LITHIUM CITRATE, 8%-18% 2-PROPANOL, 50 MM 2- REMARK 280 MERCAPTOETHANOL, AND 50 MM 2-HYDROXYETHYL DISULFIDE, VAPOR REMARK 280 DIFFUSION, HANGING DROP 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 65.16600 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 32.58300 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 32.58300 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 65.16600 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 302 LIES ON A SPECIAL POSITION. 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 163 REMARK 465 LEU A 164 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BME A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue BME A 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue XQJ A 205 DBREF 7L3D A 1 164 UNP P00720 ENLYS_BPT4 1 164 SEQADV 7L3D GLY A 12 UNP P00720 ARG 12 ENGINEERED MUTATION SEQADV 7L3D ALA A 99 UNP P00720 LEU 99 ENGINEERED MUTATION SEQADV 7L3D ARG A 137 UNP P00720 ILE 137 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 SER GLU LEU ASP LYS ALA ILE GLY ARG SEQRES 5 A 164 ASN CYS ASN GLY VAL ILE THR LYS ASP GLU ALA GLU LYS SEQRES 6 A 164 LEU PHE ASN 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 ALA VAL ARG ARG CYS ALA ALA ILE ASN MET VAL PHE SEQRES 9 A 164 GLN MET GLY GLU THR GLY VAL ALA GLY PHE THR 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 TRS A 201 8 HET BME A 202 4 HET BME A 203 4 HET CL A 204 1 HET XQJ A 205 8 HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM BME BETA-MERCAPTOETHANOL HETNAM CL CHLORIDE ION HETNAM XQJ 1-IODO-3-METHYLBENZENE HETSYN TRS TRIS BUFFER HETSYN XQJ 3-IODOTOLUENE FORMUL 2 TRS C4 H12 N O3 1+ FORMUL 3 BME 2(C2 H6 O S) FORMUL 5 CL CL 1- FORMUL 6 XQJ C7 H7 I FORMUL 7 HOH *98(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 ASN A 81 1 23 HELIX 4 AA4 LEU A 84 LEU A 91 1 8 HELIX 5 AA5 ASP A 92 GLY A 107 1 16 HELIX 6 AA6 VAL A 111 GLY A 113 5 3 HELIX 7 AA7 PHE A 114 GLN A 123 1 10 HELIX 8 AA8 ARG A 125 LYS A 135 1 11 HELIX 9 AA9 SER A 136 THR A 142 1 7 HELIX 10 AB1 THR A 142 GLY A 156 1 15 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 THR A 34 -1 O LEU A 33 N TYR A 25 SITE 1 AC1 5 GLU A 11 GLY A 30 GLN A 105 BME A 202 SITE 2 AC1 5 HOH A 311 SITE 1 AC2 7 GLY A 30 HIS A 31 LEU A 32 PHE A 104 SITE 2 AC2 7 TRS A 201 HOH A 331 HOH A 364 SITE 1 AC3 8 ASN A 68 ASP A 72 TYR A 88 ALA A 93 SITE 2 AC3 8 ARG A 96 CYS A 97 ILE A 100 HOH A 318 SITE 1 AC4 5 LYS A 124 THR A 142 ASN A 144 ARG A 145 SITE 2 AC4 5 HOH A 398 SITE 1 AC5 5 LEU A 84 MET A 102 VAL A 111 LEU A 118 SITE 2 AC5 5 LEU A 121 CRYST1 61.130 61.130 97.749 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 0.016358 0.009445 0.000000 0.00000 SCALE2 0.000000 0.018889 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010230 0.00000