HEADER PROTEIN BINDING,HYDROLASE 10-FEB-21 7LOD TITLE T4 LYSOZYME MUTANT L99A IN COMPLEX WITH 1-FLUORANYL-4-IODANYL-BENZENE COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ENDOLYSIN,LYSIS PROTEIN,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_COMMON: BACTERIOPHAGE T4; SOURCE 4 ORGANISM_TAXID: 10665; SOURCE 5 GENE: E, T4TP126; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS MUTANT, LYSOZYME, SMALL MOLECULE, L99A, COMPLEX, PROTEIN BINDING, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.S.KAMENIK,I.SINGH,P.LAK,T.E.BALIUS,K.R.LIEDL,B.K.SHOICHET REVDAT 3 18-OCT-23 7LOD 1 REMARK REVDAT 2 08-DEC-21 7LOD 1 JRNL REVDAT 1 19-MAY-21 7LOD 0 JRNL AUTH A.S.KAMENIK,I.SINGH,P.LAK,T.E.BALIUS,K.R.LIEDL,B.K.SHOICHET JRNL TITL ENERGY PENALTIES ENHANCE FLEXIBLE RECEPTOR DOCKING IN A JRNL TITL 2 MODEL CAVITY. JRNL REF PROC.NATL.ACAD.SCI.USA V. 118 2021 JRNL REFN ESSN 1091-6490 JRNL PMID 34475217 JRNL DOI 10.1073/PNAS.2106195118 REMARK 2 REMARK 2 RESOLUTION. 1.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 1.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 100736 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.030 REMARK 3 FREE R VALUE TEST SET COUNT : 5070 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 45.8400 - 3.1691 1.00 3480 208 0.2010 0.2010 REMARK 3 2 3.1691 - 2.5154 1.00 3352 190 0.2088 0.2088 REMARK 3 3 2.5154 - 2.1975 1.00 3338 173 0.2028 0.2153 REMARK 3 4 2.1975 - 1.9966 1.00 3287 181 0.1819 0.1819 REMARK 3 5 1.9966 - 1.8534 1.00 3338 158 0.2022 0.2204 REMARK 3 6 1.8534 - 1.7442 1.00 3260 197 0.1974 0.1938 REMARK 3 7 1.7442 - 1.6568 1.00 3267 167 0.1997 0.2132 REMARK 3 8 1.6568 - 1.5847 1.00 3254 180 0.1947 0.2066 REMARK 3 9 1.5847 - 1.5237 1.00 3253 202 0.2018 0.2154 REMARK 3 10 1.5237 - 1.4711 1.00 3260 162 0.2014 0.1988 REMARK 3 11 1.4711 - 1.4251 1.00 3294 161 0.2148 0.2624 REMARK 3 12 1.4251 - 1.3844 1.00 3274 149 0.2186 0.2124 REMARK 3 13 1.3844 - 1.3479 1.00 3217 188 0.2159 0.2238 REMARK 3 14 1.3479 - 1.3150 1.00 3255 157 0.2145 0.2376 REMARK 3 15 1.3150 - 1.2851 1.00 3216 202 0.2174 0.2136 REMARK 3 16 1.2851 - 1.2578 1.00 3225 191 0.2174 0.2638 REMARK 3 17 1.2578 - 1.2326 1.00 3215 163 0.2253 0.2345 REMARK 3 18 1.2326 - 1.2094 1.00 3289 157 0.2242 0.2155 REMARK 3 19 1.2094 - 1.1878 1.00 3259 158 0.2288 0.2243 REMARK 3 20 1.1878 - 1.1676 1.00 3216 187 0.2371 0.2352 REMARK 3 21 1.1676 - 1.1488 1.00 3230 171 0.2411 0.2356 REMARK 3 22 1.1488 - 1.1311 1.00 3216 183 0.2438 0.2656 REMARK 3 23 1.1311 - 1.1145 1.00 3226 156 0.2563 0.2651 REMARK 3 24 1.1145 - 1.0988 1.00 3216 177 0.2703 0.2611 REMARK 3 25 1.0988 - 1.0839 0.99 3250 161 0.2839 0.2547 REMARK 3 26 1.0839 - 1.0698 0.97 3161 137 0.3080 0.2307 REMARK 3 27 1.0698 - 1.0565 0.93 3011 129 0.3204 0.3085 REMARK 3 28 1.0565 - 1.0437 0.88 2842 150 0.3536 0.3603 REMARK 3 29 1.0437 - 1.0316 0.81 2635 136 0.3702 0.3583 REMARK 3 30 1.0316 - 1.0200 0.73 2330 139 0.3900 0.3628 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) : 24.790 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.33 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.40 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 1395 REMARK 3 ANGLE : 0.740 1873 REMARK 3 CHIRALITY : 0.061 204 REMARK 3 PLANARITY : 0.005 239 REMARK 3 DIHEDRAL : 2.462 1445 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 7LOD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-FEB-21. REMARK 100 THE DEPOSITION ID IS D_1000254731. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-NOV-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95386 REMARK 200 MONOCHROMATOR : M REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.5.32 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 100875 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.020 REMARK 200 RESOLUTION RANGE LOW (A) : 96.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 17.50 REMARK 200 R MERGE (I) : 0.04000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 28.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 76.4 REMARK 200 DATA REDUNDANCY IN SHELL : 7.90 REMARK 200 R MERGE FOR SHELL (I) : 2.61300 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: 4W57 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.87 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ISOPROPANOL, PEG 4000, TRIS-CL PH 8.0, REMARK 280 BETA-MERCAPTOETHANOL, 2-HYRDOXYETHYL DISULFIDE, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 294K 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 64.12333 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 32.06167 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 32.06167 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 64.12333 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 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 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 465 LEU A 165 REMARK 465 GLU A 166 REMARK 465 HIS A 167 REMARK 465 HIS A 168 REMARK 465 HIS A 169 REMARK 465 HIS A 170 REMARK 465 HIS A 171 REMARK 465 HIS A 172 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue Y8D 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 BME A 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 205 DBREF 7LOD A 1 164 UNP D9IEF7 D9IEF7_BPT4 1 164 SEQADV 7LOD ALA A 99 UNP D9IEF7 LEU 99 ENGINEERED MUTATION SEQADV 7LOD LEU A 165 UNP D9IEF7 EXPRESSION TAG SEQADV 7LOD GLU A 166 UNP D9IEF7 EXPRESSION TAG SEQADV 7LOD HIS A 167 UNP D9IEF7 EXPRESSION TAG SEQADV 7LOD HIS A 168 UNP D9IEF7 EXPRESSION TAG SEQADV 7LOD HIS A 169 UNP D9IEF7 EXPRESSION TAG SEQADV 7LOD HIS A 170 UNP D9IEF7 EXPRESSION TAG SEQADV 7LOD HIS A 171 UNP D9IEF7 EXPRESSION TAG SEQADV 7LOD HIS A 172 UNP D9IEF7 EXPRESSION TAG SEQRES 1 A 172 MET ASN ILE PHE GLU MET LEU ARG ILE ASP GLU GLY LEU SEQRES 2 A 172 ARG LEU LYS ILE TYR LYS ASP THR GLU GLY TYR TYR THR SEQRES 3 A 172 ILE GLY ILE GLY HIS LEU LEU THR LYS SER PRO SER LEU SEQRES 4 A 172 ASN ALA ALA LYS SER GLU LEU ASP LYS ALA ILE GLY ARG SEQRES 5 A 172 ASN CYS ASN GLY VAL ILE THR LYS ASP GLU ALA GLU LYS SEQRES 6 A 172 LEU PHE ASN GLN ASP VAL ASP ALA ALA VAL ARG GLY ILE SEQRES 7 A 172 LEU ARG ASN ALA LYS LEU LYS PRO VAL TYR ASP SER LEU SEQRES 8 A 172 ASP ALA VAL ARG ARG CYS ALA ALA ILE ASN MET VAL PHE SEQRES 9 A 172 GLN MET GLY GLU THR GLY VAL ALA GLY PHE THR ASN SER SEQRES 10 A 172 LEU ARG MET LEU GLN GLN LYS ARG TRP ASP GLU ALA ALA SEQRES 11 A 172 VAL ASN LEU ALA LYS SER ARG TRP TYR ASN GLN THR PRO SEQRES 12 A 172 ASN ARG ALA LYS ARG VAL ILE THR THR PHE ARG THR GLY SEQRES 13 A 172 THR TRP ASP ALA TYR LYS ASN LEU LEU GLU HIS HIS HIS SEQRES 14 A 172 HIS HIS HIS HET Y8D A 201 8 HET BME A 202 4 HET BME A 203 4 HET BME A 204 4 HET TRS A 205 8 HETNAM Y8D 1-FLUORANYL-4-IODANYL-BENZENE HETNAM BME BETA-MERCAPTOETHANOL HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 2 Y8D C6 H4 F I FORMUL 3 BME 3(C2 H6 O S) FORMUL 6 TRS C4 H12 N O3 1+ FORMUL 7 HOH *114(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 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 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 10 ILE A 78 LEU A 84 VAL A 87 TYR A 88 SITE 2 AC1 10 ALA A 99 MET A 102 VAL A 111 LEU A 118 SITE 3 AC1 10 PHE A 153 HOH A 404 SITE 1 AC2 7 GLY A 30 LEU A 32 ASP A 70 PHE A 104 SITE 2 AC2 7 TRS A 205 HOH A 371 HOH A 384 SITE 1 AC3 6 ASN A 68 ASP A 72 TYR A 88 ALA A 93 SITE 2 AC3 6 ARG A 96 ILE A 100 SITE 1 AC4 6 LYS A 19 ARG A 125 TRP A 126 ASP A 127 SITE 2 AC4 6 GLU A 128 HOH A 391 SITE 1 AC5 5 GLU A 11 GLY A 30 GLN A 105 BME A 202 SITE 2 AC5 5 HOH A 309 CRYST1 60.209 60.209 96.185 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 0.016609 0.009589 0.000000 0.00000 SCALE2 0.000000 0.019178 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010397 0.00000