HEADER PROTEIN BINDING,HYDROLASE 10-FEB-21 7LOG TITLE T4 LYSOZYME MUTANT L99A IN COMPLEX WITH 3-BUTYLPYRIDINE 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 7LOG 1 REMARK REVDAT 2 08-DEC-21 7LOG 1 JRNL REVDAT 1 25-AUG-21 7LOG 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. 0.99 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) : 0.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 52.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.5 REMARK 3 NUMBER OF REFLECTIONS : 108714 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.198 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 5610 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 52.1760 - 3.0760 1.00 3865 172 0.1959 0.2028 REMARK 3 2 3.0760 - 2.4415 1.00 3648 214 0.2171 0.2130 REMARK 3 3 2.4415 - 2.1328 1.00 3648 176 0.1950 0.1711 REMARK 3 4 2.1328 - 1.9378 1.00 3573 219 0.1906 0.2022 REMARK 3 5 1.9378 - 1.7989 1.00 3587 207 0.1922 0.2035 REMARK 3 6 1.7989 - 1.6929 1.00 3569 217 0.1917 0.1918 REMARK 3 7 1.6929 - 1.6081 1.00 3606 178 0.1840 0.2007 REMARK 3 8 1.6081 - 1.5381 1.00 3564 185 0.1818 0.1839 REMARK 3 9 1.5381 - 1.4789 1.00 3573 202 0.1844 0.1854 REMARK 3 10 1.4789 - 1.4278 1.00 3573 169 0.1891 0.2076 REMARK 3 11 1.4278 - 1.3832 1.00 3572 181 0.1886 0.1833 REMARK 3 12 1.3832 - 1.3436 1.00 3578 169 0.1878 0.1845 REMARK 3 13 1.3436 - 1.3083 1.00 3504 218 0.1858 0.1870 REMARK 3 14 1.3083 - 1.2763 1.00 3527 207 0.1877 0.1976 REMARK 3 15 1.2763 - 1.2473 1.00 3561 184 0.1912 0.1789 REMARK 3 16 1.2473 - 1.2208 1.00 3566 195 0.1900 0.1950 REMARK 3 17 1.2208 - 1.1964 1.00 3534 202 0.1880 0.1985 REMARK 3 18 1.1964 - 1.1738 1.00 3499 224 0.1926 0.1966 REMARK 3 19 1.1738 - 1.1528 1.00 3550 177 0.1913 0.2131 REMARK 3 20 1.1528 - 1.1333 1.00 3481 205 0.1955 0.1922 REMARK 3 21 1.1333 - 1.1150 1.00 3508 218 0.1981 0.2071 REMARK 3 22 1.1150 - 1.0978 1.00 3574 192 0.2037 0.2175 REMARK 3 23 1.0978 - 1.0817 1.00 3494 190 0.2104 0.2259 REMARK 3 24 1.0817 - 1.0664 0.98 3489 184 0.2170 0.2148 REMARK 3 25 1.0664 - 1.0520 0.95 3366 184 0.2226 0.2264 REMARK 3 26 1.0520 - 1.0384 0.91 3210 142 0.2401 0.2277 REMARK 3 27 1.0384 - 1.0254 0.86 3068 163 0.2449 0.2447 REMARK 3 28 1.0254 - 1.0130 0.82 2839 155 0.2627 0.2691 REMARK 3 29 1.0130 - 1.0013 0.75 2652 129 0.2798 0.2482 REMARK 3 30 1.0013 - 0.9900 0.66 2326 152 0.2925 0.2904 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) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.170 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.96 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.78 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 1363 REMARK 3 ANGLE : 0.774 1828 REMARK 3 CHIRALITY : 0.065 199 REMARK 3 PLANARITY : 0.005 233 REMARK 3 DIHEDRAL : 3.489 1132 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 7LOG 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_1000254734. 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 : NULL 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) : 0.9539 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 : 108816 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.990 REMARK 200 RESOLUTION RANGE LOW (A) : 52.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 16.50 REMARK 200 R MERGE (I) : 0.03600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 30.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 69.1 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.86200 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 (%): 51.90 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 64.07933 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 32.03967 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 32.03967 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 64.07933 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 MET A 1 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 THR A 109 OG1 CG2 REMARK 470 ASN A 116 OD1 ND2 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 PHE A 114 24.96 -70.75 REMARK 500 REMARK 500 REMARK: NULL DBREF 7LOG A 1 164 UNP D9IEF7 D9IEF7_BPT4 1 164 SEQADV 7LOG ALA A 99 UNP D9IEF7 LEU 99 ENGINEERED MUTATION SEQADV 7LOG LEU A 165 UNP D9IEF7 EXPRESSION TAG SEQADV 7LOG GLU A 166 UNP D9IEF7 EXPRESSION TAG SEQADV 7LOG HIS A 167 UNP D9IEF7 EXPRESSION TAG SEQADV 7LOG HIS A 168 UNP D9IEF7 EXPRESSION TAG SEQADV 7LOG HIS A 169 UNP D9IEF7 EXPRESSION TAG SEQADV 7LOG HIS A 170 UNP D9IEF7 EXPRESSION TAG SEQADV 7LOG HIS A 171 UNP D9IEF7 EXPRESSION TAG SEQADV 7LOG 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 Y8J A 201 10 HET BME A 202 4 HET BME A 203 4 HET TRS A 204 8 HETNAM Y8J 3-BUTYLPYRIDINE HETNAM BME BETA-MERCAPTOETHANOL HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 2 Y8J C9 H13 N FORMUL 3 BME 2(C2 H6 O S) FORMUL 5 TRS C4 H12 N O3 1+ FORMUL 6 HOH *143(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 VAL A 111 1 20 HELIX 6 AA6 PHE A 114 GLN A 123 1 10 HELIX 7 AA7 ARG A 125 LYS A 135 1 11 HELIX 8 AA8 SER A 136 THR A 142 1 7 HELIX 9 AA9 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 CRYST1 60.248 60.248 96.119 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 0.016598 0.009583 0.000000 0.00000 SCALE2 0.000000 0.019166 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010404 0.00000