HEADER HYDROLASE 16-AUG-14 4W54 TITLE T4 LYSOZYME L99A WITH ETHYLBENZENE BOUND 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: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET29 KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.MERSKI,B.K.SHOICHET,O.EIDAM,M.FISCHER REVDAT 7 27-SEP-23 4W54 1 REMARK REVDAT 6 25-DEC-19 4W54 1 REMARK REVDAT 5 22-NOV-17 4W54 1 REMARK REVDAT 4 06-SEP-17 4W54 1 SOURCE JRNL REMARK REVDAT 3 06-MAY-15 4W54 1 JRNL REVDAT 2 22-APR-15 4W54 1 JRNL REVDAT 1 01-APR-15 4W54 0 JRNL AUTH M.MERSKI,M.FISCHER,T.E.BALIUS,O.EIDAM,B.K.SHOICHET JRNL TITL HOMOLOGOUS LIGANDS ACCOMMODATED BY DISCRETE CONFORMATIONS OF JRNL TITL 2 A BURIED CAVITY. JRNL REF PROC.NATL.ACAD.SCI.USA V. 112 5039 2015 JRNL REFN ESSN 1091-6490 JRNL PMID 25847998 JRNL DOI 10.1073/PNAS.1500806112 REMARK 2 REMARK 2 RESOLUTION. 1.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.1_743) 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) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.97 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 19790 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1187 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 45.9868 - 3.5796 1.00 2460 157 0.1628 0.1940 REMARK 3 2 3.5796 - 2.8414 1.00 2353 150 0.1707 0.1968 REMARK 3 3 2.8414 - 2.4822 1.00 2319 148 0.1831 0.2274 REMARK 3 4 2.4822 - 2.2553 1.00 2310 147 0.1648 0.2088 REMARK 3 5 2.2553 - 2.0936 1.00 2288 146 0.1441 0.1857 REMARK 3 6 2.0936 - 1.9702 1.00 2308 148 0.1535 0.1508 REMARK 3 7 1.9702 - 1.8715 1.00 2285 145 0.1625 0.2189 REMARK 3 8 1.8715 - 1.7901 1.00 2280 146 0.1759 0.2059 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.41 REMARK 3 B_SOL : 47.39 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.070 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.72370 REMARK 3 B22 (A**2) : 0.72370 REMARK 3 B33 (A**2) : -1.44730 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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 1442 REMARK 3 ANGLE : 0.889 1953 REMARK 3 CHIRALITY : 0.056 214 REMARK 3 PLANARITY : 0.003 251 REMARK 3 DIHEDRAL : 11.061 554 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 4W54 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-AUG-14. REMARK 100 THE DEPOSITION ID IS D_1000203181. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 1.116 REMARK 200 MONOCHROMATOR : TWO FLAT SI(111) CRYSTALS, REMARK 200 MOUNTED IN A MODEL DCM FROM KHOZU REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XSCALE REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25135 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.700 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.9600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.46500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.430 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: 181L REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.58 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEGF-4000, 10% 2-PROPANOL, REMARK 280 0.1 M HEPES, 50 MM 2-MERCAPTOETHANOL, 50 MM 2-HYDROXYETHYL REMARK 280 DISULFIDE, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277K 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 64.60667 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 32.30333 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 32.30333 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 64.60667 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: 440 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8500 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 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 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 LYS A 16 NZ REMARK 470 ASN A 53 OD1 ND2 REMARK 470 LYS A 60 NZ REMARK 470 ARG A 80 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 83 CD CE NZ REMARK 470 LYS A 147 NZ REMARK 470 LYS A 162 CD CE NZ REMARK 470 ASN A 163 CG OD1 ND2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PYJ A 200 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EPE A 201 DBREF 4W54 A 1 164 UNP P00720 ENLYS_BPT4 1 164 SEQADV 4W54 GLY A 12 UNP P00720 ARG 12 VARIANT SEQADV 4W54 ALA A 99 UNP P00720 LEU 99 ENGINEERED MUTATION SEQADV 4W54 ARG A 137 UNP P00720 ILE 137 VARIANT SEQADV 4W54 LEU A 165 UNP P00720 EXPRESSION TAG SEQADV 4W54 GLU A 166 UNP P00720 EXPRESSION TAG SEQADV 4W54 HIS A 167 UNP P00720 EXPRESSION TAG SEQADV 4W54 HIS A 168 UNP P00720 EXPRESSION TAG SEQADV 4W54 HIS A 169 UNP P00720 EXPRESSION TAG SEQADV 4W54 HIS A 170 UNP P00720 EXPRESSION TAG SEQADV 4W54 HIS A 171 UNP P00720 EXPRESSION TAG SEQADV 4W54 HIS A 172 UNP P00720 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 PYJ A 200 16 HET EPE A 201 15 HETNAM PYJ PHENYLETHANE HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETSYN EPE HEPES FORMUL 2 PYJ C8 H10 FORMUL 3 EPE C8 H18 N2 O4 S FORMUL 4 HOH *133(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 ALA A 112 1 6 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 6 VAL A 87 ALA A 99 VAL A 111 LEU A 118 SITE 2 AC1 6 LEU A 121 PHE A 153 SITE 1 AC2 7 GLY A 30 LEU A 32 LYS A 35 ASP A 70 SITE 2 AC2 7 PHE A 104 MET A 106 THR A 109 CRYST1 60.300 60.300 96.910 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 0.016584 0.009575 0.000000 0.00000 SCALE2 0.000000 0.019149 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010319 0.00000