HEADER HYDROLASE 16-JUN-16 5KI8 TITLE PSEUDO T4 LYSOZYME MUTANT - Y88PHE-BR 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; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BH10B; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PBAD KEYWDS HALOGEN BONDS, T4 LYSOZYME, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR M.R.SCHOLFIELD REVDAT 6 15-NOV-23 5KI8 1 REMARK REVDAT 5 27-SEP-23 5KI8 1 REMARK REVDAT 4 27-NOV-19 5KI8 1 REMARK REVDAT 3 14-JUN-17 5KI8 1 JRNL REVDAT 2 19-APR-17 5KI8 1 JRNL REVDAT 1 12-APR-17 5KI8 0 JRNL AUTH M.R.SCHOLFIELD,M.C.FORD,A.C.CARLSSON,H.BUTTA,R.A.MEHL,P.S.HO JRNL TITL STRUCTURE-ENERGY RELATIONSHIPS OF HALOGEN BONDS IN PROTEINS. JRNL REF BIOCHEMISTRY V. 56 2794 2017 JRNL REFN ISSN 1520-4995 JRNL PMID 28345933 JRNL DOI 10.1021/ACS.BIOCHEM.7B00022 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1951 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.70 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.430 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.7 REMARK 3 NUMBER OF REFLECTIONS : 28118 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.088 REMARK 3 FREE R VALUE TEST SET COUNT : 1993 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 45.7000 - 3.7352 0.99 2107 159 0.1700 0.1900 REMARK 3 2 3.7352 - 2.9649 1.00 2005 154 0.1600 0.2000 REMARK 3 3 2.9649 - 2.5902 0.99 1984 152 0.1700 0.2000 REMARK 3 4 2.5902 - 2.3533 0.99 1949 150 0.1700 0.2100 REMARK 3 5 2.3533 - 2.1847 0.99 1954 141 0.1600 0.1900 REMARK 3 6 2.1847 - 2.0559 0.98 1917 152 0.1600 0.1900 REMARK 3 7 2.0559 - 1.9529 0.98 1911 146 0.1800 0.2300 REMARK 3 8 1.9529 - 1.8679 0.98 1909 146 0.1900 0.2400 REMARK 3 9 1.8679 - 1.7960 0.97 1898 142 0.1900 0.2300 REMARK 3 10 1.7960 - 1.7340 0.97 1891 147 0.2000 0.3100 REMARK 3 11 1.7340 - 1.6798 0.97 1875 144 0.2100 0.2300 REMARK 3 12 1.6798 - 1.6318 0.96 1849 139 0.2400 0.2600 REMARK 3 13 1.6318 - 1.5888 0.81 1566 118 0.2800 0.3100 REMARK 3 14 1.5888 - 1.5500 0.67 1310 103 0.2800 0.3400 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.169 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.220 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.64 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.62 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 1405 REMARK 3 ANGLE : 0.991 1904 REMARK 3 CHIRALITY : 0.044 209 REMARK 3 PLANARITY : 0.004 247 REMARK 3 DIHEDRAL : 12.400 563 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 5KI8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-JUN-16. REMARK 100 THE DEPOSITION ID IS D_1000222279. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : RDI CMOS_8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK 9.9.9.4L REMARK 200 DATA SCALING SOFTWARE : D*TREK 9.9.9.4L REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28167 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 45.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 1.900 REMARK 200 R MERGE (I) : 0.02600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.31000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 1L63 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.4M KPO4, 50MM 2 REMARK 280 -HYDROXYETHYLDISULFIDE, 50MM 2-MERCAPTOETHANOL, PH 6.9, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291.15K 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 63.96333 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 31.98167 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 31.98167 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 63.96333 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 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 412 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 465 HIS A 165 REMARK 465 HIS A 166 REMARK 465 HIS A 167 REMARK 465 HIS A 168 REMARK 465 HIS A 169 REMARK 465 HIS A 170 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 469 O HOH A 482 2.18 REMARK 500 O HOH A 458 O HOH A 485 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 20 -169.76 -79.34 REMARK 500 ILE A 29 75.05 -102.24 REMARK 500 PHE A 114 46.07 -79.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HED A 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5KHZ RELATED DB: PDB REMARK 900 RELATED ID: 5KI1 RELATED DB: PDB REMARK 900 RELATED ID: 5KI2 RELATED DB: PDB REMARK 900 RELATED ID: 5KI3 RELATED DB: PDB REMARK 900 RELATED ID: 5KIG RELATED DB: PDB REMARK 900 RELATED ID: 5KII RELATED DB: PDB REMARK 900 RELATED ID: 5KIM RELATED DB: PDB REMARK 900 RELATED ID: 5KIO RELATED DB: PDB DBREF 5KI8 A 1 164 UNP P00720 ENLYS_BPT4 1 164 SEQADV 5KI8 GLY A 12 UNP P00720 ARG 12 CONFLICT SEQADV 5KI8 THR A 54 UNP P00720 CYS 54 ENGINEERED MUTATION SEQADV 5KI8 ALA A 97 UNP P00720 CYS 97 ENGINEERED MUTATION SEQADV 5KI8 ARG A 137 UNP P00720 ILE 137 CONFLICT SEQADV 5KI8 HIS A 165 UNP P00720 EXPRESSION TAG SEQADV 5KI8 HIS A 166 UNP P00720 EXPRESSION TAG SEQADV 5KI8 HIS A 167 UNP P00720 EXPRESSION TAG SEQADV 5KI8 HIS A 168 UNP P00720 EXPRESSION TAG SEQADV 5KI8 HIS A 169 UNP P00720 EXPRESSION TAG SEQADV 5KI8 HIS A 170 UNP P00720 EXPRESSION TAG SEQRES 1 A 170 MET ASN ILE PHE GLU MET LEU ARG ILE ASP GLU GLY LEU SEQRES 2 A 170 ARG LEU LYS ILE TYR LYS ASP THR GLU GLY TYR TYR THR SEQRES 3 A 170 ILE GLY ILE GLY HIS LEU LEU THR LYS SER PRO SER LEU SEQRES 4 A 170 ASN ALA ALA LYS SER GLU LEU ASP LYS ALA ILE GLY ARG SEQRES 5 A 170 ASN THR ASN GLY VAL ILE THR LYS ASP GLU ALA GLU LYS SEQRES 6 A 170 LEU PHE ASN GLN ASP VAL ASP ALA ALA VAL ARG GLY ILE SEQRES 7 A 170 LEU ARG ASN ALA LYS LEU LYS PRO VAL 4BF ASP SER LEU SEQRES 8 A 170 ASP ALA VAL ARG ARG ALA ALA LEU ILE ASN MET VAL PHE SEQRES 9 A 170 GLN MET GLY GLU THR GLY VAL ALA GLY PHE THR ASN SER SEQRES 10 A 170 LEU ARG MET LEU GLN GLN LYS ARG TRP ASP GLU ALA ALA SEQRES 11 A 170 VAL ASN LEU ALA LYS SER ARG TRP TYR ASN GLN THR PRO SEQRES 12 A 170 ASN ARG ALA LYS ARG VAL ILE THR THR PHE ARG THR GLY SEQRES 13 A 170 THR TRP ASP ALA TYR LYS ASN LEU HIS HIS HIS HIS HIS SEQRES 14 A 170 HIS MODRES 5KI8 4BF A 88 TYR MODIFIED RESIDUE HET 4BF A 88 12 HET HED A 201 8 HETNAM 4BF 4-BROMO-L-PHENYLALANINE HETNAM HED 2-HYDROXYETHYL DISULFIDE HETSYN 4BF P-BROMO-L-PHENYLALANINE FORMUL 1 4BF C9 H10 BR N O2 FORMUL 2 HED C4 H10 O2 S2 FORMUL 3 HOH *197(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 113 1 22 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 HELIX 10 AB1 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 LINK C VAL A 87 N 4BF A 88 1555 1555 1.33 LINK C 4BF A 88 N ASP A 89 1555 1555 1.34 SITE 1 AC1 8 ILE A 3 PHE A 4 ASN A 68 ASP A 72 SITE 2 AC1 8 VAL A 75 4BF A 88 HOH A 301 HOH A 332 CRYST1 60.013 60.013 95.945 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 0.016663 0.009620 0.000000 0.00000 SCALE2 0.000000 0.019241 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010423 0.00000