HEADER VIRAL PROTEIN 27-NOV-18 6N7O TITLE CRYSTAL STRUCTURE OF GIL01 GP7 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GIL01 GP7; COMPND 3 CHAIN: B, A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS PHAGE PGIL01; SOURCE 3 ORGANISM_TAXID: 1075161; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR N.A.CAVENEY,N.C.J.STRYNADKA REVDAT 4 13-MAR-24 6N7O 1 REMARK REVDAT 3 08-JAN-20 6N7O 1 REMARK REVDAT 2 17-JUL-19 6N7O 1 JRNL REVDAT 1 15-MAY-19 6N7O 0 JRNL AUTH N.A.CAVENEY,A.PAVLIN,G.CABALLERO,M.BAHUN,V.HODNIK, JRNL AUTH 2 L.DE CASTRO,N.FORNELOS,M.BUTALA,N.C.J.STRYNADKA JRNL TITL STRUCTURAL INSIGHTS INTO BACTERIOPHAGE GIL01 GP7 INHIBITION JRNL TITL 2 OF HOST LEXA REPRESSOR. JRNL REF STRUCTURE V. 27 1094 2019 JRNL REFN ISSN 0969-2126 JRNL PMID 31056420 JRNL DOI 10.1016/J.STR.2019.03.019 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 32.16 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 9508 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.010 REMARK 3 FREE R VALUE TEST SET COUNT : 476 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 32.1642 - 2.4516 1.00 3102 164 0.1727 0.2105 REMARK 3 2 2.4516 - 1.9460 1.00 2981 157 0.2046 0.2300 REMARK 3 3 1.9460 - 1.7000 1.00 2949 155 0.2691 0.3082 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.860 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.25 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.30 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 : 0.006 667 REMARK 3 ANGLE : 0.678 901 REMARK 3 CHIRALITY : 0.039 106 REMARK 3 PLANARITY : 0.003 113 REMARK 3 DIHEDRAL : 18.177 277 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 6N7O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-NOV-18. REMARK 100 THE DEPOSITION ID IS D_1000238071. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUL-16 REMARK 200 TEMPERATURE (KELVIN) : 85 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08B1-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : .9801 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX300HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9511 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.470 REMARK 200 RESOLUTION RANGE LOW (A) : 32.158 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 7.497 REMARK 200 R MERGE (I) : 0.22100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.2400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.47 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.51 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.4 REMARK 200 DATA REDUNDANCY IN SHELL : 5.61 REMARK 200 R MERGE FOR SHELL (I) : 4.14500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.440 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 27.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.69 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM IODIDE, 0.1 M BIS TRIS REMARK 280 PROPANE, PH 8.5, 20% (W/V) PEG 3.35K, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 295.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 -1.000000 0.000000 0.000000 19.84500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.15000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.35000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 23.15000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.84500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 22.35000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5180 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 LYS B 38 REMARK 465 GLU B 39 REMARK 465 LEU B 40 REMARK 465 GLU B 41 REMARK 465 LYS B 42 REMARK 465 ASN B 43 REMARK 465 VAL B 44 REMARK 465 GLU B 45 REMARK 465 GLY B 46 REMARK 465 LYS B 47 REMARK 465 LYS B 48 REMARK 465 ASP B 49 REMARK 465 ASP B 50 REMARK 465 GLU A 35 REMARK 465 ASP A 36 REMARK 465 TYR A 37 REMARK 465 LYS A 38 REMARK 465 GLU A 39 REMARK 465 LEU A 40 REMARK 465 GLU A 41 REMARK 465 LYS A 42 REMARK 465 ASN A 43 REMARK 465 VAL A 44 REMARK 465 GLU A 45 REMARK 465 GLY A 46 REMARK 465 LYS A 47 REMARK 465 LYS A 48 REMARK 465 ASP A 49 REMARK 465 ASP A 50 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 102 DBREF 6N7O B 1 50 UNP Q7WSG2 Q7WSG2_9VIRU 1 50 DBREF 6N7O A 1 50 UNP Q7WSG2 Q7WSG2_9VIRU 1 50 SEQADV 6N7O GLY B -1 UNP Q7WSG2 EXPRESSION TAG SEQADV 6N7O SER B 0 UNP Q7WSG2 EXPRESSION TAG SEQADV 6N7O GLY A -1 UNP Q7WSG2 EXPRESSION TAG SEQADV 6N7O SER A 0 UNP Q7WSG2 EXPRESSION TAG SEQRES 1 B 52 GLY SER MET ARG ASP LYS LEU LEU ASP PHE ILE ILE GLU SEQRES 2 B 52 LEU SER GLN SER SER LYS GLN VAL VAL SER LYS SER TYR SEQRES 3 B 52 VAL ILE ASP ARG LEU MET GLN VAL THR LYS GLU ASP TYR SEQRES 4 B 52 LYS GLU LEU GLU LYS ASN VAL GLU GLY LYS LYS ASP ASP SEQRES 1 A 52 GLY SER MET ARG ASP LYS LEU LEU ASP PHE ILE ILE GLU SEQRES 2 A 52 LEU SER GLN SER SER LYS GLN VAL VAL SER LYS SER TYR SEQRES 3 A 52 VAL ILE ASP ARG LEU MET GLN VAL THR LYS GLU ASP TYR SEQRES 4 A 52 LYS GLU LEU GLU LYS ASN VAL GLU GLY LYS LYS ASP ASP HET IOD B 101 1 HET IOD A 101 1 HET IOD A 102 1 HETNAM IOD IODIDE ION FORMUL 3 IOD 3(I 1-) FORMUL 6 HOH *71(H2 O) HELIX 1 AA1 GLY B -1 SER B 15 1 17 HELIX 2 AA2 LYS B 22 THR B 33 1 12 HELIX 3 AA3 SER A 0 SER A 15 1 16 HELIX 4 AA4 LYS A 22 THR A 33 1 12 SHEET 1 AA1 2 VAL B 19 SER B 21 0 SHEET 2 AA1 2 VAL A 19 SER A 21 -1 O VAL A 20 N VAL B 20 SITE 1 AC1 2 GLN B 18 HOH B 227 SITE 1 AC2 2 LYS A 17 SER A 21 SITE 1 AC3 1 LYS A 17 CRYST1 39.690 44.700 46.300 90.00 90.00 90.00 P 21 21 21 8 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 0.025195 0.000000 0.000000 0.00000 SCALE2 0.000000 0.022371 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021598 0.00000