PDB Short entry for 2BL7 HEADER IMMUNE SYSTEM 02-MAR-05 2BL7 TITLE 1.6 ANGSTROM CRYSTAL STRUCTURE OF ENTA-IM: A BACTERIAL TITLE 2 IMMUNITY PROTEIN CONFERRING IMMUNITY TO THE ANTIMICROBIAL TITLE 3 ACTIVITY OF THE PEDIOCIN-LIKE BACTERIOCIN, ENTEROCIN A COMPND MOL_ID: 1; COMPND 2 MOLECULE: ENTEROCINE A IMMUNITY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS FAECIUM; SOURCE 3 ORGANISM_TAXID: 1352; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS IMMUNE SYSTEM, ENTEROCIN A, ORF2 PROTEIN, IMMUNITY, KEYWDS 2 BACTERIAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.JOHNSEN,B.DALHUS,I.LEIROS,J.NISSEN-MEYER REVDAT 3 24-FEB-09 2BL7 1 VERSN REVDAT 2 11-MAY-05 2BL7 1 JRNL REVDAT 1 07-MAR-05 2BL7 0 JRNL AUTH L.JOHNSEN,B.DALHUS,I.LEIROS,J.NISSEN-MEYER JRNL TITL 1.6-A CRYSTAL STRUCTURE OF ENTA-IM: A BACTERIAL JRNL TITL 2 IMMUNITY PROTEIN CONFERRING IMMUNITY TO THE JRNL TITL 3 ANTIMICROBIAL ACTIVITY OF THE PEDIOCIN-LIKE JRNL TITL 4 BACTERIOCIN ENTEROCIN A JRNL REF J.BIOL.CHEM. V. 280 19045 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15753083 JRNL DOI 10.1074/JBC.M501386200 REMARK 2 REMARK 2 RESOLUTION. 2.2 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.2 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.9 REMARK 3 NUMBER OF REFLECTIONS : 5907 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.2097 REMARK 3 FREE R VALUE : 0.2606 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.0 REMARK 3 FREE R VALUE TEST SET COUNT : 193 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.28 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 72 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 449 REMARK 3 BIN R VALUE (WORKING SET) : 0.218 REMARK 3 BIN FREE R VALUE : 0.210 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 3 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 16 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 660 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 47 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.9 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.760 REMARK 3 B22 (A**2) : 3.760 REMARK 3 B33 (A**2) : -7.520 REMARK 3 B12 (A**2) : 0.487 REMARK 3 B13 (A**2) : 0.000 REMARK 3 B23 (A**2) : 0.000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.13 REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.34 REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005199 REMARK 3 BOND ANGLES (DEGREES) : 1.00770 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 16.0 REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : 0.378692 REMARK 3 BSOL : 54.9115 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2BL7 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-MAR-05. REMARK 100 THE PDBE ID CODE IS EBI-23161. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 110.0 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALEIT REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6364 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 8.600 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.40000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.7 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 12.19667 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 24.39333 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 24.39333 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 12.19667 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 GENERATING THE BIOMOLECULE 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: PQS 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 HOH A2033 LIES ON A SPECIAL POSITION. REMARK 400 REMARK 400 COMPOUND REMARK 400 ENGINEERED RESIDUE IN CHAIN A, LEU 31 TO MSE REMARK 400 ENGINEERED RESIDUE IN CHAIN A, LEU 80 TO MSE 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 MSE A 1 REMARK 465 LYS A 2 REMARK 465 ILE A 83 REMARK 465 GLY A 84 REMARK 465 ARG A 85 REMARK 465 THR A 86 REMARK 465 ALA A 87 REMARK 465 GLY A 88 REMARK 465 ILE A 89 REMARK 465 ASN A 90 REMARK 465 GLY A 91 REMARK 465 LEU A 92 REMARK 465 TYR A 93 REMARK 465 ARG A 94 REMARK 465 ALA A 95 REMARK 465 ASP A 96 REMARK 465 TYR A 97 REMARK 465 GLY A 98 REMARK 465 ASP A 99 REMARK 465 LYS A 100 REMARK 465 SER A 101 REMARK 465 GLN A 102 REMARK 465 PHE A 103 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 GLU A 82 CA C O CB CG CD OE1 OE2 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 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 LYS A 20 36.14 71.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BL8 RELATED DB: PDB REMARK 900 1.6 ANGSTROM CRYSTAL STRUCTURE OF ENTA-IM REMARK 900 : A BACTERIAL IMMUNITY PROTEIN CONFERRING REMARK 900 IMMUNITY TO THE ANTIMICROBIAL ACTIVITY OF REMARK 900 THE PEDIOCIN-LIKE BACTERIOCIN, ENTEROCIN A DBREF 2BL7 A 1 103 UNP Q47785 Q47785_ENTFC 1 103 SEQADV 2BL7 MSE A 31 UNP Q47785 LEU 31 ENGINEERED MUTATION SEQADV 2BL7 MSE A 80 UNP Q47785 LEU 80 ENGINEERED MUTATION SEQRES 1 A 103 MSE LYS LYS ASN ALA LYS GLN ILE VAL HIS GLU LEU TYR SEQRES 2 A 103 ASN ASP ILE SER ILE SER LYS ASP PRO LYS TYR SER ASP SEQRES 3 A 103 ILE LEU GLU VAL MSE GLN LYS VAL TYR LEU LYS LEU GLU SEQRES 4 A 103 LYS GLN LYS TYR GLU LEU ASP PRO SER PRO LEU ILE ASN SEQRES 5 A 103 ARG LEU VAL ASN TYR LEU TYR PHE THR ALA TYR THR ASN SEQRES 6 A 103 LYS ILE ARG PHE THR GLU TYR GLN GLU GLU LEU ILE ARG SEQRES 7 A 103 ASN MSE SER GLU ILE GLY ARG THR ALA GLY ILE ASN GLY SEQRES 8 A 103 LEU TYR ARG ALA ASP TYR GLY ASP LYS SER GLN PHE MODRES 2BL7 MSE A 31 MET SELENOMETHIONINE MODRES 2BL7 MSE A 80 MET SELENOMETHIONINE HET MSE A 31 8 HET MSE A 80 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 HOH *47(H2 O1) HELIX 1 1 ASN A 4 LYS A 20 1 17 HELIX 2 2 ASP A 21 LYS A 23 5 3 HELIX 3 3 TYR A 24 LYS A 40 1 17 HELIX 4 4 LYS A 40 ASP A 46 1 7 HELIX 5 5 PRO A 47 LYS A 66 1 20 HELIX 6 6 THR A 70 SER A 81 1 12 LINK C VAL A 30 N MSE A 31 1555 1555 1.32 LINK C MSE A 31 N GLN A 32 1555 1555 1.33 LINK C ASN A 79 N MSE A 80 1555 1555 1.33 LINK C MSE A 80 N SER A 81 1555 1555 1.33 CRYST1 75.800 75.800 36.590 90.00 90.00 120.00 P 31 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 0.013193 0.007617 0.000000 0.00000 SCALE2 0.000000 0.015234 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027330 0.00000