HEADER ANTIMICROBIAL PROTEIN 30-AUG-08 2ZRR TITLE CRYSTAL STRUCTURE OF AN IMMUNITY PROTEIN THAT CONTRIBUTES TO THE SELF- TITLE 2 PROTECTION OF BACTERIOCIN-PRODUCING ENTEROCOCCUS MUNDTII 15-1A COMPND MOL_ID: 1; COMPND 2 MOLECULE: MUNDTICIN KS IMMUNITY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROCOCCUS MUNDTII; SOURCE 3 ORGANISM_TAXID: 53346; SOURCE 4 STRAIN: 15-1A; SOURCE 5 GENE: ORF8; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-28A(+) KEYWDS ANTIPARALLEL FOUR-HELIX BUNDLE, ANTIMICROBIAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.J.JEON,M.NODA,Y.MATOBA,T.KUMAGAI,M.SUGIYAMA REVDAT 2 13-MAR-24 2ZRR 1 SEQADV REVDAT 1 17-FEB-09 2ZRR 0 JRNL AUTH H.J.JEON,M.NODA,Y.MATOBA,T.KUMAGAI,M.SUGIYAMA JRNL TITL CRYSTAL STRUCTURE AND MUTAGENIC ANALYSIS OF A BACTERIOCIN JRNL TITL 2 IMMUNITY PROTEIN, MUN-IM JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 378 574 2009 JRNL REFN ISSN 0006-291X JRNL PMID 19061861 JRNL DOI 10.1016/J.BBRC.2008.11.093 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 83.4 REMARK 3 NUMBER OF REFLECTIONS : 8042 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) : 0.228 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.600 REMARK 3 FREE R VALUE TEST SET COUNT : 450 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.013 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 38.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 323 REMARK 3 BIN R VALUE (WORKING SET) : 0.3300 REMARK 3 BIN FREE R VALUE : 0.3900 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 25 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.076 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 648 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 94 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.35 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.36 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.39 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.100 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.630 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.650 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 4.290 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.660 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 7.060 ; 2.500 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 : NULL REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPH19.SOL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 2ZRR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-SEP-08. REMARK 100 THE DEPOSITION ID IS D_1000028343. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUN-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9138 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : 0.04500 REMARK 200 FOR THE DATA SET : 39.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 69.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.36800 REMARK 200 R SYM FOR SHELL (I) : 0.36800 REMARK 200 FOR SHELL : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SIRAS REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 3.1M SODIUM FORMATE, 0.1M SODIUM REMARK 280 CITRATE, PH 3.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 297K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 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 14.35500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.89000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 47.38000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 14.35500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.89000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 47.38000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 14.35500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 36.89000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 47.38000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 14.35500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 36.89000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 47.38000 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 237 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 240 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 263 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 281 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 284 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 ASN A 3 REMARK 465 LEU A 4 REMARK 465 LYS A 5 REMARK 465 TRP A 6 REMARK 465 PHE A 7 REMARK 465 SER A 8 REMARK 465 GLY A 9 REMARK 465 ASN A 93 REMARK 465 ILE A 94 REMARK 465 ARG A 95 REMARK 465 TYR A 96 REMARK 465 GLY A 97 REMARK 465 TYR A 98 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 GLU A 29 131.06 72.32 REMARK 500 LYS A 72 -81.95 -61.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUNECE DATABSE OF THIS PROTEIN HAS BEEN DEPOSITED TO DDBJ. REMARK 999 ACCESSION CODE AB454504. REMARK 999 IT WILL BE OPENED WHEN THIS FILE IS PUBLISHED. DBREF 2ZRR A 1 98 PDB 2ZRR 2ZRR 1 98 SEQADV 2ZRR MET A -19 PDB 2ZRR EXPRESSION TAG SEQADV 2ZRR GLY A -18 PDB 2ZRR EXPRESSION TAG SEQADV 2ZRR SER A -17 PDB 2ZRR EXPRESSION TAG SEQADV 2ZRR SER A -16 PDB 2ZRR EXPRESSION TAG SEQADV 2ZRR HIS A -15 PDB 2ZRR EXPRESSION TAG SEQADV 2ZRR HIS A -14 PDB 2ZRR EXPRESSION TAG SEQADV 2ZRR HIS A -13 PDB 2ZRR EXPRESSION TAG SEQADV 2ZRR HIS A -12 PDB 2ZRR EXPRESSION TAG SEQADV 2ZRR HIS A -11 PDB 2ZRR EXPRESSION TAG SEQADV 2ZRR HIS A -10 PDB 2ZRR EXPRESSION TAG SEQADV 2ZRR SER A -9 PDB 2ZRR EXPRESSION TAG SEQADV 2ZRR SER A -8 PDB 2ZRR EXPRESSION TAG SEQADV 2ZRR GLY A -7 PDB 2ZRR EXPRESSION TAG SEQADV 2ZRR LEU A -6 PDB 2ZRR EXPRESSION TAG SEQADV 2ZRR VAL A -5 PDB 2ZRR EXPRESSION TAG SEQADV 2ZRR PRO A -4 PDB 2ZRR EXPRESSION TAG SEQADV 2ZRR ARG A -3 PDB 2ZRR EXPRESSION TAG SEQADV 2ZRR GLY A -2 PDB 2ZRR EXPRESSION TAG SEQADV 2ZRR SER A -1 PDB 2ZRR EXPRESSION TAG SEQADV 2ZRR HIS A 0 PDB 2ZRR EXPRESSION TAG SEQRES 1 A 118 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 118 LEU VAL PRO ARG GLY SER HIS MET SER ASN LEU LYS TRP SEQRES 3 A 118 PHE SER GLY GLY ASP ASP ARG ARG LYS LYS ALA GLU VAL SEQRES 4 A 118 ILE ILE THR GLU LEU LEU ASP ASP LEU GLU ILE ASP LEU SEQRES 5 A 118 GLY ASN GLU SER LEU ARG LYS VAL LEU GLY SER TYR LEU SEQRES 6 A 118 LYS LYS LEU LYS ASN GLU GLY THR SER VAL PRO LEU VAL SEQRES 7 A 118 LEU SER ARG MET ASN ILE GLU ILE SER ASN ALA ILE LYS SEQRES 8 A 118 LYS ASP GLY VAL SER LEU ASN GLU ASN GLN SER LYS LYS SEQRES 9 A 118 LEU LYS GLU LEU MET SER ILE SER ASN ILE ARG TYR GLY SEQRES 10 A 118 TYR FORMUL 2 HOH *94(H2 O) HELIX 1 1 ASP A 12 GLU A 29 1 18 HELIX 2 2 ASN A 34 GLU A 51 1 18 HELIX 3 3 SER A 54 LYS A 71 1 18 HELIX 4 4 ASN A 78 SER A 90 1 13 CRYST1 28.710 73.780 94.760 90.00 90.00 90.00 I 2 2 2 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 0.034831 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013554 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010553 0.00000