HEADER IMMUNE SYSTEM 20-MAR-00 1EMV TITLE CRYSTAL STRUCTURE OF COLICIN E9 DNASE DOMAIN WITH ITS COGNATE IMMUNITY TITLE 2 PROTEIN IM9 (1.7 ANGSTROMS) COMPND MOL_ID: 1; COMPND 2 MOLECULE: IMMUNITY PROTEIN IM9; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: IMME9, MICROCIN E9 IMMUNITY PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: COLICIN E9; COMPND 8 CHAIN: B; COMPND 9 FRAGMENT: C-TERMINAL DOMAIN, DNASE DOMAIN; COMPND 10 EC: 3.1.21.1; COMPND 11 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PTRC 99A (PRJ352); SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 10 ORGANISM_TAXID: 562; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 14 EXPRESSION_SYSTEM_PLASMID: PTRC 99A (PRJ352) KEYWDS PROTEIN-PROTEIN COMPLEX, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR U.C.KUHLMANN,A.J.POMMER,G.M.MOORE,R.JAMES,C.KLEANTHOUS REVDAT 4 07-FEB-24 1EMV 1 REMARK SEQADV REVDAT 3 24-FEB-09 1EMV 1 VERSN REVDAT 2 01-APR-03 1EMV 1 JRNL REVDAT 1 13-SEP-00 1EMV 0 JRNL AUTH U.C.KUHLMANN,A.J.POMMER,G.R.MOORE,R.JAMES,C.KLEANTHOUS JRNL TITL SPECIFICITY IN PROTEIN-PROTEIN INTERACTIONS: THE STRUCTURAL JRNL TITL 2 BASIS FOR DUAL RECOGNITION IN ENDONUCLEASE COLICIN-IMMUNITY JRNL TITL 3 PROTEIN COMPLEXES. JRNL REF J.MOL.BIOL. V. 301 1163 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10966813 JRNL DOI 10.1006/JMBI.2000.3945 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 90.3 REMARK 3 NUMBER OF REFLECTIONS : 20724 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.260 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1098 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 1690 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 154 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL 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) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.538 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL 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 : 0.34 REMARK 3 BSOL : 39.54 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1EMV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAR-00. REMARK 100 THE DEPOSITION ID IS D_1000010732. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-SEP-99 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 5.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : CCP4 (TRUNCATE) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20871 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.850 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.9 REMARK 200 DATA REDUNDANCY : 19.80 REMARK 200 R MERGE (I) : 0.02600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 47.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 73.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.07100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 24% PEG 4000, 0.1M SODIUM ACETATE, PH REMARK 280 5.3, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 21.93500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 43.88500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.28000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 43.88500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.93500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.28000 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A HETERODIMERIC COMPLEX OF THE REMARK 300 E9 DNASE DOMAIN WITH ITS COGNATE IMMUNITY PROTEIN IM9 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: 1740 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11280 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -12.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 400 REMARK 400 COMPOUND REMARK 400 E9 DNASE IS METAL FREE 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 1 REMARK 465 GLU A 2 REMARK 465 GLY A 86 REMARK 465 ARG B 132 REMARK 465 GLY B 133 REMARK 465 LYS B 134 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 SER B 3 106.48 13.51 REMARK 500 ASP B 29 -123.36 49.23 REMARK 500 ASP B 44 -11.69 78.22 REMARK 500 LYS B 69 -19.98 -47.80 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 PO4 B 403 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BXI RELATED DB: PDB REMARK 900 1BXI CONTAINS THE SAME PROTEIN COMPLEX WITH METAL BOUND TO THE REMARK 900 ACTIVE SITE DBREF 1EMV A 1 86 UNP P13479 IMM9_ECOLI 1 86 DBREF 1EMV B 2 134 UNP P09883 CEA9_ECOLI 450 582 SEQADV 1EMV MET B 1 UNP P09883 CLONING ARTIFACT SEQRES 1 A 86 MET GLU LEU LYS HIS SER ILE SER ASP TYR THR GLU ALA SEQRES 2 A 86 GLU PHE LEU GLN LEU VAL THR THR ILE CYS ASN ALA ASP SEQRES 3 A 86 THR SER SER GLU GLU GLU LEU VAL LYS LEU VAL THR HIS SEQRES 4 A 86 PHE GLU GLU MET THR GLU HIS PRO SER GLY SER ASP LEU SEQRES 5 A 86 ILE TYR TYR PRO LYS GLU GLY ASP ASP ASP SER PRO SER SEQRES 6 A 86 GLY ILE VAL ASN THR VAL LYS GLN TRP ARG ALA ALA ASN SEQRES 7 A 86 GLY LYS SER GLY PHE LYS GLN GLY SEQRES 1 B 134 MET GLU SER LYS ARG ASN LYS PRO GLY LYS ALA THR GLY SEQRES 2 B 134 LYS GLY LYS PRO VAL GLY ASP LYS TRP LEU ASP ASP ALA SEQRES 3 B 134 GLY LYS ASP SER GLY ALA PRO ILE PRO ASP ARG ILE ALA SEQRES 4 B 134 ASP LYS LEU ARG ASP LYS GLU PHE LYS SER PHE ASP ASP SEQRES 5 B 134 PHE ARG LYS ALA VAL TRP GLU GLU VAL SER LYS ASP PRO SEQRES 6 B 134 GLU LEU SER LYS ASN LEU ASN PRO SER ASN LYS SER SER SEQRES 7 B 134 VAL SER LYS GLY TYR SER PRO PHE THR PRO LYS ASN GLN SEQRES 8 B 134 GLN VAL GLY GLY ARG LYS VAL TYR GLU LEU HIS HIS ASP SEQRES 9 B 134 LYS PRO ILE SER GLN GLY GLY GLU VAL TYR ASP MET ASP SEQRES 10 B 134 ASN ILE ARG VAL THR THR PRO LYS ARG HIS ILE ASP ILE SEQRES 11 B 134 HIS ARG GLY LYS HET PO4 B 403 5 HETNAM PO4 PHOSPHATE ION FORMUL 3 PO4 O4 P 3- FORMUL 4 HOH *154(H2 O) HELIX 1 1 SER A 6 TYR A 10 5 5 HELIX 2 2 THR A 11 ASN A 24 1 14 HELIX 3 3 SER A 29 GLU A 45 1 17 HELIX 4 4 SER A 50 TYR A 55 1 6 HELIX 5 5 SER A 63 ASN A 78 1 16 HELIX 6 6 SER B 3 LYS B 7 5 5 HELIX 7 7 LYS B 21 ALA B 26 1 6 HELIX 8 8 PRO B 35 ARG B 43 1 9 HELIX 9 9 SER B 49 LYS B 63 1 15 HELIX 10 10 ASP B 64 LYS B 69 1 6 HELIX 11 11 ASN B 72 SER B 80 1 9 HELIX 12 12 PRO B 88 GLN B 92 5 5 HELIX 13 13 PRO B 106 GLY B 110 5 5 HELIX 14 14 THR B 123 HIS B 131 1 9 SHEET 1 A 2 GLY B 9 LYS B 10 0 SHEET 2 A 2 GLU B 46 PHE B 47 -1 N PHE B 47 O GLY B 9 SHEET 1 B 3 ALA B 32 PRO B 33 0 SHEET 2 B 3 ILE B 119 THR B 122 -1 N VAL B 121 O ALA B 32 SHEET 3 B 3 GLU B 100 HIS B 103 -1 N GLU B 100 O THR B 122 SITE 1 AC1 6 SER A 28 ARG B 5 HIS B 102 HIS B 103 SITE 2 AC1 6 HOH B 404 HOH B 423 CRYST1 43.870 52.560 87.770 90.00 90.00 90.00 P 21 21 21 4 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 0.022795 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019026 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011393 0.00000