10 20 30 40 50 60 70 80 1V74 - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER ANTIBIOTIC/IMMUNE SYSTEM 10-DEC-03 1V74
TITLE RIBONUCLEASE-INHIBITOR COMPLEX
COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLICIN D; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: COLICIN D CATALYTIC DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: COLICIN D IMMUNITY PROTEIN; COMPND 8 CHAIN: B; COMPND 9 SYNONYM: MICROCIN D IMMUNITY PROTEIN; COMPND 10 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI K12; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 83333; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: K12; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PCOLD-CA23; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 11 ORGANISM_TAXID: 562; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 14 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 15 EXPRESSION_SYSTEM_PLASMID: PJF129
KEYWDS COLICIN D - IMMD COMPLEX, CYTOTOXICITY, TRANSFER RNASE, KEYWDS 2 PROTEIN-PROTEIN INHIBITION, ANTIBIOTIC/IMMUNE SYSTEM COMPLEX
EXPDTA X-RAY DIFFRACTION
AUTHOR M.GRAILLE,L.MORA,R.H.BUCKINGHAM,H.VAN TILBEURGH,M.DE AUTHOR 2 ZAMAROCZY
REVDAT 3 24-FEB-09 1V74 1 VERSN REVDAT 2 26-APR-05 1V74 1 JRNL REVDAT 1 30-MAR-04 1V74 0
JRNL AUTH M.GRAILLE,L.MORA,R.H.BUCKINGHAM,H.VAN TILBEURGH, JRNL AUTH 2 M.DE ZAMAROCZY JRNL TITL STRUCTURAL INHIBITION OF THE COLICIN D TRNASE BY JRNL TITL 2 THE TRNA-MIMICKING IMMUNITY PROTEIN JRNL REF EMBO J. V. 23 1474 2004 JRNL REFN ISSN 0261-4189 JRNL PMID 15014439 JRNL DOI 10.1038/SJ.EMBOJ.7600162
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 19396 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) : 0.194 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 930 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2300 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 139 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1569 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 16 REMARK 3 SOLVENT ATOMS : 195 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.00 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) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.17 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) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.20 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.10 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 20.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.69 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 : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1V74 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-DEC-03. REMARK 100 THE RCSB ID CODE IS RCSB006289.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-SEP-02 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8; 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : BM30A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20818 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.980 REMARK 200 RESOLUTION RANGE LOW (A) : 99.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 13.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.98 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.27800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.600 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 (%): 61.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% PEG 400, 0.2M MGSO4, PH 8, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291K. 24% PEG 8000, REMARK 280 0.1M NA CITRATE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 73.96700 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 31.02850 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 31.02850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 36.98350 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 31.02850 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 31.02850 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 110.95050 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 31.02850 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 31.02850 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 36.98350 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 31.02850 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 31.02850 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 110.95050 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 73.96700 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 PRESENT IN THE ASYMETRIC UNIT
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 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 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 LYS A 646 101.01 -162.28 REMARK 500 ASN B 2 100.69 -57.65 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 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 19 DISTANCE = 16.50 ANGSTROMS REMARK 525 HOH A 38 DISTANCE = 18.66 ANGSTROMS REMARK 525 HOH A 120 DISTANCE = 19.02 ANGSTROMS
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 1PE A 1001
DBREF 1V74 A 591 697 UNP P17998 CEAD_ECOLI 591 697 DBREF 1V74 B 1 87 UNP P11899 IMMD_ECOLI 1 87
SEQRES 1 A 107 LEU ASN ASP PRO LEU ASP SER GLY ARG PHE SER ARG LYS SEQRES 2 A 107 GLN LEU ASP LYS LYS TYR LYS HIS ALA GLY ASP PHE GLY SEQRES 3 A 107 ILE SER ASP THR LYS LYS ASN ARG GLU THR LEU THR LYS SEQRES 4 A 107 PHE ARG ASP ALA ILE GLU GLU HIS LEU SER ASP LYS ASP SEQRES 5 A 107 THR VAL GLU LYS GLY THR TYR ARG ARG GLU LYS GLY SER SEQRES 6 A 107 LYS VAL TYR PHE ASN PRO ASN THR MET ASN VAL VAL ILE SEQRES 7 A 107 ILE LYS SER ASN GLY GLU PHE LEU SER GLY TRP LYS ILE SEQRES 8 A 107 ASN PRO ASP ALA ASP ASN GLY ARG ILE TYR LEU GLU THR SEQRES 9 A 107 GLY GLU LEU SEQRES 1 B 87 MET ASN LYS MET ALA MET ILE ASP LEU ALA LYS LEU PHE SEQRES 2 B 87 LEU ALA SER LYS ILE THR ALA ILE GLU PHE SER GLU ARG SEQRES 3 B 87 ILE CYS VAL GLU ARG ARG ARG LEU TYR GLY VAL LYS ASP SEQRES 4 B 87 LEU SER PRO ASN ILE LEU ASN CYS GLY GLU GLU LEU PHE SEQRES 5 B 87 MET ALA ALA GLU ARG PHE GLU PRO ASP ALA ASP ARG ALA SEQRES 6 B 87 ASN TYR GLU ILE ASP ASP ASN GLY LEU LYS VAL GLU VAL SEQRES 7 B 87 ARG SER ILE LEU GLU LYS PHE LYS LEU
HET 1PE A1001 16
HETNAM 1PE PENTAETHYLENE GLYCOL
HETSYN 1PE PEG400
FORMUL 3 1PE C10 H22 O6 FORMUL 4 HOH *195(H2 O)
HELIX 1 1 SER A 601 TYR A 609 1 9 HELIX 2 2 LYS A 610 GLY A 616 5 7 HELIX 3 3 ASN A 623 ASP A 640 1 18 HELIX 4 4 ALA A 685 GLY A 695 1 11 HELIX 5 5 MET B 4 ALA B 15 1 12 HELIX 6 6 THR B 19 TYR B 35 1 17 HELIX 7 7 SER B 41 ARG B 57 1 17 HELIX 8 8 ASP B 70 PHE B 85 1 16
SHEET 1 A 4 VAL A 644 GLU A 645 0 SHEET 2 A 4 LYS A 656 PHE A 659 -1 O PHE A 659 N VAL A 644 SHEET 3 A 4 ASN A 665 ILE A 669 -1 O ILE A 669 N LYS A 656 SHEET 4 A 4 PHE A 675 LYS A 680 -1 O SER A 677 N ILE A 668 SHEET 1 B 2 THR A 648 TYR A 649 0 SHEET 2 B 2 GLU A 696 LEU A 697 1 O LEU A 697 N THR A 648
SITE 1 AC1 5 HOH A 192 ARG A 599 TYR A 658 SER A 671 SITE 2 AC1 5 ASN B 72
CRYST1 62.057 62.057 147.934 90.00 90.00 90.00 P 41 21 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 0.016114 0.000000 0.000000 0.00000
SCALE2 0.000000 0.016114 0.000000 0.00000
SCALE3 0.000000 0.000000 0.006760 0.00000