HEADER TOXIN 09-SEP-13 4MMJ TITLE CRYSTAL STRUCTURE OF YAFQ FROM E.COLI STRAIN BL21(DE3) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADDICTION MODULE TOXIN, RELE/STBE FAMILY; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PREDICTED TOXIN OF THE YAFQ-DINJ TOXIN-ANTITOXIN SYSTEM, COMPND 5 TOXIN OF THE YAFQ-DINJ TOXIN-ANTITOXIN SYSTEM, SUBUNIT OF DINJ-YAFQ COMPND 6 COMPLEX; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI BL21(DE3); SOURCE 3 ORGANISM_TAXID: 469008; SOURCE 4 STRAIN: BL21(DE3); SOURCE 5 GENE: YAFQ; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS TOXIN, ANTITOXIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.LIANG,Z.GAO,Q.LIU,Y.DONG REVDAT 5 08-NOV-23 4MMJ 1 REMARK SEQADV REVDAT 4 24-OCT-18 4MMJ 1 SOURCE AUTHOR REVDAT 3 15-NOV-17 4MMJ 1 REMARK REVDAT 2 20-AUG-14 4MMJ 1 JRNL REVDAT 1 25-JUN-14 4MMJ 0 JRNL AUTH Y.LIANG,Z.GAO,F.WANG,Y.ZHANG,Y.DONG,Q.LIU JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF ESCHERICHIA JRNL TITL 2 COLI TOXIN-ANTITOXIN COMPLEX DINJ-YAFQ JRNL REF J.BIOL.CHEM. V. 289 21191 2014 JRNL REFN ISSN 0021-9258 JRNL PMID 24923448 JRNL DOI 10.1074/JBC.M114.559773 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 12162 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.710 REMARK 3 FREE R VALUE TEST SET COUNT : 573 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 38.0095 - 2.8571 1.00 3035 150 0.1876 0.2145 REMARK 3 2 2.8571 - 2.2678 1.00 2914 132 0.2141 0.2345 REMARK 3 3 2.2678 - 1.9812 0.99 2868 141 0.2070 0.2401 REMARK 3 4 1.9812 - 1.8000 0.97 2772 150 0.2500 0.3179 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.660 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL 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 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 : 0.007 810 REMARK 3 ANGLE : 1.093 1098 REMARK 3 CHIRALITY : 0.081 114 REMARK 3 PLANARITY : 0.004 138 REMARK 3 DIHEDRAL : 12.871 309 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 4MMJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000082097. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-JUL-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BSRF REMARK 200 BEAMLINE : 1W2B 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 : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12280 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 49.1000 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) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : 0.24200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 10.20 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: 4MMG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.33 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M (NH4)2SO4, 30%PEG8000, 10MM REMARK 280 PR(AC)3, PH 7.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z 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 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 33.41250 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 33.41250 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 20.75750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 46.19800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 20.75750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 46.19800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 33.41250 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 20.75750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 46.19800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 33.41250 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 20.75750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 46.19800 REMARK 290 SMTRY3 8 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: 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 201 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 316 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 SER A -2 REMARK 465 THR A -1 REMARK 465 GLY A 0 REMARK 465 MET A 1 REMARK 465 ILE A 2 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 ASN A 39 60.45 60.60 REMARK 500 SER A 54 -125.41 52.97 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 SO4 A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 103 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4MMG RELATED DB: PDB REMARK 900 SAME PROTEIN BUT FROM DIFFERENT E.COLI STRAIN REMARK 900 RELATED ID: 4ML2 RELATED DB: PDB REMARK 900 WILD TYPE REMARK 900 RELATED ID: 4ML0 RELATED DB: PDB DBREF 4MMJ A 1 92 UNP C6EA63 C6EA63_ECOBD 1 92 SEQADV 4MMJ SER A -2 UNP C6EA63 EXPRESSION TAG SEQADV 4MMJ THR A -1 UNP C6EA63 EXPRESSION TAG SEQADV 4MMJ GLY A 0 UNP C6EA63 EXPRESSION TAG SEQADV 4MMJ GLN A 87 UNP C6EA63 HIS 87 ENGINEERED MUTATION SEQRES 1 A 95 SER THR GLY MET ILE GLN ARG ASP ILE GLU TYR SER GLY SEQRES 2 A 95 GLN PHE SER LYS ASP VAL LYS LEU ALA GLN LYS ARG HIS SEQRES 3 A 95 LYS ASP MET ASN LYS LEU LYS TYR LEU MET THR LEU LEU SEQRES 4 A 95 ILE ASN ASN THR LEU PRO LEU PRO ALA VAL TYR LYS ASP SEQRES 5 A 95 HIS PRO LEU GLN SER SER TRP LYS GLY TYR ARG ASP ALA SEQRES 6 A 95 HIS VAL GLU PRO ASP TRP ILE LEU ILE TYR LYS LEU THR SEQRES 7 A 95 ASP LYS LEU LEU ARG PHE GLU ARG THR GLY THR GLN ALA SEQRES 8 A 95 ALA LEU PHE GLY HET SO4 A 101 5 HET SO4 A 102 5 HET SO4 A 103 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 3(O4 S 2-) FORMUL 5 HOH *128(H2 O) HELIX 1 1 SER A 9 ARG A 22 1 14 HELIX 2 2 ASP A 25 ASN A 38 1 14 HELIX 3 3 PRO A 44 LYS A 48 5 5 HELIX 4 4 GLN A 53 LYS A 57 5 5 HELIX 5 5 THR A 86 GLY A 92 1 7 SHEET 1 A 5 ASP A 5 TYR A 8 0 SHEET 2 A 5 LEU A 78 GLY A 85 1 O LEU A 79 N GLU A 7 SHEET 3 A 5 TRP A 68 LEU A 74 -1 N ILE A 71 O ARG A 83 SHEET 4 A 5 ARG A 60 GLU A 65 -1 N ARG A 60 O TYR A 72 SHEET 5 A 5 HIS A 50 PRO A 51 -1 N HIS A 50 O ASP A 61 CISPEP 1 LEU A 41 PRO A 42 0 -1.29 SITE 1 AC1 8 HIS A 23 HIS A 50 ASP A 61 HIS A 63 SITE 2 AC1 8 GLN A 87 PHE A 91 HOH A 242 HOH A 313 SITE 1 AC2 8 ARG A 22 LYS A 24 SER A 55 ASP A 67 SITE 2 AC2 8 THR A 86 HOH A 214 HOH A 225 HOH A 239 SITE 1 AC3 6 LYS A 48 HIS A 63 PRO A 66 HOH A 204 SITE 2 AC3 6 HOH A 230 HOH A 281 CRYST1 41.515 92.396 66.825 90.00 90.00 90.00 C 2 2 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 0.024088 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010823 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014964 0.00000