HEADER TOXIN 06-SEP-13 4ML2 TITLE CRYSTAL STRUCTURE OF WILD-TYPE YAFQ COMPND MOL_ID: 1; COMPND 2 MOLECULE: MRNA INTERFERASE YAFQ; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ENDORIBONUCLEASE YAFQ, TOXIN YAFQ; COMPND 5 EC: 3.1.-.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: YAFQ, B0225, JW0215; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS TOXIN, ANTITOXIN EXPDTA X-RAY DIFFRACTION AUTHOR Y.J.LIANG,Z.Q.GAO,Q.S.LIU,Y.H.DONG REVDAT 4 08-NOV-23 4ML2 1 REMARK SEQADV REVDAT 3 15-NOV-17 4ML2 1 REMARK REVDAT 2 20-AUG-14 4ML2 1 JRNL REVDAT 1 25-JUN-14 4ML2 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. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 22746 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.189 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 1163 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 28.7949 - 2.9990 1.00 2844 144 0.1796 0.1789 REMARK 3 2 2.9990 - 2.3808 1.00 2714 153 0.1753 0.1989 REMARK 3 3 2.3808 - 2.0799 1.00 2696 148 0.1700 0.1648 REMARK 3 4 2.0799 - 1.8898 1.00 2708 132 0.1685 0.1834 REMARK 3 5 1.8898 - 1.7544 1.00 2673 142 0.1638 0.2003 REMARK 3 6 1.7544 - 1.6510 1.00 2629 157 0.1639 0.1913 REMARK 3 7 1.6510 - 1.5683 1.00 2675 156 0.1816 0.2196 REMARK 3 8 1.5683 - 1.5000 1.00 2644 131 0.2180 0.2581 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.40 REMARK 3 B_SOL : 45.10 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 15.210 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) : -1.20610 REMARK 3 B22 (A**2) : -2.05020 REMARK 3 B33 (A**2) : -0.64310 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 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 : 0.006 810 REMARK 3 ANGLE : 1.084 1098 REMARK 3 CHIRALITY : 0.076 112 REMARK 3 PLANARITY : 0.005 135 REMARK 3 DIHEDRAL : 12.545 304 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 4ML2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 09-SEP-13. REMARK 100 THE DEPOSITION ID IS D_1000082044. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-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 : 22754 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 10.00 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 72.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 0.16700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 16.30 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 (%): 60.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M (NH4)2SO4, 30% PEG8000, PH 7.0, REMARK 280 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 37.50750 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 37.50750 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 20.64950 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.91600 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 20.64950 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.91600 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 37.50750 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 20.64950 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.91600 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 37.50750 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 20.64950 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 44.91600 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 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 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: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 385 O HOH A 400 1.83 REMARK 500 O HOH A 383 O HOH A 398 1.94 REMARK 500 O1 SO4 A 103 O HOH A 386 1.96 REMARK 500 O HOH A 260 O HOH A 398 2.01 REMARK 500 O HOH A 388 O HOH A 408 2.06 REMARK 500 O HOH A 331 O HOH A 376 2.06 REMARK 500 O HOH A 377 O HOH A 409 2.07 REMARK 500 O HOH A 391 O HOH A 396 2.10 REMARK 500 O HOH A 371 O HOH A 395 2.14 REMARK 500 O HOH A 323 O HOH A 386 2.14 REMARK 500 OD1 ASP A 5 O HOH A 253 2.17 REMARK 500 O HOH A 338 O HOH A 362 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 GLN A 53 -165.73 -115.18 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 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 104 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 105 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ML0 RELATED DB: PDB REMARK 900 RELATED ID: 4MMJ RELATED DB: PDB REMARK 900 RELATED ID: 4MMG RELATED DB: PDB REMARK 900 SAME PROTEIN BUT FROM DIFFERENT E.COLI STRAIN DBREF 4ML2 A 1 92 UNP Q47149 YAFQ_ECOLI 1 92 SEQADV 4ML2 SER A -2 UNP Q47149 EXPRESSION TAG SEQADV 4ML2 THR A -1 UNP Q47149 EXPRESSION TAG SEQADV 4ML2 GLY A 0 UNP Q47149 EXPRESSION TAG SEQRES 1 A 95 SER THR GLY MET ILE GLN ARG ASP ILE GLU TYR SER GLY SEQRES 2 A 95 GLN TYR 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 GLY 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 HIS ALA SEQRES 8 A 95 ALA LEU PHE GLY HET SO4 A 101 5 HET SO4 A 102 5 HET SO4 A 103 5 HET SO4 A 104 5 HET SO4 A 105 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 5(O4 S 2-) FORMUL 7 HOH *217(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 69 O GLY A 85 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 -2.51 SITE 1 AC1 8 HIS A 23 HIS A 50 ASP A 61 HIS A 63 SITE 2 AC1 8 HIS A 87 HOH A 320 HOH A 337 HOH A 393 SITE 1 AC2 9 LYS A 48 HIS A 63 PRO A 66 HOH A 213 SITE 2 AC2 9 HOH A 215 HOH A 224 HOH A 298 HOH A 346 SITE 3 AC2 9 HOH A 353 SITE 1 AC3 10 ARG A 22 GLY A 54 THR A 86 ALA A 89 SITE 2 AC3 10 HOH A 203 HOH A 251 HOH A 263 HOH A 323 SITE 3 AC3 10 HOH A 373 HOH A 386 SITE 1 AC4 10 PRO A 44 ALA A 45 PRO A 51 ARG A 60 SITE 2 AC4 10 HOH A 214 HOH A 231 HOH A 294 HOH A 315 SITE 3 AC4 10 HOH A 351 HOH A 369 SITE 1 AC5 6 LYS A 73 ARG A 80 HOH A 279 HOH A 307 SITE 2 AC5 6 HOH A 379 HOH A 399 CRYST1 41.299 89.832 75.015 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 0.024214 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011132 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013331 0.00000