HEADER HYDROLASE 05-OCT-12 4HFL TITLE CRYSTAL STRUCTURE OF THE TYPE VI EFFECTOR TAE4 FROM ENTEROBACTER TITLE 2 CLOACAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE CYTOPLASMIC PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTER CLOACAE; SOURCE 3 ORGANISM_TAXID: 550; SOURCE 4 STRAIN: ATCC 13047 / DSM 30054 / NBRC 13535 / NCDC 279-56; SOURCE 5 GENE: ECL_01542; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS AMIDASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.ZHANG,Z.Q.GAO,Y.H.DONG REVDAT 4 08-NOV-23 4HFL 1 SEQADV REVDAT 3 15-NOV-17 4HFL 1 REMARK REVDAT 2 24-JUL-13 4HFL 1 JRNL REVDAT 1 16-JAN-13 4HFL 0 JRNL AUTH H.ZHANG,H.ZHANG,Z.Q.GAO,W.J.WANG,G.F.LIU,J.H.XU,X.D.SU, JRNL AUTH 2 Y.H.DONG JRNL TITL STRUCTURE OF THE TYPE VI EFFECTOR-IMMUNITY COMPLEX JRNL TITL 2 (TAE4-TAI4) PROVIDES NOVEL INSIGHTS INTO THE INHIBITION JRNL TITL 3 MECHANISM OF THE EFFECTOR BY ITS IMMUNITY PROTEIN. JRNL REF J.BIOL.CHEM. V. 288 5928 2013 JRNL REFN ISSN 0021-9258 JRNL PMID 23288853 JRNL DOI 10.1074/JBC.M112.434357 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.29 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 12134 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.760 REMARK 3 FREE R VALUE TEST SET COUNT : 578 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 23.2919 - 3.1752 0.99 2975 133 0.2013 0.2366 REMARK 3 2 3.1752 - 2.5212 1.00 2902 149 0.2029 0.2234 REMARK 3 3 2.5212 - 2.2028 0.99 2850 137 0.2310 0.2991 REMARK 3 4 2.2028 - 2.0015 0.98 2829 159 0.2202 0.3109 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.37 REMARK 3 B_SOL : 48.54 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.740 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) : 4.12340 REMARK 3 B22 (A**2) : 4.12340 REMARK 3 B33 (A**2) : -8.24680 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 : 0.009 1275 REMARK 3 ANGLE : 1.136 1727 REMARK 3 CHIRALITY : 0.083 186 REMARK 3 PLANARITY : 0.004 220 REMARK 3 DIHEDRAL : 12.587 449 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 4.2922 -33.8640 3.2202 REMARK 3 T TENSOR REMARK 3 T11: 0.0802 T22: 0.2113 REMARK 3 T33: 0.1234 T12: -0.0727 REMARK 3 T13: -0.0190 T23: 0.0382 REMARK 3 L TENSOR REMARK 3 L11: 1.2161 L22: 1.1359 REMARK 3 L33: 1.8672 L12: -0.2312 REMARK 3 L13: 0.5572 L23: 0.1509 REMARK 3 S TENSOR REMARK 3 S11: 0.0026 S12: -0.1741 S13: -0.0414 REMARK 3 S21: 0.0043 S22: 0.0398 S23: 0.1156 REMARK 3 S31: -0.1296 S32: -0.4242 S33: -0.0123 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 4HFL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000075404. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-JUN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BSRF REMARK 200 BEAMLINE : 3W1A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 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 : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12215 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 44.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.5 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.14200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 11.10 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: PDB ENTRY 4HFF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5M AMMONIUM SULFATE, 0.1M SODIUM REMARK 280 CITRATE TRIBASIC DEHYDRATE PH5.6, 1.0M LITHIUM SULFATE REMARK 280 MONOHYDRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 28.96800 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 14.48400 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 14.48400 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 28.96800 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1230 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15170 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL 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 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 28.96800 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 HIS A -12 REMARK 465 MET A -11 REMARK 465 ALA A -10 REMARK 465 SER A -9 REMARK 465 MET A -8 REMARK 465 THR A -7 REMARK 465 GLY A -6 REMARK 465 GLY A -5 REMARK 465 GLN A -4 REMARK 465 GLN A -3 REMARK 465 MET A -2 REMARK 465 GLY A -1 REMARK 465 ARG A 0 REMARK 465 GLY A 145 REMARK 465 SER A 146 REMARK 465 PRO A 147 REMARK 465 GLY A 148 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 VAL A 70 -168.75 -119.93 REMARK 500 ASN A 135 -38.96 -146.54 REMARK 500 ASP A 139 -75.55 -130.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4HFK RELATED DB: PDB DBREF 4HFL A 1 163 UNP D5C6F6 D5C6F6_ENTCC 1 163 SEQADV 4HFL HIS A -12 UNP D5C6F6 EXPRESSION TAG SEQADV 4HFL MET A -11 UNP D5C6F6 EXPRESSION TAG SEQADV 4HFL ALA A -10 UNP D5C6F6 EXPRESSION TAG SEQADV 4HFL SER A -9 UNP D5C6F6 EXPRESSION TAG SEQADV 4HFL MET A -8 UNP D5C6F6 EXPRESSION TAG SEQADV 4HFL THR A -7 UNP D5C6F6 EXPRESSION TAG SEQADV 4HFL GLY A -6 UNP D5C6F6 EXPRESSION TAG SEQADV 4HFL GLY A -5 UNP D5C6F6 EXPRESSION TAG SEQADV 4HFL GLN A -4 UNP D5C6F6 EXPRESSION TAG SEQADV 4HFL GLN A -3 UNP D5C6F6 EXPRESSION TAG SEQADV 4HFL MET A -2 UNP D5C6F6 EXPRESSION TAG SEQADV 4HFL GLY A -1 UNP D5C6F6 EXPRESSION TAG SEQADV 4HFL ARG A 0 UNP D5C6F6 EXPRESSION TAG SEQRES 1 A 176 HIS MET ALA SER MET THR GLY GLY GLN GLN MET GLY ARG SEQRES 2 A 176 MET SER HIS MET ARG PRO ALA PHE GLY ALA ALA TRP ASN SEQRES 3 A 176 ARG PHE LYS GLU VAL ASN VAL ASN VAL GLU GLN VAL GLY SEQRES 4 A 176 LYS LEU LEU GLY GLY LYS VAL GLN HIS ASN ILE ASP ALA SEQRES 5 A 176 GLY ILE PHE LYS ASN ALA CYS PRO ILE ARG MET SER TYR SEQRES 6 A 176 VAL LEU ASN TYR CYS GLY ILE PRO VAL PRO SER ASN SER SEQRES 7 A 176 LYS TYR ALA THR VAL THR GLY SER ASP LYS LYS ARG TYR SEQRES 8 A 176 MET PHE ARG VAL LYS ASP MET ILE ALA PHE LEU PRO THR SEQRES 9 A 176 VAL LEU GLY LYS ALA ASP ILE SER VAL SER SER PRO THR SEQRES 10 A 176 PRO ALA GLN PHE ALA GLY LYS GLN GLY ILE ILE ILE PHE SEQRES 11 A 176 THR GLY HIS GLY TRP LEU ASP ALA THR GLY HIS VAL THR SEQRES 12 A 176 LEU TRP ASN GLY ASN ILE CYS SER ASP ASP CYS HIS PHE SEQRES 13 A 176 LEU GLY SER PRO GLY ASN GLY SER PHE ILE PRO THR ASN SEQRES 14 A 176 ALA THR PHE TRP SER LEU LYS FORMUL 2 HOH *98(H2 O) HELIX 1 1 ALA A 7 VAL A 18 1 12 HELIX 2 2 ASN A 21 GLY A 30 1 10 HELIX 3 3 GLY A 30 ALA A 39 1 10 HELIX 4 4 ALA A 45 CYS A 57 1 13 HELIX 5 5 ARG A 81 GLY A 94 1 14 HELIX 6 6 THR A 104 ALA A 109 5 6 SHEET 1 A 2 THR A 69 THR A 71 0 SHEET 2 A 2 ARG A 77 MET A 79 -1 O TYR A 78 N VAL A 70 SHEET 1 B 4 ILE A 98 SER A 101 0 SHEET 2 B 4 ILE A 153 SER A 161 -1 O PHE A 159 N ILE A 98 SHEET 3 B 4 GLY A 113 HIS A 120 -1 N ILE A 116 O THR A 158 SHEET 4 B 4 ALA A 125 TRP A 132 -1 O HIS A 128 N PHE A 117 SSBOND 1 CYS A 137 CYS A 141 1555 1555 2.03 CRYST1 84.283 84.283 43.452 90.00 90.00 120.00 P 32 2 1 6 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 0.011865 0.006850 0.000000 0.00000 SCALE2 0.000000 0.013700 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023014 0.00000