HEADER HYDROLASE 22-SEP-15 5DWC TITLE CRYSTAL STRUCTURE OF RESTRICTION ENDONUCLEASE AGEI COMPND MOL_ID: 1; COMPND 2 MOLECULE: TYPE-2 RESTRICTION ENZYME AGEI; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: R.AGEI,ENDONUCLEASE AGEI,TYPE II RESTRICTION ENZYME AGEI; COMPND 5 EC: 3.1.21.4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THALASSOBIUS GELATINOVORUS; SOURCE 3 ORGANISM_TAXID: 53501; SOURCE 4 GENE: AGEIR; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: ER2566; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PRRS-AGEIRM KEYWDS RESTRICTION ENDONUCLEASE, PD-(D/E)XK NUCLEASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.TAMULAITIENE,I.RAMONAITE,S.GRAZULIS,V.SIKSNYS REVDAT 5 10-JAN-24 5DWC 1 REMARK REVDAT 4 17-JAN-18 5DWC 1 REMARK REVDAT 3 03-MAY-17 5DWC 1 JRNL REVDAT 2 11-JAN-17 5DWC 1 JRNL REVDAT 1 28-SEP-16 5DWC 0 JRNL AUTH G.TAMULAITIENE,V.JOVAISAITE,G.TAMULAITIS,I.SONGAILIENE, JRNL AUTH 2 E.MANAKOVA,M.ZAREMBA,S.GRAZULIS,S.Y.XU,V.SIKSNYS JRNL TITL RESTRICTION ENDONUCLEASE AGEI IS A MONOMER WHICH DIMERIZES JRNL TITL 2 TO CLEAVE DNA. JRNL REF NUCLEIC ACIDS RES. V. 45 3547 2017 JRNL REFN ESSN 1362-4962 JRNL PMID 28039325 JRNL DOI 10.1093/NAR/GKW1310 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.3 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.33 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 9756 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.214 REMARK 3 FREE R VALUE : 0.256 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.750 REMARK 3 FREE R VALUE TEST SET COUNT : 867 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 33.3290 - 5.7151 1.00 1317 176 0.1672 0.1943 REMARK 3 2 5.7151 - 4.5399 1.00 1349 141 0.1650 0.2279 REMARK 3 3 4.5399 - 3.9671 1.00 1344 145 0.1639 0.1964 REMARK 3 4 3.9671 - 3.6049 1.00 1339 161 0.2012 0.2137 REMARK 3 5 3.6049 - 3.3467 1.00 1335 136 0.2229 0.2704 REMARK 3 6 3.3467 - 3.1496 1.00 1335 155 0.2384 0.2882 REMARK 3 7 3.1496 - 2.9920 1.00 1356 126 0.2532 0.3530 REMARK 3 8 2.9920 - 2.8618 1.00 1347 140 0.2628 0.2788 REMARK 3 9 2.8618 - 2.7517 1.00 1365 137 0.2665 0.3419 REMARK 3 10 2.7517 - 2.6568 1.00 1338 138 0.2835 0.3303 REMARK 3 11 2.6568 - 2.5737 1.00 1347 139 0.2738 0.3715 REMARK 3 12 2.5737 - 2.5002 1.00 1315 143 0.2967 0.3343 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) : 0.380 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.740 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.96 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 : 0.002 2171 REMARK 3 ANGLE : 0.676 2938 REMARK 3 CHIRALITY : 0.026 321 REMARK 3 PLANARITY : 0.003 388 REMARK 3 DIHEDRAL : 13.220 807 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 5.2321 0.3455 15.8391 REMARK 3 T TENSOR REMARK 3 T11: 0.1627 T22: 0.1667 REMARK 3 T33: 0.1554 T12: 0.0159 REMARK 3 T13: 0.0160 T23: -0.0025 REMARK 3 L TENSOR REMARK 3 L11: 0.8943 L22: 2.0066 REMARK 3 L33: 0.9572 L12: 0.1175 REMARK 3 L13: -0.0307 L23: 0.7983 REMARK 3 S TENSOR REMARK 3 S11: 0.0688 S12: -0.0211 S13: 0.0135 REMARK 3 S21: -0.2533 S22: -0.0102 S23: -0.1799 REMARK 3 S31: -0.1070 S32: -0.0168 S33: 0.0077 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 5DWC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-SEP-15. REMARK 100 THE DEPOSITION ID IS D_1000213876. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-NOV-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I911-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9100 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM 7.0.6 REMARK 200 DATA SCALING SOFTWARE : SCALA 3.3.20 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9795 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 33.329 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 5.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.11800 REMARK 200 FOR THE DATA SET : 12.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 REMARK 200 R MERGE FOR SHELL (I) : 0.64700 REMARK 200 R SYM FOR SHELL (I) : 0.64700 REMARK 200 FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP 6.0 REMARK 200 STARTING MODEL: 5DWB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALLIZATION BUFFER WAS 0.1 M NACL, REMARK 280 0.1 M NA-HEPES (PH 7.5), 22% PEG3350, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 291K 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 18.60650 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.45750 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.63450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.45750 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.60650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.63450 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 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 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 12890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 GLY A 8 REMARK 465 ARG A 9 REMARK 465 GLY A 10 REMARK 465 ALA A 278 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 -72.61 -108.76 REMARK 500 ARG A 174 64.71 -69.75 REMARK 500 LYS A 200 106.09 -162.32 REMARK 500 PRO A 221 104.65 -53.71 REMARK 500 GLN A 265 -102.39 -108.22 REMARK 500 REMARK 500 REMARK: NULL DBREF 5DWC A 1 278 UNP Q9KHV6 T2A1_THAGE 1 278 SEQRES 1 A 278 MET ARG LEU ASP LEU ASP PHE GLY ARG GLY LEU VAL ALA SEQRES 2 A 278 HIS VAL MET LEU ASP ASN VAL SER GLU GLU GLN TYR GLN SEQRES 3 A 278 GLN ILE SER ASP TYR PHE VAL PRO LEU VAL ASN LYS PRO SEQRES 4 A 278 LYS LEU LYS SER ARG ASP ALA ILE GLY GLN ALA PHE VAL SEQRES 5 A 278 MET ALA THR GLU VAL CYS PRO ASP ALA ASN PRO SER ASP SEQRES 6 A 278 LEU TRP HIS HIS VAL LEU TYR ARG ILE TYR ILE ARG GLU SEQRES 7 A 278 LYS ILE GLY THR ASP PRO SER GLN SER TRP VAL ARG THR SEQRES 8 A 278 SER GLY GLU ALA PHE GLU VAL ALA LEU VAL GLU ARG TYR SEQRES 9 A 278 ASN PRO VAL LEU ALA ARG HIS GLY ILE ARG LEU THR ALA SEQRES 10 A 278 LEU PHE LYS GLY GLN LYS GLY LEU ALA LEU THR ARG MET SEQRES 11 A 278 GLY VAL ALA ASP ARG VAL GLY SER ARG LYS VAL ASP VAL SEQRES 12 A 278 MET ILE GLU LYS GLN GLY GLY GLY ARG SER PRO ASP ALA SEQRES 13 A 278 GLU GLY PHE GLY VAL VAL GLY GLY ILE HIS ALA LYS VAL SEQRES 14 A 278 SER LEU ALA GLU ARG VAL SER ASP ASP ILE PRO ALA SER SEQRES 15 A 278 ARG ILE MET MET GLY GLU GLY LEU LEU SER VAL LEU SER SEQRES 16 A 278 THR LEU ASP VAL LYS SER PHE PRO PRO PRO HIS GLY ASP SEQRES 17 A 278 LEU VAL ASN ARG GLY GLU LEU GLY THR PRO ASP ARG PRO SEQRES 18 A 278 SER ASP LYS ARG ASN TYR ILE GLU GLY HIS GLY ASP PHE SEQRES 19 A 278 SER ALA CSO PHE SER TYR ASN LEU ARG THR SER PRO SER SEQRES 20 A 278 ASN ALA THR THR PRO SER GLY ARG HIS ILE TYR VAL SER SEQRES 21 A 278 GLY PHE SER GLY GLN ASP ASP GLU PHE THR ASP TYR LEU SEQRES 22 A 278 VAL ALA GLN LEU ALA MODRES 5DWC CSO A 237 CYS MODIFIED RESIDUE HET CSO A 237 7 HETNAM CSO S-HYDROXYCYSTEINE FORMUL 1 CSO C3 H7 N O3 S FORMUL 2 HOH *19(H2 O) HELIX 1 AA1 SER A 21 ASN A 37 1 17 HELIX 2 AA2 LYS A 42 CYS A 58 1 17 HELIX 3 AA3 ASN A 62 HIS A 69 1 8 HELIX 4 AA4 VAL A 70 LYS A 79 1 10 HELIX 5 AA5 ASP A 83 GLN A 86 5 4 HELIX 6 AA6 SER A 87 ALA A 109 1 23 HELIX 7 AA7 LYS A 123 MET A 130 1 8 HELIX 8 AA8 VAL A 132 GLY A 137 1 6 HELIX 9 AA9 ARG A 174 ASP A 177 5 4 HELIX 10 AB1 ASP A 178 GLU A 188 1 11 HELIX 11 AB2 SER A 222 GLY A 230 1 9 HELIX 12 AB3 ASP A 267 LEU A 277 1 11 SHEET 1 AA1 2 ARG A 2 LEU A 5 0 SHEET 2 AA1 2 ALA A 13 MET A 16 -1 O ALA A 13 N LEU A 5 SHEET 1 AA2 6 ILE A 113 ALA A 117 0 SHEET 2 AA2 6 VAL A 143 GLN A 148 -1 O GLU A 146 N ARG A 114 SHEET 3 AA2 6 PHE A 159 LYS A 168 -1 O ILE A 165 N VAL A 143 SHEET 4 AA2 6 LEU A 191 THR A 196 1 O LEU A 191 N GLY A 164 SHEET 5 AA2 6 ALA A 236 SER A 239 1 O PHE A 238 N THR A 196 SHEET 6 AA2 6 ILE A 257 VAL A 259 1 O TYR A 258 N CSO A 237 LINK C ALA A 236 N CSO A 237 1555 1555 1.33 LINK C CSO A 237 N PHE A 238 1555 1555 1.33 CISPEP 1 PRO A 204 PRO A 205 0 7.34 CRYST1 37.213 59.269 120.915 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 0.026872 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016872 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008270 0.00000