HEADER UNKNOWN FUNCTION 20-SEP-18 6HPA TITLE CRYSTAL STRUCTURE OF A BA3943 MUTANT,A CE4 FAMILY PSEUDOENZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: PUTATIVE POLYSACCHARIDE DEACETYLASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS ANTHRACIS; SOURCE 3 ORGANISM_TAXID: 1392; SOURCE 4 GENE: YLXY, BA_3943, A9486_19545, BASH2_01993, CN272_11110, SOURCE 5 COL95_11150; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET26B KEYWDS POLYSACCHARIDE, DEACETYLASE, PEPTIDOGLYCAN, PSEUDOENZYME, KEYWDS 2 SPORULATION., UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR A.MOLFETAS,N.TOMATSIDOU,M.KOKKINIDIS REVDAT 2 01-MAY-24 6HPA 1 REMARK REVDAT 1 09-OCT-19 6HPA 0 JRNL AUTH A.MOLFETAS,A.TOMATSIDOU,V.BOURIOTIS,M.KOKKINIDIS JRNL TITL THE RESURRECTION OF A DEAN ENZYME JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.44 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 38043 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.166 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.680 REMARK 3 FREE R VALUE TEST SET COUNT : 1781 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 39.4542 - 3.6527 1.00 3042 148 0.1453 0.1667 REMARK 3 2 3.6527 - 2.8995 1.00 2913 149 0.1559 0.1782 REMARK 3 3 2.8995 - 2.5331 1.00 2887 142 0.1673 0.2181 REMARK 3 4 2.5331 - 2.3015 1.00 2904 106 0.1710 0.2157 REMARK 3 5 2.3015 - 2.1365 0.88 2533 114 0.1615 0.2155 REMARK 3 6 2.1365 - 2.0106 1.00 2843 134 0.1606 0.2178 REMARK 3 7 2.0106 - 1.9099 0.97 2457 118 0.1644 0.1803 REMARK 3 8 1.9099 - 1.8268 0.99 2630 139 0.1734 0.2348 REMARK 3 9 1.8268 - 1.7564 1.00 2809 156 0.1728 0.2304 REMARK 3 10 1.7564 - 1.6958 1.00 2817 126 0.1849 0.2157 REMARK 3 11 1.6958 - 1.6428 1.00 2801 154 0.2103 0.2201 REMARK 3 12 1.6428 - 1.5958 1.00 2829 153 0.2413 0.2847 REMARK 3 13 1.5958 - 1.5538 1.00 2797 142 0.2686 0.3229 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) : 0.170 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.770 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 : 0.005 2329 REMARK 3 ANGLE : 0.779 3154 REMARK 3 CHIRALITY : 0.051 340 REMARK 3 PLANARITY : 0.005 404 REMARK 3 DIHEDRAL : 10.966 1433 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 6HPA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 20-SEP-18. REMARK 100 THE DEPOSITION ID IS D_1200011882. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAR-16 REMARK 200 TEMPERATURE (KELVIN) : 124 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALBA REMARK 200 BEAMLINE : XALOC REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.072710 REMARK 200 MONOCHROMATOR : SI(111) CHANNEL-CUT, CRYOCOOLED REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38119 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.554 REMARK 200 RESOLUTION RANGE LOW (A) : 78.883 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 12.53 REMARK 200 R MERGE (I) : 0.10800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.56 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.600 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: BC1960 REMARK 200 REMARK 200 REMARK: CUBIC REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULPHATE 2.8 M TRIS BUFFER REMARK 280 PH=8, PH 8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 28.60500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.44150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.40800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.44150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.60500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.40800 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: 720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13700 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 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 29 -142.06 64.88 REMARK 500 TRP A 96 -178.58 -176.22 REMARK 500 ASN A 127 51.34 -142.52 REMARK 500 SER A 145 175.65 70.65 REMARK 500 SER A 185 14.05 58.83 REMARK 500 MET A 205 -136.15 -105.62 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 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 303 DBREF1 6HPA A 1 273 UNP A0A1Q4M7R6_BACAN DBREF2 6HPA A A0A1Q4M7R6 26 298 SEQADV 6HPA ASP A 93 UNP A0A1Q4M7R ASN 118 ENGINEERED MUTATION SEQRES 1 A 273 GLN ASP ASN LEU TYR GLU GLU ILE GLN LYS HIS ALA LYS SEQRES 2 A 273 GLN TYR GLU ILE ALA PRO GLN ASN ALA MET ILE ASP LYS SEQRES 3 A 273 ILE TRP LYS ALA THR PRO GLY TYR ASN GLY ARG GLN VAL SEQRES 4 A 273 ASP MET GLU ALA SER TYR ASN ASN MET LYS LYS LEU LYS SEQRES 5 A 273 LYS PHE ASP GLN LYS HIS LEU GLU PHE LYS GLU VAL SER SEQRES 6 A 273 PRO SER VAL HIS LEU GLU ASP LEU SER PRO ALA PRO ILE SEQRES 7 A 273 TYR ARG GLY HIS PRO ASN LYS LYS MET VAL GLY LEU THR SEQRES 8 A 273 ILE ASP VAL ALA TRP GLY ASN GLU TYR LEU PRO ARG ILE SEQRES 9 A 273 LEU GLU ILE LEU LYS LYS HIS ASP VAL LYS ALA THR PHE SEQRES 10 A 273 PHE LEU GLU GLY ARG TRP VAL LYS GLU ASN LEU ARG PHE SEQRES 11 A 273 ALA LYS MET ILE VAL ASP ALA ASN GLN GLU VAL GLY ASN SEQRES 12 A 273 HIS SER TYR THR HIS PRO ASN MET LYS THR LEU SER SER SEQRES 13 A 273 ASP GLU ILE ARG ASP GLN LEU GLN LYS THR ASN ARG MET SEQRES 14 A 273 ILE GLU ALA ALA THR ASN GLN LYS VAL ARG TRP PHE ALA SEQRES 15 A 273 PRO PRO SER GLY SER PHE ARG ASP GLU VAL VAL LYS ILE SEQRES 16 A 273 ALA ASP ASP PHE GLN MET GLY THR ILE MET TRP THR VAL SEQRES 17 A 273 ASP THR ILE ASP TRP LYS ARG PRO GLU PRO ASP VAL LEU SEQRES 18 A 273 LEU GLN ARG VAL MET ARG LYS ILE HIS PRO GLY ALA ILE SEQRES 19 A 273 VAL LEU MET HIS PRO THR SER SER THR THR GLU ALA LEU SEQRES 20 A 273 ASP THR MET ILE THR LYS LEU LYS GLU GLN GLY TYR LYS SEQRES 21 A 273 VAL GLY ASN ILE THR GLU LEU LEU ASP GLU LYS ARG VAL HET SO4 A 301 5 HET SO4 A 302 5 HET TRS A 303 8 HETNAM SO4 SULFATE ION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 TRS C4 H12 N O3 1+ FORMUL 5 HOH *253(H2 O) HELIX 1 AA1 ASN A 3 GLU A 16 1 14 HELIX 2 AA2 ASP A 40 LYS A 49 1 10 HELIX 3 AA3 ASP A 55 LEU A 59 5 5 HELIX 4 AA4 HIS A 69 LEU A 73 5 5 HELIX 5 AA5 GLY A 97 GLU A 99 5 3 HELIX 6 AA6 TYR A 100 ASP A 112 1 13 HELIX 7 AA7 GLU A 120 ASN A 127 1 8 HELIX 8 AA8 ASN A 127 ALA A 137 1 11 HELIX 9 AA9 ASN A 150 LEU A 154 5 5 HELIX 10 AB1 SER A 155 ASN A 175 1 21 HELIX 11 AB2 PRO A 183 SER A 187 5 5 HELIX 12 AB3 ARG A 189 PHE A 199 1 11 HELIX 13 AB4 ILE A 211 ARG A 215 5 5 HELIX 14 AB5 GLU A 217 ILE A 229 1 13 HELIX 15 AB6 THR A 240 GLN A 257 1 18 HELIX 16 AB7 ASN A 263 ASP A 269 1 7 SHEET 1 AA1 2 MET A 23 ASP A 25 0 SHEET 2 AA1 2 LYS A 29 THR A 31 -1 O THR A 31 N MET A 23 SHEET 1 AA2 2 GLY A 36 VAL A 39 0 SHEET 2 AA2 2 PHE A 61 VAL A 64 -1 O LYS A 62 N GLN A 38 SHEET 1 AA3 5 GLU A 140 ASN A 143 0 SHEET 2 AA3 5 THR A 116 LEU A 119 1 N LEU A 119 O GLY A 142 SHEET 3 AA3 5 MET A 87 VAL A 94 1 N VAL A 94 O PHE A 118 SHEET 4 AA3 5 ILE A 234 MET A 237 1 O VAL A 235 N GLY A 89 SHEET 5 AA3 5 VAL A 208 ASP A 209 1 N VAL A 208 O LEU A 236 SHEET 1 AA4 4 GLU A 140 ASN A 143 0 SHEET 2 AA4 4 THR A 116 LEU A 119 1 N LEU A 119 O GLY A 142 SHEET 3 AA4 4 MET A 87 VAL A 94 1 N VAL A 94 O PHE A 118 SHEET 4 AA4 4 LYS A 260 GLY A 262 1 O GLY A 262 N LEU A 90 SHEET 1 AA5 2 TRP A 180 PHE A 181 0 SHEET 2 AA5 2 GLY A 202 THR A 203 1 O GLY A 202 N PHE A 181 SITE 1 AC1 9 ASP A 93 HIS A 144 HIS A 148 PRO A 184 SITE 2 AC1 9 SER A 185 HIS A 238 HOH A 401 HOH A 489 SITE 3 AC1 9 HOH A 537 SITE 1 AC2 5 LYS A 114 ARG A 224 ARG A 227 LYS A 228 SITE 2 AC2 5 HOH A 477 SITE 1 AC3 9 ALA A 30 LEU A 70 LEU A 73 SER A 74 SITE 2 AC3 9 PRO A 75 ALA A 76 ARG A 129 ASP A 197 SITE 3 AC3 9 HOH A 464 CRYST1 57.210 58.816 78.883 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 0.017479 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017002 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012677 0.00000