HEADER HYDROLASE 12-MAR-26 11TT TITLE CRYSTAL STRUCTURE OF APO ALPHA/BETA-HYDROLASE MACROLIDE ESTERASE ESTT TITLE 2 FROM SPHINGOBACTERIUM THALPOPHILUM (S102A MUTANT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA/BETA-HYDROLASE MACROLIDE ESTERASE ESTT; COMPND 3 CHAIN: A; COMPND 4 EC: 3.1.1.24; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SPHINGOBACTERIUM THALPOPHILUM; SOURCE 3 ORGANISM_TAXID: 259; SOURCE 4 GENE: CATD_1, NCTC11429_00166; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 511693 KEYWDS ALPHA/BETA-HYDROLASE, ESTERASE, MACROLIDE RESISTANCE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR E.T.R.KELLY,J.BLANCHET,A.M.BERGHUIS REVDAT 1 08-APR-26 11TT 0 JRNL AUTH E.T.R.KELLY,I.MYZIUK,M.Z.HEMMINGS,Z.MULLA,J.BLANCHET, JRNL AUTH 2 A.RUZZINI,A.M.BERGHUIS JRNL TITL HYDRATION AND HYDROLYSIS DEFINE ANTIBIOTIC RESISTANCE JRNL TITL 2 CONFERRED BY MACROLIDE ESTERASES JRNL REF BIORXIV 2026 JRNL REFN ISSN 2692-8205 JRNL DOI 10.64898/2026.03.24.713787 REMARK 2 REMARK 2 RESOLUTION. 2.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.21.2_5419: ???) 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) : 2.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 74.9 REMARK 3 NUMBER OF REFLECTIONS : 20295 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.184 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.250 REMARK 3 FREE R VALUE TEST SET COUNT : 2081 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 29.0900 - 5.3700 1.00 1609 188 0.2152 0.2405 REMARK 3 2 5.3600 - 4.2600 1.00 1605 192 0.1618 0.2028 REMARK 3 3 4.2600 - 3.7200 0.99 1618 175 0.1547 0.2152 REMARK 3 4 3.7200 - 3.3800 0.99 1597 186 0.1701 0.1931 REMARK 3 5 3.3800 - 3.1400 0.99 1609 168 0.1830 0.2386 REMARK 3 6 3.1400 - 2.9600 0.95 1542 175 0.1793 0.2482 REMARK 3 7 2.9600 - 2.8100 0.90 1465 168 0.2058 0.2704 REMARK 3 8 2.8100 - 2.6900 0.85 1379 164 0.1899 0.2577 REMARK 3 9 2.6900 - 2.5800 0.79 1261 142 0.1984 0.3281 REMARK 3 10 2.5800 - 2.4900 0.68 1099 129 0.2032 0.2742 REMARK 3 11 2.4900 - 2.4200 0.58 947 107 0.2075 0.2645 REMARK 3 12 2.4200 - 2.3500 0.49 797 87 0.2004 0.2646 REMARK 3 13 2.3500 - 2.2800 0.41 668 76 0.2066 0.2880 REMARK 3 14 2.2800 - 2.2300 0.37 574 74 0.1999 0.2688 REMARK 3 15 2.2300 - 2.1800 0.27 444 50 0.1972 0.3627 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 : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.290 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 2080 REMARK 3 ANGLE : 0.827 2834 REMARK 3 CHIRALITY : 0.052 322 REMARK 3 PLANARITY : 0.006 370 REMARK 3 DIHEDRAL : 14.496 728 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 11TT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAR-26. REMARK 100 THE DEPOSITION ID IS D_1000305981. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAY-24 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : CLSI REMARK 200 BEAMLINE : 08B1-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.18 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26538 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.180 REMARK 200 RESOLUTION RANGE LOW (A) : 29.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 74.9 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.3700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 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 : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 9.6, 0.2 MGAC, 20% PEG REMARK 280 3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277.15K 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 23.38900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 38.50200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.15450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 38.50200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.38900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.15450 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 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 GLU A 10 REMARK 465 GLY A 71 REMARK 465 SER A 72 REMARK 465 PRO A 138 REMARK 465 GLU A 139 REMARK 465 MET A 140 REMARK 465 ASP A 141 REMARK 465 THR A 142 REMARK 465 ARG A 143 REMARK 465 ILE A 144 REMARK 465 LEU A 145 REMARK 465 ASP A 146 REMARK 465 PHE A 147 REMARK 465 HIS A 148 REMARK 465 ALA A 149 REMARK 465 LYS A 150 REMARK 465 ALA A 151 REMARK 465 ALA A 152 REMARK 465 ILE A 282 REMARK 465 LYS A 283 REMARK 465 VAL A 284 REMARK 465 SER A 285 REMARK 465 ASN A 286 REMARK 465 GLN A 287 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 MET A 1 CG SD CE REMARK 470 LYS A 2 CG CD CE NZ REMARK 470 HIS A 8 CG ND1 CD2 CE1 NE2 REMARK 470 ILE A 11 CG1 CG2 CD1 REMARK 470 LYS A 22 CG CD CE NZ REMARK 470 GLU A 69 CG CD OE1 OE2 REMARK 470 LYS A 86 CG CD CE NZ REMARK 470 TRP A 156 CG CD1 CD2 NE1 CE2 CE3 CZ2 REMARK 470 TRP A 156 CZ3 CH2 REMARK 470 GLN A 164 CG CD OE1 NE2 REMARK 470 GLU A 168 CG CD OE1 OE2 REMARK 470 LYS A 171 CG CD CE NZ REMARK 470 LYS A 181 CG CD CE NZ REMARK 470 LYS A 196 CG CD CE NZ REMARK 470 ARG A 241 CG CD NE CZ NH1 NH2 REMARK 470 HIS A 280 CG ND1 CD2 CE1 NE2 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 2 63.36 -103.81 REMARK 500 GLU A 51 60.14 78.21 REMARK 500 THR A 66 123.50 -36.09 REMARK 500 ALA A 102 -119.95 60.21 REMARK 500 THR A 127 -166.50 -129.31 REMARK 500 ASN A 197 99.19 -173.63 REMARK 500 REMARK 500 REMARK: NULL DBREF1 11TT A 1 287 UNP A0A4U9U5V9_9SPHI DBREF2 11TT A A0A4U9U5V9 1 287 SEQADV 11TT ALA A 102 UNP A0A4U9U5V SER 102 ENGINEERED MUTATION SEQRES 1 A 287 MET LYS ASP LYS MET ILE ILE HIS GLY GLU ILE GLU ILE SEQRES 2 A 287 CYS THR GLU SER PHE GLY ASN PRO LYS ASN PRO ALA ILE SEQRES 3 A 287 LEU LEU LEU ALA GLY ALA THR VAL SER MET LEU TYR TRP SEQRES 4 A 287 ASP GLU ASP PHE CYS ARG ARG LEU ALA ASP LYS GLU PHE SEQRES 5 A 287 TYR VAL ILE ARG TYR ASP ASN ARG ASP VAL GLY THR SER SEQRES 6 A 287 THR ASN TYR GLU PRO GLY SER ALA PRO TYR ASN ILE VAL SEQRES 7 A 287 ASP PHE GLU GLU ASP ALA ILE LYS ILE LEU ASP GLY TYR SEQRES 8 A 287 ASN LEU ASP ASN ALA HIS PHE VAL GLY ILE ALA LEU GLY SEQRES 9 A 287 GLY LEU ILE ALA GLN ILE ALA ALA ILE ARG HIS PRO HIS SEQRES 10 A 287 ARG VAL GLU SER LEU THR LEU ILE ALA THR GLY PRO TRP SEQRES 11 A 287 GLY VAL VAL ASP ILE ASP ILE PRO GLU MET ASP THR ARG SEQRES 12 A 287 ILE LEU ASP PHE HIS ALA LYS ALA ALA ASP VAL ASN TRP SEQRES 13 A 287 SER GLN GLU GLU ASN VAL VAL GLN TYR MET LEU GLU GLY SEQRES 14 A 287 ALA LYS LEU MET SER GLY ARG LYS PRO PHE ASP LYS THR SEQRES 15 A 287 ARG ALA GLU ASN LEU ILE ARG SER GLU TYR ALA ARG ALA SEQRES 16 A 287 LYS ASN TYR ILE SER MET PHE ASN HIS ALA THR LEU GLY SEQRES 17 A 287 GLY GLY GLU ASP TYR TYR ASN ARG LEU ASP GLU ILE GLN SEQRES 18 A 287 GLN PRO THR LEU VAL ILE HIS GLY THR ASP ASP LEU VAL SEQRES 19 A 287 TRP HIS PHE ASN SER THR ARG ILE LEU LEU ASP LYS ILE SEQRES 20 A 287 SER ASN SER THR LEU ILE PRO LEU GLU GLY THR GLY HIS SEQRES 21 A 287 GLU LEU HIS THR HIS ASP TRP ASP THR ILE ILE ASP GLY SEQRES 22 A 287 ILE SER LYS HIS ILE GLY HIS ALA ILE LYS VAL SER ASN SEQRES 23 A 287 GLN FORMUL 2 HOH *95(H2 O) HELIX 1 AA1 SER A 35 TRP A 39 5 5 HELIX 2 AA2 ASP A 40 ASP A 49 1 10 HELIX 3 AA3 ASN A 76 TYR A 91 1 16 HELIX 4 AA4 ALA A 102 HIS A 115 1 14 HELIX 5 AA5 GLN A 158 LEU A 172 1 15 HELIX 6 AA6 ASP A 180 ALA A 195 1 16 HELIX 7 AA7 ASN A 197 LEU A 207 5 11 HELIX 8 AA8 GLY A 210 TYR A 214 5 5 HELIX 9 AA9 ARG A 216 ILE A 220 5 5 HELIX 10 AB1 HIS A 236 ASN A 238 5 3 HELIX 11 AB2 SER A 239 ILE A 247 1 9 HELIX 12 AB3 HIS A 263 HIS A 265 5 3 HELIX 13 AB4 ASP A 266 ALA A 281 1 16 SHEET 1 AA1 8 LYS A 4 ILE A 7 0 SHEET 2 AA1 8 GLU A 12 PHE A 18 -1 O ILE A 13 N ILE A 6 SHEET 3 AA1 8 TYR A 53 TYR A 57 -1 O VAL A 54 N PHE A 18 SHEET 4 AA1 8 ALA A 25 LEU A 29 1 N ILE A 26 O TYR A 53 SHEET 5 AA1 8 ALA A 96 ILE A 101 1 O VAL A 99 N LEU A 29 SHEET 6 AA1 8 VAL A 119 ILE A 125 1 O ILE A 125 N GLY A 100 SHEET 7 AA1 8 THR A 224 GLY A 229 1 O LEU A 225 N LEU A 124 SHEET 8 AA1 8 SER A 250 LEU A 255 1 O THR A 251 N VAL A 226 CRYST1 46.778 74.309 77.004 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 0.021378 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013457 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012986 0.00000 MASTER 277 0 0 13 8 0 0 6 2124 1 0 23 END