HEADER HYDROLASE 02-JAN-23 8HWP TITLE CRYSTAL STRUCTURE OF MUTANT GDSL ESTERASE OF PHOTOBACTERIUM SP. J15 TITLE 2 S12A IN COMPLEX WITH BUTYRATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GDSL-FAMILY ESTERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PHOTOBACTERIUM SP. J15; SOURCE 3 ORGANISM_TAXID: 265901; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GDSL ESTERASE, BUTYRATE, COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR N.N.A.RAHMAN,T.C.LEOW,M.A.JONET REVDAT 2 29-MAY-24 8HWP 1 REMARK REVDAT 1 28-JUN-23 8HWP 0 JRNL AUTH N.N.A.RAHMAN,T.C.LEOW,M.A.JONET JRNL TITL CRYSTAL STRUCTURE OF MUTANT GDSL ESTERASE OF PHOTOBACTERIUM JRNL TITL 2 SP. J15 IN COMPLEX WITH BUTYRATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.73 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 1.73 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 117000 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.242 REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.275 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.180 REMARK 3 FREE R VALUE TEST SET COUNT : 2037 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 32.9457 - 4.2640 1.00 2689 161 0.1768 0.2021 REMARK 3 2 4.2640 - 3.3856 1.00 2563 160 0.2062 0.2323 REMARK 3 3 3.3856 - 2.9579 1.00 2556 129 0.2474 0.3179 REMARK 3 4 2.9579 - 2.6876 1.00 2507 155 0.2650 0.2858 REMARK 3 5 2.6876 - 2.4950 0.99 2500 129 0.2706 0.3010 REMARK 3 6 2.4950 - 2.3480 0.99 2497 130 0.2632 0.2894 REMARK 3 7 2.3480 - 2.2304 0.99 2495 129 0.2493 0.2700 REMARK 3 8 2.2304 - 2.1333 0.99 2467 129 0.2610 0.2994 REMARK 3 9 2.1333 - 2.0512 0.99 2500 114 0.2594 0.3159 REMARK 3 10 2.0512 - 1.9805 0.99 2459 142 0.2657 0.3019 REMARK 3 11 1.9805 - 1.9185 0.99 2450 142 0.2663 0.3100 REMARK 3 12 1.9185 - 1.8637 0.99 2449 140 0.2557 0.3066 REMARK 3 13 1.8637 - 1.8146 0.99 2439 124 0.2650 0.3187 REMARK 3 14 1.8146 - 1.7704 0.97 2391 117 0.2931 0.3787 REMARK 3 15 1.7704 - 1.7301 0.93 2309 136 0.3027 0.3428 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) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.070 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.78 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 : 0.009 2575 REMARK 3 ANGLE : 1.044 3489 REMARK 3 CHIRALITY : 0.059 383 REMARK 3 PLANARITY : 0.007 458 REMARK 3 DIHEDRAL : 3.025 1502 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 8HWP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-FEB-23. REMARK 100 THE DEPOSITION ID IS D_1300034485. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-APR-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 117000 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.730 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.73 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.3 REMARK 200 DATA REDUNDANCY IN SHELL : 1.80 REMARK 200 R MERGE FOR SHELL (I) : 0.33900 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: HKL-3000 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.96 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.61 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM ACETATE AS SALT, 30% REMARK 280 (W/V) POLYETHYLENE GLYCOL 4,000 AS PRECIPITANT IN 0.1 M SODIUM REMARK 280 ACETATE TRIHYDRATE BUFFER AT PH 4.6, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293.15K 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 27.50350 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 59.83900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.31300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 59.83900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.50350 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.31300 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 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 ASP A 11 -153.88 -120.60 REMARK 500 ASP A 115 40.08 -154.17 REMARK 500 ASP A 302 -147.49 -103.52 REMARK 500 LEU A 304 -45.41 -154.81 REMARK 500 REMARK 500 REMARK: NULL DBREF1 8HWP A 1 328 UNP A0A0K0PV22_9GAMM DBREF2 8HWP A A0A0K0PV22 20 347 SEQADV 8HWP ALA A 12 UNP A0A0K0PV2 SER 31 ENGINEERED MUTATION SEQRES 1 A 328 ALA GLU PHE ASP ARG ILE THR ASN PHE GLY ASP ALA LEU SEQRES 2 A 328 SER ASP ILE GLY ASN LYS HIS MET ILE THR VAL ASP MET SEQRES 3 A 328 ASN GLN ALA THR SER GLY LYS ILE GLY ILE ARG ALA ASP SEQRES 4 A 328 LYS PRO ASN PHE ASP GLY ARG PHE SER ASN GLY PRO VAL SEQRES 5 A 328 TRP THR GLU TYR LEU ALA GLY PHE LEU ALA LYS PRO ALA SEQRES 6 A 328 PRO VAL ARG GLY HIS GLY GLU ILE ASP SER GLN VAL VAL SEQRES 7 A 328 LEU LYS ASP GLN ALA GLY LYS GLN ILE THR TYR HIS TYR SEQRES 8 A 328 HIS HIS ASN ALA LEU PRO GLY THR ASN TRP ALA VAL GLY SEQRES 9 A 328 GLY ALA MET SER GLY LEU GLY ASN PHE LEU ASP ILE ASP SEQRES 10 A 328 ALA ALA ASN GLY PHE THR ALA LYS SER GLY LEU ASP VAL SEQRES 11 A 328 LEU THR ASN THR GLY GLN GLN ILE LYS LEU ARG ILE ALA SEQRES 12 A 328 ASN LYS GLY GLN PHE THR GLY ASN GLU LEU VAL SER TYR SEQRES 13 A 328 MET SER GLY THR ASN ASN LEU TRP PHE THR LEU PHE GLY SEQRES 14 A 328 ASP LEU ASP GLN THR GLY ASN LYS ALA ALA GLY PHE ALA SEQRES 15 A 328 LEU THR ASP ILE GLU THR LEU ILE ASP ALA GLY ALA LYS SEQRES 16 A 328 GLN VAL LEU ALA ALA ASN ILE PRO ASP PHE VAL ASP ALA SEQRES 17 A 328 PRO TRP PHE ALA GLY GLN GLN LYS LYS THR THR ARG PHE SEQRES 18 A 328 ILE GLN SER HIS ASN GLN ALA LEU LYS ALA GLY LEU ASP SEQRES 19 A 328 GLN LEU ALA ALA ALA HIS PRO ASP VAL GLU ILE TYR TYR SEQRES 20 A 328 PHE ASP ALA PHE ASP LEU PHE ASN LYS VAL SER ASN GLU SEQRES 21 A 328 VAL LYS THR LYS GLY LYS TYR GLN ASP LYS GLU LEU ALA SEQRES 22 A 328 ILE THR LEU THR ASN VAL THR GLY GLU ALA TYR SER TYR SEQRES 23 A 328 ALA THR GLY LYS VAL ILE ALA GLN PRO ASN ARG ASN LEU SEQRES 24 A 328 PHE TRP ASP GLY LEU HIS PRO THR THR ALA MET HIS LYS SEQRES 25 A 328 ILE MET ALA LYS GLU ALA ALA SER LEU VAL ILE SER GLY SEQRES 26 A 328 ARG THR LEU HET BUA A 401 6 HETNAM BUA BUTANOIC ACID FORMUL 2 BUA C4 H8 O2 HELIX 1 AA1 GLY A 17 THR A 30 1 14 HELIX 2 AA2 VAL A 52 ALA A 62 1 11 HELIX 3 AA3 ASN A 133 GLY A 146 1 14 HELIX 4 AA4 GLY A 159 PHE A 168 1 10 HELIX 5 AA5 THR A 174 ALA A 192 1 19 HELIX 6 AA6 ALA A 208 ALA A 212 5 5 HELIX 7 AA7 GLN A 214 HIS A 240 1 27 HELIX 8 AA8 ASP A 249 GLY A 265 1 17 HELIX 9 AA9 GLN A 294 ASN A 296 5 3 HELIX 10 AB1 THR A 307 SER A 324 1 18 SHEET 1 AA1 4 ARG A 5 GLY A 10 0 SHEET 2 AA1 4 GLU A 152 MET A 157 1 O SER A 155 N THR A 7 SHEET 3 AA1 4 GLN A 196 ALA A 200 1 O ALA A 200 N TYR A 156 SHEET 4 AA1 4 GLU A 244 PHE A 248 1 O TYR A 246 N VAL A 197 SHEET 1 AA2 3 GLN A 86 HIS A 93 0 SHEET 2 AA2 3 ILE A 73 LYS A 80 -1 N LEU A 79 O ILE A 87 SHEET 3 AA2 3 THR A 123 SER A 126 -1 O LYS A 125 N VAL A 78 SHEET 1 AA3 2 ASN A 112 PHE A 113 0 SHEET 2 AA3 2 LEU A 131 THR A 132 -1 O LEU A 131 N PHE A 113 SHEET 1 AA4 2 TYR A 267 ASP A 269 0 SHEET 2 AA4 2 ILE A 274 LEU A 276 -1 O LEU A 276 N TYR A 267 SHEET 1 AA5 2 ASN A 278 GLU A 282 0 SHEET 2 AA5 2 ASN A 298 PHE A 300 1 O LEU A 299 N ASN A 278 CISPEP 1 LYS A 40 PRO A 41 0 9.23 CRYST1 55.007 56.626 119.678 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 0.018180 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017660 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008356 0.00000