HEADER LYASE 21-JUN-23 8JT4 TITLE SUBSTRATE -BINDING MODE GUIDED PROTEIN DESIGN OF ALGINATE LYASE FLALYA TITLE 2 FOR ALTERED END-PRODUCT DISTRIBUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALGINATE LYASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FLAVOBACTERIUM SP. UMI-01; SOURCE 3 ORGANISM_TAXID: 1441053; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS MUTATION, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR X.ZHANG,D.F.YANG REVDAT 1 26-JUN-24 8JT4 0 JRNL AUTH X.ZHANG,D.F.YANG JRNL TITL SUBSTRATE -BINDING MODE GUIDED PROTEIN DESIGN OF ALGINATE JRNL TITL 2 LYASE FLALYA FOR ALTERED END-PRODUCT DISTRIBUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 53484 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.193 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.70 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 2166 REMARK 3 ANGLE : 0.844 2928 REMARK 3 CHIRALITY : 0.085 310 REMARK 3 PLANARITY : 0.007 373 REMARK 3 DIHEDRAL : 12.630 1301 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 8JT4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 27-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1300038825. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL02U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979183 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 S 9M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 53504 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 31.180 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 8.800 REMARK 200 R MERGE (I) : 0.06089 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.6100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.50 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.25440 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: BUCCANEER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: BULK REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: DL-MALIC ACID, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,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 17.47200 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 34.94400 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 THR A 214 -84.82 -119.66 REMARK 500 ASP A 220 30.28 -150.77 REMARK 500 ASP A 221 -163.87 -101.67 REMARK 500 GLN A 241 50.53 -94.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 532 DISTANCE = 6.10 ANGSTROMS DBREF1 8JT4 A 1 260 UNP A0A068PC91_9FLAO DBREF2 8JT4 A A0A068PC91 29 288 SEQADV 8JT4 ASP A 176 UNP A0A068PC9 HIS 204 CONFLICT SEQADV 8JT4 LEU A 261 UNP A0A068PC9 EXPRESSION TAG SEQRES 1 A 261 SER LYS THR ALA LYS ILE ASP TRP SER HIS TRP THR VAL SEQRES 2 A 261 THR VAL PRO GLU GLU ASN PRO ASP LYS PRO GLY LYS PRO SEQRES 3 A 261 TYR SER LEU GLY TYR PRO GLU ILE LEU ASN TYR ALA GLU SEQRES 4 A 261 ASP LYS ILE ALA SER LYS TYR MET TYR ASP ASP PRO LYS SEQRES 5 A 261 ASP LYS SER VAL VAL PHE TYR ALA PHE PRO SER GLY VAL SEQRES 6 A 261 THR THR ALA ASN THR HIS TYR SER ARG SER GLU LEU ARG SEQRES 7 A 261 GLU THR MET GLU THR GLY SER ASN LYS VAL ASN TRP THR SEQRES 8 A 261 PHE ALA LYS GLY GLY LYS MET ARG GLY THR TYR ALA ILE SEQRES 9 A 261 ASP ASP ILE SER LYS GLU PRO ASP GLY LYS TYR SER ARG SEQRES 10 A 261 VAL ILE ILE ALA GLN ILE HIS GLY VAL LEU THR ASP GLU SEQRES 11 A 261 GLN ARG ASP LEU ILE GLY GLN LYS ASP ASN ASN ALA PRO SEQRES 12 A 261 PRO ILE LEU LYS VAL TYR TRP ASP LYS GLY LYS ILE ARG SEQRES 13 A 261 VAL LYS THR LYS VAL LEU LYS ASP LEU ASN ALA PRO TYR SEQRES 14 A 261 LYS GLU MET LEU SER GLU ASP ALA TRP GLY ASP ASP GLU SEQRES 15 A 261 GLY ARG ASN PHE LYS GLU LYS ILE ASP LEU ASN THR ARG SEQRES 16 A 261 PHE THR LEU GLU VAL LYS VAL SER ASP GLY ARG MET GLU SEQRES 17 A 261 VAL ILE LEU ASN ASP THR GLU SER LEU VAL TYR ASP ASP SEQRES 18 A 261 ILE HIS MET LYS LYS TRP GLY ILE PHE GLU ASN TYR PHE SEQRES 19 A 261 LYS ALA GLY ASN TYR PHE GLN SER LYS THR PRO GLY THR SEQRES 20 A 261 PHE ALA LYS VAL LYS ILE TYR SER LEU GLN VAL THR HIS SEQRES 21 A 261 LEU FORMUL 2 HOH *232(H2 O) HELIX 1 AA1 PRO A 32 ASP A 40 5 9 HELIX 2 AA2 ILE A 42 LYS A 45 5 4 HELIX 3 AA3 THR A 128 GLY A 136 1 9 HELIX 4 AA4 PRO A 168 LEU A 173 1 6 HELIX 5 AA5 SER A 174 ASP A 176 5 3 HELIX 6 AA6 ASP A 221 TRP A 227 1 7 SHEET 1 AA1 4 LYS A 5 ILE A 6 0 SHEET 2 AA1 4 ALA A 249 THR A 259 1 O LEU A 256 N LYS A 5 SHEET 3 AA1 4 SER A 55 ALA A 60 -1 N PHE A 58 O VAL A 251 SHEET 4 AA1 4 MET A 47 ASP A 50 -1 N TYR A 48 O VAL A 57 SHEET 1 AA2 6 LYS A 5 ILE A 6 0 SHEET 2 AA2 6 ALA A 249 THR A 259 1 O LEU A 256 N LYS A 5 SHEET 3 AA2 6 GLY A 96 ILE A 107 -1 N ALA A 103 O LYS A 252 SHEET 4 AA2 6 PHE A 196 SER A 203 -1 O VAL A 202 N GLY A 96 SHEET 5 AA2 6 ARG A 206 LEU A 211 -1 O GLU A 208 N LYS A 201 SHEET 6 AA2 6 GLU A 215 TYR A 219 -1 O TYR A 219 N MET A 207 SHEET 1 AA3 8 LYS A 22 LEU A 29 0 SHEET 2 AA3 8 TRP A 11 ASN A 19 -1 N GLU A 17 O TYR A 27 SHEET 3 AA3 8 ARG A 74 GLU A 79 -1 O ARG A 78 N THR A 12 SHEET 4 AA3 8 GLU A 231 PHE A 240 -1 O ALA A 236 N LEU A 77 SHEET 5 AA3 8 VAL A 118 VAL A 126 -1 N HIS A 124 O TYR A 233 SHEET 6 AA3 8 LEU A 146 ASP A 151 -1 O TRP A 150 N VAL A 118 SHEET 7 AA3 8 LYS A 154 LEU A 162 -1 O ARG A 156 N TYR A 149 SHEET 8 AA3 8 TRP A 178 ASP A 180 -1 O GLY A 179 N VAL A 161 SHEET 1 AA4 6 TRP A 90 THR A 91 0 SHEET 2 AA4 6 GLU A 231 PHE A 240 -1 O ASN A 232 N TRP A 90 SHEET 3 AA4 6 VAL A 118 VAL A 126 -1 N HIS A 124 O TYR A 233 SHEET 4 AA4 6 LEU A 146 ASP A 151 -1 O TRP A 150 N VAL A 118 SHEET 5 AA4 6 LYS A 154 LEU A 162 -1 O ARG A 156 N TYR A 149 SHEET 6 AA4 6 ARG A 184 ASN A 185 -1 O ARG A 184 N VAL A 157 CISPEP 1 TYR A 31 PRO A 32 0 1.41 CRYST1 71.998 71.998 52.416 90.00 90.00 120.00 P 31 3 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 0.013889 0.008019 0.000000 0.00000 SCALE2 0.000000 0.016038 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019078 0.00000