HEADER LYASE 15-FEB-22 7WXJ TITLE CRYSTAL STRUCTURE OF PL-5 FAMILY POLYSACCHARIDE LYASE PANPL FROM TITLE 2 PANDORAEA APISTA AT PH3.5 IN APO FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: POLY(BETA-D-MANNURONATE) LYASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PANPL, POLYSACCHARIDE LYASE; COMPND 5 EC: 4.2.2.3; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PANDORAEA APISTA; SOURCE 3 ORGANISM_TAXID: 93218; SOURCE 4 STRAIN: TF81F4; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: LEMO-21 KEYWDS PL-5 POLYSACCHARIDE LYASE, IN APO FORM, AT PH3.5, PANDORAEA APISTA, KEYWDS 2 LYASE EXPDTA X-RAY DIFFRACTION AUTHOR P.DASH,R.ACHARYA REVDAT 2 29-NOV-23 7WXJ 1 REMARK REVDAT 1 10-AUG-22 7WXJ 0 JRNL AUTH P.DASH,R.ACHARYA JRNL TITL DISTINCT MODES OF HIDDEN STRUCTURAL DYNAMICS IN THE JRNL TITL 2 FUNCTIONING OF AN ALLOSTERIC POLYSACCHARIDE LYASE. JRNL REF ACS CENT.SCI. V. 8 933 2022 JRNL REFN ESSN 2374-7951 JRNL PMID 35912344 JRNL DOI 10.1021/ACSCENTSCI.2C00277 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 64.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 89.2 REMARK 3 NUMBER OF REFLECTIONS : 15373 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 799 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 64.5700 - 3.8100 1.00 2768 180 0.1605 0.1832 REMARK 3 2 3.8100 - 3.0300 1.00 2748 138 0.1846 0.2050 REMARK 3 3 3.0300 - 2.6500 1.00 2753 117 0.1993 0.2672 REMARK 3 4 2.6500 - 2.4000 1.00 2684 151 0.2035 0.2790 REMARK 3 5 2.4000 - 2.2300 0.80 2141 140 0.2162 0.2965 REMARK 3 6 2.2300 - 2.1000 0.55 1480 73 0.2385 0.3023 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) : 0.222 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.634 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.28 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.21 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 : 0.003 2496 REMARK 3 ANGLE : 0.487 3402 REMARK 3 CHIRALITY : 0.038 355 REMARK 3 PLANARITY : 0.003 453 REMARK 3 DIHEDRAL : 4.012 350 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 7WXJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1300027526. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-MAR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07234 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS JAN 26, 2018 BUILT=20180409 REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15375 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.099 REMARK 200 RESOLUTION RANGE LOW (A) : 64.575 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 89.2 REMARK 200 DATA REDUNDANCY : 5.100 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.14 REMARK 200 COMPLETENESS FOR SHELL (%) : 48.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.14600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.400 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: 7FHX REMARK 200 REMARK 200 REMARK: NEEDLES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 32.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.81 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M CITRIC ACID PH 3.5, 25% W/V REMARK 280 POLYETHYLENE GLYCOL 3,350, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 49.50300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.04800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 49.50300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.04800 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 MET A -28 REMARK 465 GLY A -27 REMARK 465 SER A -26 REMARK 465 SER A -25 REMARK 465 HIS A -24 REMARK 465 HIS A -23 REMARK 465 HIS A -22 REMARK 465 HIS A -21 REMARK 465 HIS A -20 REMARK 465 HIS A -19 REMARK 465 SER A -18 REMARK 465 SER A -17 REMARK 465 GLY A -16 REMARK 465 LEU A -15 REMARK 465 VAL A -14 REMARK 465 PRO A -13 REMARK 465 ARG A -12 REMARK 465 GLY A -11 REMARK 465 SER A -10 REMARK 465 HIS A -9 REMARK 465 MET A -8 REMARK 465 LEU A -7 REMARK 465 GLU A -6 REMARK 465 VAL A -5 REMARK 465 LEU A -4 REMARK 465 PHE A -3 REMARK 465 GLN A -2 REMARK 465 GLY A -1 REMARK 465 PRO A 0 REMARK 465 MET A 1 REMARK 465 ARG A 2 REMARK 465 PHE A 3 REMARK 465 GLN A 4 REMARK 465 SER A 5 REMARK 465 LEU A 6 REMARK 465 SER A 7 REMARK 465 LEU A 8 REMARK 465 ALA A 9 REMARK 465 GLY A 10 REMARK 465 SER A 11 REMARK 465 VAL A 12 REMARK 465 ALA A 13 REMARK 465 MET A 14 REMARK 465 LEU A 15 REMARK 465 LEU A 16 REMARK 465 HIS A 17 REMARK 465 ILE A 18 REMARK 465 ASN A 19 REMARK 465 ALA A 20 REMARK 465 PHE A 21 REMARK 465 ALA A 22 REMARK 465 ALA A 23 REMARK 465 GLN A 24 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 ARG A 48 CD NE CZ NH1 NH2 REMARK 470 LYS A 82 CD CE NZ REMARK 470 ARG A 101 CZ NH1 NH2 REMARK 470 LYS A 168 CG CD CE NZ REMARK 470 LYS A 220 CE NZ REMARK 470 ARG A 268 CZ NH1 NH2 REMARK 470 LYS A 287 CE NZ 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 85 54.45 -154.80 REMARK 500 ASN A 113 -47.57 68.92 REMARK 500 ASP A 115 40.68 -91.14 REMARK 500 ASN A 170 -145.10 -92.46 REMARK 500 LYS A 220 -115.33 53.67 REMARK 500 ALA A 288 -111.39 52.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE REFERENCE IS GENBANK: AJE99968.1. REMARK 999 THE 29 N-TERMINAL RESIDUES ARE EXPRESSION TAGS. DBREF 7WXJ A -28 338 PDB 7WXJ 7WXJ -28 338 SEQRES 1 A 367 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 367 LEU VAL PRO ARG GLY SER HIS MET LEU GLU VAL LEU PHE SEQRES 3 A 367 GLN GLY PRO MET ARG PHE GLN SER LEU SER LEU ALA GLY SEQRES 4 A 367 SER VAL ALA MET LEU LEU HIS ILE ASN ALA PHE ALA ALA SEQRES 5 A 367 GLN ASN ASP CYS PRO ALA PRO PRO PRO GLY SER PRO ASP SEQRES 6 A 367 ILE ARG ALA ILE GLY TYR TYR THR ASP ALA ALA ARG SER SEQRES 7 A 367 VAL ILE ASP PRO ARG LEU LYS THR GLN ASN ASP ALA ALA SEQRES 8 A 367 VAL LYS PRO LEU ASN ALA PHE ALA ALA HIS VAL ALA LYS SEQRES 9 A 367 PHE ALA ASP ALA TYR ALA LYS GLY ALA ASP GLU ALA ALA SEQRES 10 A 367 GLY ARG CYS ALA LEU THR TRP LEU ASP ALA TRP ALA ARG SEQRES 11 A 367 SER GLY ALA MET LEU GLY ARG MET ALA HIS VAL ASN ASN SEQRES 12 A 367 ASP GLN SER ASP TYR MET ARG GLN TRP THR HIS GLY ALA SEQRES 13 A 367 ALA ALA MET ALA TYR LEU ARG THR GLN ALA LEU ALA SER SEQRES 14 A 367 GLU GLN GLN ARG THR ASP ILE GLU THR TRP LEU LYS ARG SEQRES 15 A 367 LEU SER ALA ALA ASN LEU ALA TYR TRP ASP ASN PRO LYS SEQRES 16 A 367 HIS LYS ARG ASN ASN HIS TYR TYR TRP THR GLY VAL GLY SEQRES 17 A 367 ILE MET ALA THR ALA VAL ALA THR ARG ASP ASP THR LEU SEQRES 18 A 367 LEU ASN THR ALA GLN GLY ILE TYR ARG ALA GLY ILE ASP SEQRES 19 A 367 ALA ILE GLU PRO ASP GLY ARG LEU PRO MET GLU MET ALA SEQRES 20 A 367 ARG LYS ARG LEU ALA LEU HIS TYR HIS ASP TYR ALA THR SEQRES 21 A 367 ALA PRO LEU VAL LEU MET ALA GLU MET ALA ARG LEU GLN SEQRES 22 A 367 GLY GLU ASP TRP TYR THR TYR ARG GLN GLY ALA LEU GLU SEQRES 23 A 367 ARG LEU ALA ALA ARG VAL ALA ASP GLY TYR ARG ASP PRO SEQRES 24 A 367 SER TRP PHE ASN THR GLN SER GLY ALA VAL GLN GLU THR SEQRES 25 A 367 ALA THR PRO LYS ALA SER SER GLY TRP VAL GLU PHE TYR SEQRES 26 A 367 ARG LEU ARG SER PRO ASP PRO MET ARG PHE ASP ALA MET SEQRES 27 A 367 HIS ALA ALA GLY PRO PHE GLN ASP PRO ARG MET GLY GLY SEQRES 28 A 367 ASN LEU THR LEU MET ALA GLN GLU GLY ILE VAL PRO LEU SEQRES 29 A 367 PRO GLN GLN FORMUL 2 HOH *186(H2 O) HELIX 1 AA1 ASP A 52 VAL A 63 1 12 HELIX 2 AA2 VAL A 63 LYS A 82 1 20 HELIX 3 AA3 ASP A 85 SER A 102 1 18 HELIX 4 AA4 ASP A 115 GLN A 136 1 22 HELIX 5 AA5 ALA A 137 ALA A 139 5 3 HELIX 6 AA6 SER A 140 TRP A 162 1 23 HELIX 7 AA7 ASN A 170 ARG A 188 1 19 HELIX 8 AA8 ASP A 189 ALA A 206 1 18 HELIX 9 AA9 LEU A 213 ALA A 218 1 6 HELIX 10 AB1 ARG A 219 ARG A 221 5 3 HELIX 11 AB2 LEU A 222 GLN A 244 1 23 HELIX 12 AB3 ASP A 247 TYR A 251 5 5 HELIX 13 AB4 GLY A 254 ASP A 269 1 16 HELIX 14 AB5 PRO A 270 GLY A 278 1 9 HELIX 15 AB6 LYS A 287 SER A 290 5 4 HELIX 16 AB7 GLY A 291 ARG A 297 1 7 HELIX 17 AB8 ASP A 302 ARG A 305 5 4 HELIX 18 AB9 PHE A 306 ALA A 312 1 7 HELIX 19 AC1 PRO A 318 GLY A 321 5 4 HELIX 20 AC2 LEU A 324 GLY A 331 1 8 SHEET 1 AA1 2 GLN A 316 ASP A 317 0 SHEET 2 AA1 2 GLY A 322 ASN A 323 -1 O GLY A 322 N ASP A 317 SSBOND 1 CYS A 27 CYS A 91 1555 1555 2.04 CISPEP 1 GLY A 313 PRO A 314 0 0.71 CRYST1 99.006 46.096 64.586 90.00 91.08 90.00 C 1 2 1 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 0.010100 0.000000 0.000190 0.00000 SCALE2 0.000000 0.021694 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015486 0.00000