HEADER LYASE 29-JUN-19 6KCW TITLE STRUCTURE OF ALGINATE LYASE ALY36B 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: CHITINOPHAGA SP. MD30; SOURCE 3 ORGANISM_TAXID: 2033437; SOURCE 4 GENE: CK934_20815; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS ALGINATE LYASE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR F.DONG,X.L.CHEN,Y.Z.ZHANG REVDAT 3 27-MAR-24 6KCW 1 REMARK REVDAT 2 13-JAN-21 6KCW 1 JRNL REVDAT 1 24-JUN-20 6KCW 0 JRNL AUTH F.DONG,F.XU,X.L.CHEN,P.Y.LI,C.Y.LI,F.C.LI,Y.CHEN,P.WANG, JRNL AUTH 2 Y.Z.ZHANG JRNL TITL ALGINATE LYASE ALY36B IS A NEW BACTERIAL MEMBER OF THE JRNL TITL 2 POLYSACCHARIDE LYASE FAMILY 36 AND CATALYZES BY A NOVEL JRNL TITL 3 MECHANISM WITH LYSINE AS BOTH THE CATALYTIC BASE AND JRNL TITL 4 CATALYTIC ACID. JRNL REF J.MOL.BIOL. V. 431 4897 2019 JRNL REFN ESSN 1089-8638 JRNL PMID 31682837 JRNL DOI 10.1016/J.JMB.2019.10.023 REMARK 2 REMARK 2 RESOLUTION. 2.28 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1_2155 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.28 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 10500 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 511 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 46.8600 - 3.6215 0.98 2634 125 0.1674 0.1919 REMARK 3 2 3.6215 - 2.8746 0.98 2513 127 0.2031 0.2319 REMARK 3 3 2.8746 - 2.5113 0.99 2493 137 0.2388 0.2972 REMARK 3 4 2.5113 - 2.2817 0.94 2349 122 0.2410 0.3394 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.410 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.15 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 6KCW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1300012724. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-18 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 : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10564 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.280 REMARK 200 RESOLUTION RANGE LOW (A) : 46.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.13700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 25.0600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.28 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 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: SAD REMARK 200 SOFTWARE USED: AUTOSOL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: POTASSIUM PHOSPHATE MONOBASIC/ SODIUM REMARK 280 PHOSPHATE DIBASIC, POLYETHYLENE GLYCOL (PEG) 8,000, AND SODIUM REMARK 280 CHLORIDE., VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 26.88500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.74600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.88500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.74600 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: 310 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9640 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 454 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OH TYR A 153 O4 PO4 A 301 1.27 REMARK 500 OE2 GLU A 118 O HOH A 401 1.84 REMARK 500 OD2 ASP A 251 O HOH A 402 1.92 REMARK 500 OH TYR A 57 O HOH A 403 2.04 REMARK 500 O VAL A 84 O HOH A 404 2.06 REMARK 500 OD2 ASP A 128 O HOH A 401 2.09 REMARK 500 O LYS A 225 O HOH A 404 2.12 REMARK 500 O HOH A 442 O HOH A 473 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 ALA A 48 90.37 -165.41 REMARK 500 SER A 73 -135.73 58.45 REMARK 500 SER A 105 -134.59 55.33 REMARK 500 TYR A 161 -166.79 -101.90 REMARK 500 ARG A 195 55.22 -96.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 302 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 27 O REMARK 620 2 ASN A 29 OD1 80.5 REMARK 620 3 GLY A 61 O 80.7 93.2 REMARK 620 4 ASP A 251 OD1 79.3 151.7 102.9 REMARK 620 5 ASP A 251 OD2 127.6 151.7 94.6 50.7 REMARK 620 6 HOH A 406 O 143.4 63.6 93.7 136.7 88.8 REMARK 620 7 HOH A 408 O 99.3 84.8 177.9 79.1 87.1 85.1 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 302 DBREF1 6KCW A 19 259 UNP A0A249T061_9BACT DBREF2 6KCW A A0A249T061 53 293 SEQADV 6KCW LEU A 260 UNP A0A249T06 EXPRESSION TAG SEQADV 6KCW GLU A 261 UNP A0A249T06 EXPRESSION TAG SEQADV 6KCW HIS A 262 UNP A0A249T06 EXPRESSION TAG SEQRES 1 A 244 ALA ILE PRO SER SER LEU SER ILE ASN TRP ASN ASN TYR SEQRES 2 A 244 ALA THR GLY ALA TYR SER SER GLY ASN ALA ALA SER ASP SEQRES 3 A 244 PHE GLY ASN ALA GLY GLY TRP ASN GLN SER ARG SER TYR SEQRES 4 A 244 ILE SER ASP GLY THR LEU ARG VAL THR LEU LEU LYS ASN SEQRES 5 A 244 ALA LEU SER GLY ALA GLY GLY LEU ILE SER ASN ILE ASP SEQRES 6 A 244 VAL SER ASP GLY THR GLU TYR GLU LEU ASP TYR ASP VAL SEQRES 7 A 244 ARG PHE HIS SER GLN PHE ASP TRP SER ARG GLY GLY LYS SEQRES 8 A 244 VAL GLY PHE GLY PHE SER ILE GLY GLU GLY ASN THR GLY SEQRES 9 A 244 GLY ASP PRO GLY TRP ASP GLY ASN GLY GLY THR LEU ARG SEQRES 10 A 244 MET MET TRP TYR GLN THR ASP ALA GLY ARG VAL PHE PHE SEQRES 11 A 244 GLN PRO TYR ILE TYR HIS LYS ASP GLN PRO GLY GLN TYR SEQRES 12 A 244 GLY ASP THR PHE GLY LYS SER TYR PRO SER SER GLY SER SEQRES 13 A 244 ILE THR LYS GLY THR THR TYR HIS VAL HIS VAL TYR ILE SEQRES 14 A 244 LYS SER ASN THR GLY SER ASN ARG ASP GLY ARG ALA GLN SEQRES 15 A 244 ILE ILE ILE ASN GLY THR THR VAL LEU ASP THR ALA ILE SEQRES 16 A 244 ARG TRP THR THR ASN ASP ALA GLN ARG LEU ILE LYS ASN SEQRES 17 A 244 MET THR PHE HIS THR PHE ARG GLY GLY SER GLN THR TYR SEQRES 18 A 244 TRP GLN SER PRO VAL ASP SER TYR ILE TYR TYR ASP ASN SEQRES 19 A 244 LEU VAL LEU ARG LYS ILE ARG LEU GLU HIS HET PO4 A 301 5 HET CA A 302 1 HETNAM PO4 PHOSPHATE ION HETNAM CA CALCIUM ION FORMUL 2 PO4 O4 P 3- FORMUL 3 CA CA 2+ FORMUL 4 HOH *73(H2 O) HELIX 1 AA1 SER A 37 GLY A 46 1 10 HELIX 2 AA2 LEU A 72 GLY A 77 1 6 HELIX 3 AA3 PRO A 125 GLY A 129 5 5 HELIX 4 AA4 ASN A 218 ARG A 222 5 5 HELIX 5 AA5 GLN A 237 GLN A 241 5 5 SHEET 1 AA1 5 SER A 23 ILE A 26 0 SHEET 2 AA1 5 SER A 246 ARG A 259 -1 O LEU A 255 N LEU A 24 SHEET 3 AA1 5 THR A 62 LEU A 67 -1 N LEU A 63 O TYR A 250 SHEET 4 AA1 5 SER A 56 SER A 59 -1 N TYR A 57 O ARG A 64 SHEET 5 AA1 5 GLY A 34 ALA A 35 -1 N GLY A 34 O ILE A 58 SHEET 1 AA2 6 SER A 23 ILE A 26 0 SHEET 2 AA2 6 SER A 246 ARG A 259 -1 O LEU A 255 N LEU A 24 SHEET 3 AA2 6 GLU A 89 PHE A 98 -1 N ASP A 95 O ASP A 251 SHEET 4 AA2 6 THR A 180 LYS A 188 -1 O TYR A 181 N VAL A 96 SHEET 5 AA2 6 GLY A 197 ILE A 203 -1 O ILE A 202 N HIS A 184 SHEET 6 AA2 6 THR A 206 ILE A 213 -1 O LEU A 209 N ILE A 201 SHEET 1 AA3 5 LEU A 78 GLY A 87 0 SHEET 2 AA3 5 ILE A 224 ARG A 233 -1 O MET A 227 N ILE A 82 SHEET 3 AA3 5 GLY A 107 GLY A 117 -1 N SER A 115 O LYS A 225 SHEET 4 AA3 5 GLY A 131 GLN A 140 -1 O LEU A 134 N PHE A 114 SHEET 5 AA3 5 VAL A 146 TYR A 153 -1 O GLN A 149 N MET A 137 LINK O ASN A 27 CA CA A 302 1555 1555 2.21 LINK OD1 ASN A 29 CA CA A 302 1555 1555 2.20 LINK O GLY A 61 CA CA A 302 1555 1555 2.31 LINK OD1 ASP A 251 CA CA A 302 1555 1555 2.48 LINK OD2 ASP A 251 CA CA A 302 1555 1555 2.67 LINK CA CA A 302 O HOH A 406 1555 1555 2.13 LINK CA CA A 302 O HOH A 408 1555 1555 2.67 CISPEP 1 TYR A 169 PRO A 170 0 0.62 CISPEP 2 GLY A 234 GLY A 235 0 -3.92 SITE 1 AC1 6 LYS A 109 GLY A 122 ARG A 135 TYR A 151 SITE 2 AC1 6 TYR A 153 HOH A 418 SITE 1 AC2 6 ASN A 27 ASN A 29 GLY A 61 ASP A 251 SITE 2 AC2 6 HOH A 406 HOH A 408 CRYST1 53.770 89.492 46.856 90.00 90.00 90.00 P 21 21 2 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 0.018598 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011174 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021342 0.00000