HEADER HYDROLASE 21-MAY-20 7C6C TITLE CRYSTAL STRUCTURE OF NATIVE CHITOSANASE FROM BACILLUS SUBTILIS MY002 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHITOSANASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.132; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168; SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: CSN, BSU26890; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CHITOSANASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.GOU,Z.C.LIU,T.XIE,G.G.WANG REVDAT 3 29-NOV-23 7C6C 1 JRNL REVDAT 2 07-APR-21 7C6C 1 JRNL REVDAT 1 31-MAR-21 7C6C 0 JRNL AUTH Y.LI,Y.GOU,Z.LIU,T.XIE,G.WANG JRNL TITL STRUCTURE-BASED RATIONAL DESIGN OF CHITOSANASE CSNMY002 FOR JRNL TITL 2 HIGH YIELDS OF CHITOBIOSE. JRNL REF COLLOIDS SURF B V. 202 11692 2021 JRNL REF 2 BIOINTERFACES JRNL REFN ESSN 1873-4367 JRNL PMID 33744813 JRNL DOI 10.1016/J.COLSURFB.2021.111692 REMARK 2 REMARK 2 RESOLUTION. 1.26 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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) : 1.26 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.08 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 79201 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.151 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.166 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 3859 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 28.0830 - 3.8173 0.85 2508 133 0.1732 0.1678 REMARK 3 2 3.8173 - 3.0311 0.95 2674 134 0.1658 0.2006 REMARK 3 3 3.0311 - 2.6483 0.99 2739 151 0.1661 0.1731 REMARK 3 4 2.6483 - 2.4063 1.00 2743 157 0.1631 0.1607 REMARK 3 5 2.4063 - 2.2339 1.00 2731 145 0.1505 0.1603 REMARK 3 6 2.2339 - 2.1022 1.00 2716 159 0.1501 0.1663 REMARK 3 7 2.1022 - 1.9970 1.00 2728 145 0.1471 0.1618 REMARK 3 8 1.9970 - 1.9101 1.00 2721 141 0.1551 0.1905 REMARK 3 9 1.9101 - 1.8365 1.00 2728 128 0.1514 0.1697 REMARK 3 10 1.8365 - 1.7732 1.00 2689 140 0.1497 0.1726 REMARK 3 11 1.7732 - 1.7177 1.00 2714 143 0.1427 0.1581 REMARK 3 12 1.7177 - 1.6686 1.00 2755 118 0.1345 0.1483 REMARK 3 13 1.6686 - 1.6247 1.00 2655 148 0.1259 0.1381 REMARK 3 14 1.6247 - 1.5851 1.00 2684 142 0.1216 0.1373 REMARK 3 15 1.5851 - 1.5491 1.00 2727 140 0.1205 0.1337 REMARK 3 16 1.5491 - 1.5161 1.00 2672 141 0.1191 0.1597 REMARK 3 17 1.5161 - 1.4858 1.00 2674 173 0.1242 0.1544 REMARK 3 18 1.4858 - 1.4577 1.00 2683 158 0.1234 0.1460 REMARK 3 19 1.4577 - 1.4317 1.00 2684 134 0.1242 0.1662 REMARK 3 20 1.4317 - 1.4074 1.00 2715 116 0.1234 0.1479 REMARK 3 21 1.4074 - 1.3847 1.00 2701 121 0.1263 0.1593 REMARK 3 22 1.3847 - 1.3634 1.00 2694 127 0.1211 0.1406 REMARK 3 23 1.3634 - 1.3434 1.00 2696 124 0.1249 0.1411 REMARK 3 24 1.3434 - 1.3245 1.00 2709 111 0.1265 0.1473 REMARK 3 25 1.3245 - 1.3066 1.00 2712 126 0.1222 0.1518 REMARK 3 26 1.3066 - 1.2896 1.00 2676 129 0.1313 0.1536 REMARK 3 27 1.2896 - 1.2735 1.00 2654 160 0.1366 0.1553 REMARK 3 28 1.2735 - 1.2581 0.95 2560 115 0.1532 0.1841 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) : 0.080 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.76 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.14 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 : 0.004 2022 REMARK 3 ANGLE : 0.768 2738 REMARK 3 CHIRALITY : 0.076 287 REMARK 3 PLANARITY : 0.006 367 REMARK 3 DIHEDRAL : 4.464 2166 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 7C6C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-MAY-20. REMARK 100 THE DEPOSITION ID IS D_1300017078. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97854 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 79276 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.258 REMARK 200 RESOLUTION RANGE LOW (A) : 28.083 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.06800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.26 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.26400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 6.000 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: 4OLT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.64 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15 M DL-MALIC ACID PH7.0 AND 20% REMARK 280 (W/V) PEG3350, PH 6.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K 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 23.69050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.60550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.83300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.60550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.69050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.83300 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 ALA A 1 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 O HOH A 527 O HOH A 643 2.18 REMARK 500 O HOH A 402 O HOH A 632 2.19 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 TYR A 118 -58.27 -122.23 REMARK 500 TYR A 118 -58.16 -122.21 REMARK 500 ASN A 222 56.57 -102.67 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 735 DISTANCE = 6.92 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LMR A 301 DBREF 7C6C A 1 242 UNP O07921 CHIS_BACSU 36 277 SEQRES 1 A 242 ALA GLY LEU ASN LYS ASP GLN LYS ARG ARG ALA GLU GLN SEQRES 2 A 242 LEU THR SER ILE PHE GLU ASN GLY THR THR GLU ILE GLN SEQRES 3 A 242 TYR GLY TYR VAL GLU ARG LEU ASP ASP GLY ARG GLY TYR SEQRES 4 A 242 THR CYS GLY ARG ALA GLY PHE THR THR ALA THR GLY ASP SEQRES 5 A 242 ALA LEU GLU VAL VAL GLU VAL TYR THR LYS ALA VAL PRO SEQRES 6 A 242 ASN ASN LYS LEU LYS LYS TYR LEU PRO GLU LEU ARG ARG SEQRES 7 A 242 LEU ALA LYS GLU GLU SER ASP ASP THR SER ASN LEU LYS SEQRES 8 A 242 GLY PHE ALA SER ALA TRP LYS SER LEU ALA ASN ASP LYS SEQRES 9 A 242 GLU PHE ARG ALA ALA GLN ASP LYS VAL ASN ASP HIS LEU SEQRES 10 A 242 TYR TYR GLN PRO ALA MET LYS ARG SER ASP ASN ALA GLY SEQRES 11 A 242 LEU LYS THR ALA LEU ALA ARG ALA VAL MET TYR ASP THR SEQRES 12 A 242 VAL ILE GLN HIS GLY ASP GLY ASP ASP PRO ASP SER PHE SEQRES 13 A 242 TYR ALA LEU ILE LYS ARG THR ASN LYS LYS ALA GLY GLY SEQRES 14 A 242 SER PRO LYS ASP GLY ILE ASP GLU LYS LYS TRP LEU ASN SEQRES 15 A 242 LYS PHE LEU ASP VAL ARG TYR ASP ASP LEU MET ASN PRO SEQRES 16 A 242 ALA ASN HIS ASP THR ARG ASP GLU TRP ARG GLU SER VAL SEQRES 17 A 242 ALA ARG VAL ASP VAL LEU ARG SER ILE ALA LYS GLU ASN SEQRES 18 A 242 ASN TYR ASN LEU ASN GLY PRO ILE HIS VAL ARG SER ASN SEQRES 19 A 242 GLU TYR GLY ASN PHE VAL ILE LYS HET LMR A 301 9 HETNAM LMR (2S)-2-HYDROXYBUTANEDIOIC ACID HETSYN LMR L-MALATE FORMUL 2 LMR C4 H6 O5 FORMUL 3 HOH *335(H2 O) HELIX 1 AA1 ASN A 4 GLY A 21 1 18 HELIX 2 AA2 GLY A 51 VAL A 64 1 14 HELIX 3 AA3 LEU A 69 LYS A 71 5 3 HELIX 4 AA4 TYR A 72 GLU A 83 1 12 HELIX 5 AA5 GLY A 92 LEU A 100 1 9 HELIX 6 AA6 ASP A 103 TYR A 118 1 16 HELIX 7 AA7 TYR A 118 ALA A 129 1 12 HELIX 8 AA8 THR A 133 GLY A 148 1 16 HELIX 9 AA9 SER A 155 GLY A 168 1 14 HELIX 10 AB1 SER A 170 GLY A 174 5 5 HELIX 11 AB2 ASP A 176 ASN A 194 1 19 HELIX 12 AB3 ASN A 197 ASP A 199 5 3 HELIX 13 AB4 THR A 200 GLU A 206 1 7 HELIX 14 AB5 VAL A 208 GLU A 220 1 13 SHEET 1 AA1 3 VAL A 30 ARG A 32 0 SHEET 2 AA1 3 TYR A 39 CYS A 41 -1 O THR A 40 N GLU A 31 SHEET 3 AA1 3 PHE A 46 THR A 47 -1 O PHE A 46 N CYS A 41 SHEET 1 AA2 2 ILE A 229 SER A 233 0 SHEET 2 AA2 2 GLY A 237 ILE A 241 -1 O ILE A 241 N ILE A 229 CISPEP 1 GLY A 227 PRO A 228 0 -0.93 SITE 1 AC1 8 LYS A 62 ALA A 209 ASP A 212 SER A 233 SITE 2 AC1 8 ASN A 234 GLU A 235 HOH A 412 HOH A 429 CRYST1 47.381 77.666 79.211 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 0.021106 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012876 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012625 0.00000