HEADER HYDROLASE 21-MAY-20 7C6D TITLE CRYSTAL STRUCTURE OF E19A MUTANT CHITOSANASE FROM BACILLUS SUBTILIS TITLE 2 MY002 COMPLEXED WITH 6 GLCN. COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHITOSANASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.132; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: 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 7C6D 1 JRNL REVDAT 2 07-APR-21 7C6D 1 JRNL REVDAT 1 31-MAR-21 7C6D 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. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.98 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.390 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 3 NUMBER OF REFLECTIONS : 51437 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.137 REMARK 3 R VALUE (WORKING SET) : 0.136 REMARK 3 FREE R VALUE : 0.160 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.750 REMARK 3 FREE R VALUE TEST SET COUNT : 2445 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 24.9780 - 3.7262 1.00 3129 158 0.1551 0.1663 REMARK 3 2 3.7262 - 2.9591 1.00 3008 132 0.1476 0.1943 REMARK 3 3 2.9591 - 2.5855 1.00 2956 147 0.1488 0.1577 REMARK 3 4 2.5855 - 2.3493 1.00 2929 150 0.1458 0.1512 REMARK 3 5 2.3493 - 2.1810 1.00 2923 158 0.1366 0.1542 REMARK 3 6 2.1810 - 2.0525 1.00 2900 158 0.1352 0.1645 REMARK 3 7 2.0525 - 1.9497 1.00 2899 152 0.1382 0.1534 REMARK 3 8 1.9497 - 1.8649 1.00 2927 138 0.1305 0.1608 REMARK 3 9 1.8649 - 1.7931 1.00 2916 113 0.1222 0.1538 REMARK 3 10 1.7931 - 1.7313 1.00 2879 158 0.1179 0.1425 REMARK 3 11 1.7313 - 1.6771 1.00 2886 144 0.1141 0.1487 REMARK 3 12 1.6771 - 1.6292 1.00 2895 141 0.1080 0.1463 REMARK 3 13 1.6292 - 1.5863 1.00 2887 133 0.1023 0.1396 REMARK 3 14 1.5863 - 1.5476 0.99 2868 141 0.0973 0.1568 REMARK 3 15 1.5476 - 1.5125 0.97 2816 130 0.0972 0.1277 REMARK 3 16 1.5125 - 1.4803 0.94 2694 142 0.0998 0.1441 REMARK 3 17 1.4803 - 1.4510 0.87 2480 150 0.0995 0.1696 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) : 0.090 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 13.420 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.28 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 : 0.005 2074 REMARK 3 ANGLE : 0.844 2800 REMARK 3 CHIRALITY : 0.076 309 REMARK 3 PLANARITY : 0.006 363 REMARK 3 DIHEDRAL : 10.610 1270 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 7C6D 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_1300017080. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97853 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51501 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 24.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 12.00 REMARK 200 R MERGE (I) : 0.05200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 47.2000 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) : 1.48 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.13300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.147 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: 7C6C REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.64 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES PH7.5, 0.2M AMMONIUM REMARK 280 SULFATE AND 25%(W/V) PEG 3350, 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 23.48050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.55450 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.96050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.55450 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.48050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.96050 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: 2350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 31.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: 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 -59.05 -120.59 REMARK 500 ASN A 222 59.55 -103.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7C6C RELATED DB: PDB DBREF 7C6D A 1 242 UNP O07921 CHIS_BACSU 36 277 SEQADV 7C6D ALA A 19 UNP O07921 GLU 54 ENGINEERED MUTATION 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 ALA 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 GCS B 1 12 HET GCS B 2 11 HET GCS B 3 11 HET GCS B 4 11 HET GCS B 5 11 HET GCS B 6 11 HETNAM GCS 2-AMINO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN GCS BETA-D-GLUCOSAMINE; 2-AMINO-2-DEOXY-BETA-D-GLUCOSE; 2- HETSYN 2 GCS AMINO-2-DEOXY-D-GLUCOSE; 2-AMINO-2-DEOXY-GLUCOSE; D- HETSYN 3 GCS GLUCOSAMINE FORMUL 2 GCS 6(C6 H13 N O5) FORMUL 3 HOH *320(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 LINK O4 GCS B 1 C1 GCS B 2 1555 1555 1.43 LINK O4 GCS B 2 C1 GCS B 3 1555 1555 1.45 LINK O4 GCS B 3 C1 GCS B 4 1555 1555 1.43 LINK O4 GCS B 4 C1 GCS B 5 1555 1555 1.43 LINK O4 GCS B 5 C1 GCS B 6 1555 1555 1.44 CISPEP 1 GLY A 227 PRO A 228 0 -2.30 CRYST1 46.961 77.921 79.109 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 0.021294 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012834 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012641 0.00000