HEADER HYDROLASE 06-OCT-24 9JTP TITLE CRYSTAL STRUCTURE OF CHITINASE (E167Q) FROM THE CARNIVOROUS PLANT TITLE 2 DROSERA ADELAE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BASIC CHITINASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 OTHER_DETAILS: CHITINASE SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSERA ADELAE; SOURCE 3 ORGANISM_TAXID: 173387; SOURCE 4 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: GS115; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PPIC9K KEYWDS CHITINASE, CLASS I CHITINASE, E167Q, DROSERA ADELAE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR K.YONEDA,Y.SUIZU,Y.NARUSE,H.SAKURABA,T.OHSHIMA REVDAT 2 10-DEC-25 9JTP 1 JRNL REVDAT 1 13-AUG-25 9JTP 0 JRNL AUTH K.YONEDA,Y.NARUSE,Y.SUIZU,T.ARAKI,Y.HOSHI,H.SAKURABA, JRNL AUTH 2 J.HAYASHI,T.OHSHIMA JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF CHITINASE FROM JRNL TITL 2 CARNIVOROUS PLANT DROSERA ADELAE. JRNL REF FEBS OPEN BIO V. 15 1930 2025 JRNL REFN ESSN 2211-5463 JRNL PMID 40874485 JRNL DOI 10.1002/2211-5463.70110 REMARK 2 REMARK 2 RESOLUTION. 1.57 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 3 NUMBER OF REFLECTIONS : 25329 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1303 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.57 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.61 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1210 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 61.27 REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE SET COUNT : 46 REMARK 3 BIN FREE R VALUE : 0.2550 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1857 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 166 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : -0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.113 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.108 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.078 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.221 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.940 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1919 ; 0.010 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 1667 ; 0.001 ; 0.018 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2615 ; 1.597 ; 1.648 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3834 ; 1.515 ; 1.575 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 242 ; 6.303 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 102 ;37.151 ;23.333 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 262 ;11.767 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ;18.193 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 243 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2311 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 497 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 972 ; 2.030 ; 2.248 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 970 ; 2.030 ; 2.247 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1212 ; 2.799 ; 3.371 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1213 ; 2.798 ; 3.371 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 947 ; 2.525 ; 2.367 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 948 ; 2.523 ; 2.368 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1404 ; 3.624 ; 3.504 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2317 ; 4.887 ;27.376 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2295 ; 4.830 ;27.103 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 9JTP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-OCT-24. REMARK 100 THE DEPOSITION ID IS D_1300052210. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-23 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 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 : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26673 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.570 REMARK 200 RESOLUTION RANGE LOW (A) : 47.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.7 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.02900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 33.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.57 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 60.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.40400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 8000 40% 2-PROPANOL 0.1 M REMARK 280 IMIDAZOLE PH 6.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K 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 21.56000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.44700 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.62350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 36.44700 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.56000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.62350 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 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 LEU A 93 59.15 -97.05 REMARK 500 ASN A 170 71.37 -111.30 REMARK 500 TYR A 199 142.76 82.48 REMARK 500 ASN A 277 33.61 -157.01 REMARK 500 REMARK 500 REMARK: NULL DBREF1 9JTP A 79 321 UNP A0A1L7NZT5_9CARY DBREF2 9JTP A A0A1L7NZT5 79 321 SEQADV 9JTP GLN A 167 UNP A0A1L7NZT GLU 167 ENGINEERED MUTATION SEQRES 1 A 243 ASP VAL SER SER ILE ILE THR SER GLN ILE PHE ASN GLN SEQRES 2 A 243 MET LEU LEU HIS ARG ASN ASP ASN ALA CYS PRO ALA ASN SEQRES 3 A 243 GLY PHE TYR SER TYR GLN ALA PHE ILE ASN ALA ALA ARG SEQRES 4 A 243 LYS PHE SER GLY PHE GLY THR THR GLY ASP THR ASN THR SEQRES 5 A 243 ARG LYS ASN GLU LEU ALA ALA PHE PHE GLY GLN THR SER SEQRES 6 A 243 HIS GLU THR THR GLY GLY TRP SER THR ALA PRO ASP GLY SEQRES 7 A 243 PRO TYR ALA TRP GLY TYR CYS PHE LYS GLN GLN GLN GLY SEQRES 8 A 243 ASN PRO GLY ASP TYR CYS VAL PRO SER SER THR TYR PRO SEQRES 9 A 243 CYS ALA PRO GLY LYS LYS TYR TYR GLY ARG GLY PRO ILE SEQRES 10 A 243 GLN ILE SER TYR ASN TYR ASN TYR GLY LEU CYS GLY ALA SEQRES 11 A 243 ALA ILE ASN GLN PRO LEU LEU SER ASN PRO GLY LEU VAL SEQRES 12 A 243 ALA SER ASP ALA ASP ILE SER PHE GLU THR ALA ILE TRP SEQRES 13 A 243 PHE TRP MET THR PRO GLN GLY ASN LYS PRO SER CYS HIS SEQRES 14 A 243 ALA VAL ALA THR GLY GLN TRP ASN PRO SER SER ALA ASP SEQRES 15 A 243 GLN ALA ALA GLY ARG VAL PRO GLY TYR GLY VAL ILE THR SEQRES 16 A 243 ASN ILE ILE ASN GLY GLY VAL GLU CYS GLY GLN GLY GLU SEQRES 17 A 243 LYS ALA GLU VAL ALA ASN ARG ILE GLY PHE TYR GLN ARG SEQRES 18 A 243 TYR CYS SER ILE PHE GLY ILE SER PRO GLY GLN ASN LEU SEQRES 19 A 243 ASP CYS TYR ASN GLN ARG PRO PHE SER HET ACY A 401 4 HETNAM ACY ACETIC ACID FORMUL 2 ACY C2 H4 O2 FORMUL 3 HOH *166(H2 O) HELIX 1 AA1 ASP A 79 ILE A 83 5 5 HELIX 2 AA2 THR A 85 LEU A 93 1 9 HELIX 3 AA3 SER A 108 ARG A 117 1 10 HELIX 4 AA4 ASP A 127 THR A 146 1 20 HELIX 5 AA5 GLY A 156 TRP A 160 5 5 HELIX 6 AA6 TYR A 199 ASN A 211 1 13 HELIX 7 AA7 GLY A 219 ASP A 224 1 6 HELIX 8 AA8 ASP A 224 THR A 238 1 15 HELIX 9 AA9 SER A 245 THR A 251 1 7 HELIX 10 AB1 SER A 257 ALA A 263 1 7 HELIX 11 AB2 GLY A 268 CYS A 282 1 15 HELIX 12 AB3 LYS A 287 PHE A 304 1 18 SSBOND 1 CYS A 101 CYS A 163 1555 1555 2.06 SSBOND 2 CYS A 175 CYS A 183 1555 1555 2.02 SSBOND 3 CYS A 282 CYS A 314 1555 1555 2.09 CRYST1 43.120 63.247 72.894 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 0.023191 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015811 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013719 0.00000 CONECT 181 656 CONECT 656 181 CONECT 752 810 CONECT 810 752 CONECT 1546 1792 CONECT 1792 1546 CONECT 1859 1860 1861 1862 CONECT 1860 1859 CONECT 1861 1859 CONECT 1862 1859 MASTER 255 0 1 12 0 0 0 6 2027 1 10 19 END