HEADER HYDROLASE 10-NOV-23 8X2W TITLE CRYSTAL STRUCTURE OF THE ANCESTRAL GH19 CHITINASE, ANC4+LOOPII TITLE 2 (P12K/N13H/S58T/N193G/Y194F/D197R) COMPND MOL_ID: 1; COMPND 2 MOLECULE: THE ANCESTRAL GH19 CHITINASE, ANC4+LOOPII COMPND 3 (P12K/N13H/S58T/N193G/Y194F/D197R); COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS GH19 CHITINASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR D.KOZOME,P.LAURINO REVDAT 1 03-APR-24 8X2W 0 JRNL AUTH D.KOZOME,P.LAURINO JRNL TITL BEYOND THE ACTIVE SITE: THE ADDITION OF A REMOTE LOOP JRNL TITL 2 REVEALS A NEW COMPLEX BIOLOGICAL FUNCTION FOR CHITINASE JRNL TITL 3 ENZYMES JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 36817 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.460 REMARK 3 FREE R VALUE TEST SET COUNT : 2009 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 49.4300 - 3.3700 1.00 2667 156 0.1764 0.1806 REMARK 3 2 3.3700 - 2.6800 1.00 2531 148 0.1940 0.2181 REMARK 3 3 2.6800 - 2.3400 1.00 2509 147 0.1922 0.2247 REMARK 3 4 2.3400 - 2.1300 1.00 2507 146 0.1847 0.2071 REMARK 3 5 2.1300 - 1.9700 1.00 2468 139 0.1870 0.2041 REMARK 3 6 1.9700 - 1.8600 1.00 2486 142 0.1853 0.2027 REMARK 3 7 1.8600 - 1.7600 1.00 2455 143 0.1866 0.1938 REMARK 3 8 1.7600 - 1.6900 1.00 2481 143 0.1873 0.2098 REMARK 3 9 1.6900 - 1.6200 1.00 2428 138 0.1810 0.2047 REMARK 3 10 1.6200 - 1.5700 1.00 2484 144 0.1834 0.2395 REMARK 3 11 1.5700 - 1.5200 1.00 2451 140 0.1856 0.2200 REMARK 3 12 1.5200 - 1.4700 1.00 2449 144 0.2131 0.2293 REMARK 3 13 1.4700 - 1.4400 1.00 2423 137 0.2175 0.2368 REMARK 3 14 1.4400 - 1.4000 1.00 2469 142 0.2368 0.2739 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.147 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.191 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.56 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 : 0.009 1860 REMARK 3 ANGLE : 1.061 2543 REMARK 3 CHIRALITY : 0.093 256 REMARK 3 PLANARITY : 0.011 343 REMARK 3 DIHEDRAL : 5.612 256 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 8X2W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-NOV-23. REMARK 100 THE DEPOSITION ID IS D_1300042506. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUL-23 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 : SPRING-8 REMARK 200 BEAMLINE : BL32XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 46885 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 49.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 52.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 1.20.1_4487 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 UL OF ANC4+LOOP REMARK 280 II+P12K/N13H/S58T/N193G/Y194F/D197R (6.0 MG/ML IN 10 MM SODIUM REMARK 280 ACETATE PH 5.0, 150 MM NACL) + 1 UL OF 25% (W/V) POLYETHYLENE REMARK 280 GLYCOL 3,350, 0.1 M BIS-TRIS, PH 6.5, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.79500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.11000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.79500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.11000 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 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 GLN A 90 CG CD OE1 NE2 REMARK 470 ARG A 228 CG CD NE CZ NH1 NH2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 197 CA - N - CD ANGL. DEV. = -10.1 DEGREES 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 GLN A 80 51.48 -115.06 REMARK 500 TRP A 109 141.57 84.70 REMARK 500 ASN A 187 40.44 -160.93 REMARK 500 REMARK 500 REMARK: NULL DBREF 8X2W A 0 231 PDB 8X2W 8X2W 0 231 SEQRES 1 A 232 MET VAL SER ARG SER MET PHE ASP GLN LEU PHE LYS HIS SEQRES 2 A 232 ARG ASN SER PHE TYR THR TYR ASP ALA PHE ILE ALA ALA SEQRES 3 A 232 ALA LYS SER PHE PRO SER PHE GLY THR THR GLY ASP THR SEQRES 4 A 232 ASP VAL ARG LYS ARG GLU ILE ALA ALA PHE PHE ALA HIS SEQRES 5 A 232 VAL SER HIS GLU THR THR GLY GLY TRP PRO THR ALA PRO SEQRES 6 A 232 ASP GLY PRO TYR ALA TRP GLY LEU VAL TYR ILE GLU GLU SEQRES 7 A 232 ILE ASN GLN SER ASN ASP TYR CYS ASP PRO SER THR GLN SEQRES 8 A 232 TYR PRO CYS ALA PRO GLY LYS GLN TYR TYR GLY ARG GLY SEQRES 9 A 232 PRO LEU GLN LEU SER TRP ASN TYR ASN TYR GLY PRO CYS SEQRES 10 A 232 GLY ASP ALA LEU GLY LEU ASP LEU LEU ASN ASN PRO ASP SEQRES 11 A 232 LEU VAL ALA GLN ASP PRO VAL ILE ALA PHE LYS THR ALA SEQRES 12 A 232 LEU TRP PHE TRP MET THR PRO GLN SER PRO LYS PRO SER SEQRES 13 A 232 CYS HIS ASP VAL MET THR GLY ASN TRP THR PRO SER SER SEQRES 14 A 232 ALA ASP LEU ALA ALA GLY ARG VAL PRO GLY PHE GLY VAL SEQRES 15 A 232 THR THR ASN ILE ILE ASN GLY GLY LEU GLU CYS GLY LYS SEQRES 16 A 232 GLY ASN PRO ALA GLN ALA GLU ASN ARG VAL GLY PHE TYR SEQRES 17 A 232 LYS ARG PHE CYS ASN GLN LEU GLY VAL SER PRO GLY SER SEQRES 18 A 232 ASN LEU ASP CYS ALA ASN MET ARG PRO PHE GLY FORMUL 2 HOH *118(H2 O) HELIX 1 AA1 SER A 2 PHE A 10 1 9 HELIX 2 AA2 THR A 18 LYS A 27 1 10 HELIX 3 AA3 ASP A 37 THR A 57 1 21 HELIX 4 AA4 TRP A 109 GLY A 121 1 13 HELIX 5 AA5 ASP A 129 ASP A 134 1 6 HELIX 6 AA6 ASP A 134 THR A 148 1 15 HELIX 7 AA7 SER A 155 THR A 161 1 7 HELIX 8 AA8 SER A 167 ALA A 173 1 7 HELIX 9 AA9 GLY A 178 CYS A 192 1 15 HELIX 10 AB1 PRO A 197 GLY A 215 1 19 SSBOND 1 CYS A 85 CYS A 93 1555 1555 2.04 SSBOND 2 CYS A 192 CYS A 224 1555 1555 2.07 CISPEP 1 SER A 151 PRO A 152 0 9.73 CRYST1 37.320 69.590 70.220 90.00 90.00 90.00 P 2 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 0.026795 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014370 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014241 0.00000