HEADER HYDROLASE 10-NOV-23 8X2V TITLE CRYSTAL STRUCTURE OF THE ANCESTRAL GH19 CHITINASE, ANC4+LOOPII TITLE 2 (P12K/N13H MUTANT) COMPND MOL_ID: 1; COMPND 2 MOLECULE: GH19 CHITINASE; COMPND 3 CHAIN: A; COMPND 4 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 8X2V 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. 1.29 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) : 1.29 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 47016 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.172 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.250 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 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 49.5300 - 3.1100 1.00 3429 154 0.1537 0.1471 REMARK 3 2 3.1100 - 2.4700 1.00 3293 149 0.1764 0.2067 REMARK 3 3 2.4700 - 2.1600 1.00 3248 143 0.1723 0.1642 REMARK 3 4 2.1600 - 1.9600 1.00 3218 139 0.1755 0.1838 REMARK 3 5 1.9600 - 1.8200 1.00 3225 145 0.1729 0.2128 REMARK 3 6 1.8200 - 1.7100 1.00 3184 143 0.1701 0.1977 REMARK 3 7 1.7100 - 1.6300 1.00 3174 137 0.1623 0.1973 REMARK 3 8 1.6300 - 1.5500 1.00 3185 141 0.1594 0.2026 REMARK 3 9 1.5500 - 1.4900 1.00 3183 144 0.1767 0.2027 REMARK 3 10 1.4900 - 1.4400 1.00 3198 142 0.1821 0.2250 REMARK 3 11 1.4400 - 1.4000 1.00 3162 140 0.1919 0.2148 REMARK 3 12 1.4000 - 1.3600 1.00 3196 142 0.1973 0.2156 REMARK 3 13 1.3600 - 1.3200 1.00 3136 138 0.1989 0.2471 REMARK 3 14 1.3200 - 1.2900 1.00 3185 143 0.2156 0.2458 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) : 0.117 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 17.225 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.41 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.90 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 : 0.007 1881 REMARK 3 ANGLE : 0.958 2574 REMARK 3 CHIRALITY : 0.080 257 REMARK 3 PLANARITY : 0.009 349 REMARK 3 DIHEDRAL : 5.694 259 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 8X2V 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_1300042507. 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) : 1.0 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 : 47133 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.290 REMARK 200 RESOLUTION RANGE LOW (A) : 49.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 33.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.8700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.29 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 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: 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 (%): 31.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 UL OF ANC4+LOOP II+P12K/N13H (6.0 REMARK 280 MG/ML IN 10 MM SODIUM ACETATE PH 5.0, 150 MM NACL) + 1 UL OF 25% REMARK 280 (W/V) POLYETHYLENE GLYCOL 3350, 0.1 M BIS-TRIS, PH 6.5, VAPOR REMARK 280 DIFFUSION, SITTING 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 34.91500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 35.13500 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.91500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.13500 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 PHE A 10 56.96 -116.79 REMARK 500 TRP A 109 140.92 84.05 REMARK 500 ASN A 187 38.67 -159.40 REMARK 500 ASN A 226 33.17 -97.19 REMARK 500 REMARK 500 REMARK: NULL DBREF 8X2V A 0 231 PDB 8X2V 8X2V 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 SER 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 ASN TYR TYR SEQRES 17 A 232 LYS ASP 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 *134(H2 O) HELIX 1 AA1 SER A 2 PHE A 10 1 9 HELIX 2 AA2 THR A 18 SER A 28 1 11 HELIX 3 AA3 ASP A 37 SER 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 2.10 CISPEP 1 SER A 151 PRO A 152 0 12.92 CRYST1 37.290 69.830 70.270 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 0.026817 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014320 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014231 0.00000