HEADER HYDROLASE 07-DEC-22 8HNE TITLE CRYSTAL STRUCTURE OF THE ANCESTRAL GH19 CHITINASE ANC4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANC4, ANCESTRAL 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 13-DEC-23 8HNE 0 JRNL AUTH D.KOZOME,P.LAURINO JRNL TITL EMERGENCE OF ANTIFUNGAL ACTIVITY IN GH19 CHITINASES THROUGH JRNL TITL 2 GAIN-OF-FUNCTION IN A REMOTE LOOP. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.13 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) : 1.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.47 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 73261 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.241 REMARK 3 R VALUE (WORKING SET) : 0.241 REMARK 3 FREE R VALUE : 0.251 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.730 REMARK 3 FREE R VALUE TEST SET COUNT : 2002 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 39.4700 - 2.7200 1.00 5427 150 0.2357 0.2250 REMARK 3 2 2.7200 - 2.1600 1.00 5196 149 0.2576 0.2953 REMARK 3 3 2.1600 - 1.8900 1.00 5126 143 0.2691 0.2740 REMARK 3 4 1.8900 - 1.7200 1.00 5148 143 0.2678 0.2600 REMARK 3 5 1.7200 - 1.5900 1.00 5108 146 0.2476 0.2653 REMARK 3 6 1.5900 - 1.5000 1.00 5096 141 0.2358 0.2513 REMARK 3 7 1.5000 - 1.4200 1.00 5075 150 0.2262 0.2304 REMARK 3 8 1.4200 - 1.3600 1.00 5058 141 0.2184 0.2482 REMARK 3 9 1.3600 - 1.3100 1.00 5068 140 0.2132 0.2328 REMARK 3 10 1.3100 - 1.2600 1.00 5055 140 0.2100 0.2162 REMARK 3 11 1.2600 - 1.2200 1.00 5042 143 0.2127 0.2370 REMARK 3 12 1.2200 - 1.1900 1.00 5011 144 0.2120 0.2169 REMARK 3 13 1.1900 - 1.1600 1.00 5045 143 0.2221 0.2394 REMARK 3 14 1.1600 - 1.1300 0.95 4804 129 0.2466 0.2659 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) : 0.118 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.023 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 8.18 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.88 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 1793 REMARK 3 ANGLE : 1.091 2441 REMARK 3 CHIRALITY : 0.075 245 REMARK 3 PLANARITY : 0.009 324 REMARK 3 DIHEDRAL : 11.608 270 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 8HNE COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-DEC-22. REMARK 100 THE DEPOSITION ID IS D_1300033998. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-APR-22 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 : BL45XU 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 PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 73261 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.130 REMARK 200 RESOLUTION RANGE LOW (A) : 39.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.17200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.1400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.13 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.17 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.22980 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 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% (W/V) POLYETHYLENE GLYCOL REMARK 280 MONOMETHYL ETHER 2000, 0.1M MES MONOHYDRATE PH 6.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 316K 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 16.07000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.46500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.12000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.46500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.07000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.12000 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 TRP A 96 138.97 83.91 REMARK 500 ASN A 174 36.62 -160.07 REMARK 500 REMARK 500 REMARK: NULL DBREF 8HNE A 0 218 PDB 8HNE 8HNE 0 218 SEQRES 1 A 219 MET VAL SER ARG SER MET PHE ASP GLN LEU PHE PRO ASN SEQRES 2 A 219 ARG ASN SER PHE TYR THR TYR ASP ALA PHE ILE ALA ALA SEQRES 3 A 219 ALA LYS SER PHE PRO SER PHE GLY THR THR GLY ASP THR SEQRES 4 A 219 ASP VAL ARG LYS ARG GLU ILE ALA ALA PHE PHE ALA HIS SEQRES 5 A 219 VAL SER HIS GLU THR SER GLY LEU VAL TYR ILE GLU GLU SEQRES 6 A 219 ILE ASN GLN SER ASN ASP TYR CYS ASP PRO SER THR GLN SEQRES 7 A 219 TYR PRO CYS ALA PRO GLY LYS GLN TYR TYR GLY ARG GLY SEQRES 8 A 219 PRO LEU GLN LEU SER TRP ASN TYR ASN TYR GLY PRO CYS SEQRES 9 A 219 GLY ASP ALA LEU GLY LEU ASP LEU LEU ASN ASN PRO ASP SEQRES 10 A 219 LEU VAL ALA GLN ASP PRO VAL ILE ALA PHE LYS THR ALA SEQRES 11 A 219 LEU TRP PHE TRP MET THR PRO GLN SER PRO LYS PRO SER SEQRES 12 A 219 CYS HIS ASP VAL MET THR GLY ASN TRP THR PRO SER SER SEQRES 13 A 219 ALA ASP LEU ALA ALA GLY ARG VAL PRO GLY PHE GLY VAL SEQRES 14 A 219 THR THR ASN ILE ILE ASN GLY GLY LEU GLU CYS GLY LYS SEQRES 15 A 219 GLY ASN PRO ALA GLN ALA GLU ASN ARG VAL ASN TYR TYR SEQRES 16 A 219 LYS ASP PHE CYS ASN GLN LEU GLY VAL SER PRO GLY SER SEQRES 17 A 219 ASN LEU ASP CYS ALA ASN MET ARG PRO PHE GLY HET MES A 301 25 HET MES A 302 25 HET 1PG A 303 41 HETNAM MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID HETNAM 1PG 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)- HETNAM 2 1PG ETHANOL FORMUL 2 MES 2(C6 H13 N O4 S) FORMUL 4 1PG C11 H24 O6 FORMUL 5 HOH *214(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 96 GLY A 108 1 13 HELIX 5 AA5 ASN A 114 GLN A 120 5 7 HELIX 6 AA6 ASP A 121 THR A 135 1 15 HELIX 7 AA7 SER A 142 THR A 148 1 7 HELIX 8 AA8 SER A 154 ALA A 160 1 7 HELIX 9 AA9 GLY A 165 CYS A 179 1 15 HELIX 10 AB1 PRO A 184 GLY A 202 1 19 SSBOND 1 CYS A 72 CYS A 80 1555 1555 2.06 SSBOND 2 CYS A 179 CYS A 211 1555 1555 2.10 CISPEP 1 SER A 138 PRO A 139 0 4.05 CRYST1 32.140 76.240 78.930 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 0.031114 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013116 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012669 0.00000