HEADER HYDROLASE 07-DEC-22 8HNF TITLE CRYSTAL STRUCTURE OF THE ANCESTRAL GH19 CHITINASE ANC5 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ANC5, 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 8HNF 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. 1.57 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) : 1.57 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 28607 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.176 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 1435 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 38.6900 - 3.3800 0.99 2766 146 0.1570 0.1580 REMARK 3 2 3.3800 - 2.6900 1.00 2754 132 0.1711 0.1892 REMARK 3 3 2.6900 - 2.3500 1.00 2722 147 0.1628 0.1888 REMARK 3 4 2.3500 - 2.1300 1.00 2748 119 0.1676 0.2005 REMARK 3 5 2.1300 - 1.9800 1.00 2737 130 0.1695 0.2238 REMARK 3 6 1.9800 - 1.8600 1.00 2683 177 0.1964 0.2354 REMARK 3 7 1.8600 - 1.7700 1.00 2709 144 0.1945 0.2575 REMARK 3 8 1.7700 - 1.6900 1.00 2706 166 0.2222 0.2932 REMARK 3 9 1.6900 - 1.6300 1.00 2706 144 0.2680 0.3316 REMARK 3 10 1.6300 - 1.5700 0.97 2641 130 0.3248 0.3565 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) : 0.219 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.809 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.28 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 : 0.010 1967 REMARK 3 ANGLE : 1.092 2678 REMARK 3 CHIRALITY : 0.056 264 REMARK 3 PLANARITY : 0.012 354 REMARK 3 DIHEDRAL : 12.860 287 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 8HNF 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_1300034000. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAY-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 : BL41XU 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 : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28613 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.570 REMARK 200 RESOLUTION RANGE LOW (A) : 38.690 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 2.000 REMARK 200 R MERGE (I) : 0.06581 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.3600 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) : 1.63 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.48420 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 (%): 38.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 27% (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 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 36.71350 REMARK 290 SMTRY3 2 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 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 GLY A 238 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE2 GLU A 208 OH TYR A 232 2.14 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O PRO A 68 OG SER A 158 1554 2.06 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 LEU A 10 59.36 -101.01 REMARK 500 TRP A 116 141.35 90.63 REMARK 500 GLN A 157 64.29 -115.62 REMARK 500 SER A 158 124.59 58.77 REMARK 500 ASN A 194 36.64 -155.70 REMARK 500 LYS A 201 21.85 -145.97 REMARK 500 REMARK 500 REMARK: NULL DBREF 8HNF A 0 238 PDB 8HNF 8HNF 0 238 SEQRES 1 A 239 MET ILE SER ARG SER MET PHE ASP GLN LEU LEU LYS HIS SEQRES 2 A 239 ARG ASN ASP GLY ALA CYS PRO ALA LYS GLY PHE TYR THR SEQRES 3 A 239 TYR ASP ALA PHE ILE ALA ALA ALA LYS SER PHE PRO SER SEQRES 4 A 239 PHE GLY THR THR GLY ASP THR ASP VAL ARG LYS ARG GLU SEQRES 5 A 239 ILE ALA ALA PHE LEU GLY GLN THR SER HIS GLU THR THR SEQRES 6 A 239 GLY GLY TRP PRO THR ALA PRO ASP GLY PRO TYR ALA TRP SEQRES 7 A 239 GLY TYR CYS PHE LEU LYS GLU ILE ASN PRO SER SER ASP SEQRES 8 A 239 TYR CYS ASP PRO SER PRO GLN TYR PRO CYS ALA PRO GLY SEQRES 9 A 239 LYS GLN TYR TYR GLY ARG GLY PRO ILE GLN LEU SER TRP SEQRES 10 A 239 ASN TYR ASN TYR GLY PRO CYS GLY GLU ALA LEU GLY VAL SEQRES 11 A 239 ASP LEU LEU ASN ASN PRO ASP LEU VAL ALA THR ASP PRO SEQRES 12 A 239 VAL ILE SER PHE LYS THR ALA LEU TRP PHE TRP MET THR SEQRES 13 A 239 PRO GLN SER PRO LYS PRO SER CYS HIS ASP VAL ILE THR SEQRES 14 A 239 GLY ARG TRP THR PRO SER ALA ALA ASP ARG ALA ALA GLY SEQRES 15 A 239 ARG VAL PRO GLY TYR GLY VAL ILE THR ASN ILE ILE ASN SEQRES 16 A 239 GLY GLY LEU GLU CYS GLY LYS GLY PRO ASP ALA GLN VAL SEQRES 17 A 239 GLU ASP ARG ILE GLY PHE TYR LYS ARG TYR CYS ASP ILE SEQRES 18 A 239 LEU GLY VAL SER TYR GLY ASN ASN LEU ASP CYS TYR ASN SEQRES 19 A 239 GLN ARG PRO PHE GLY HET MES A 301 25 HET 1PG A 302 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 C6 H13 N O4 S FORMUL 3 1PG C11 H24 O6 FORMUL 4 HOH *86(H2 O) HELIX 1 AA1 SER A 2 LEU A 10 1 9 HELIX 2 AA2 THR A 25 SER A 35 1 11 HELIX 3 AA3 ASP A 44 THR A 63 1 20 HELIX 4 AA4 GLY A 73 TRP A 77 5 5 HELIX 5 AA5 TRP A 116 GLY A 128 1 13 HELIX 6 AA6 ASN A 134 THR A 140 5 7 HELIX 7 AA7 ASP A 141 THR A 155 1 15 HELIX 8 AA8 SER A 162 THR A 168 1 7 HELIX 9 AA9 SER A 174 ALA A 180 1 7 HELIX 10 AB1 GLY A 185 CYS A 199 1 15 HELIX 11 AB2 ASP A 204 GLY A 222 1 19 SSBOND 1 CYS A 18 CYS A 80 1555 1555 2.07 SSBOND 2 CYS A 92 CYS A 100 1555 1555 2.04 SSBOND 3 CYS A 199 CYS A 231 1555 1555 2.09 CISPEP 1 SER A 158 PRO A 159 0 6.57 CISPEP 2 SER A 158 PRO A 159 0 1.70 CRYST1 36.888 73.427 39.279 90.00 99.97 90.00 P 1 21 1 2 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 0.027109 0.000000 0.004765 0.00000 SCALE2 0.000000 0.013619 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025849 0.00000