HEADER HYDROLASE 05-FEB-22 7TVL TITLE VIRAL AMG CHITOSANASE V-CSN, APO STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: VIRAL CHITOSANASE V-CSN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 OTHER_DETAILS: N-TERMINAL GSH FROM EXPRESSION TAG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: UNCLASSIFIED SEQUENCES; SOURCE 3 ORGANISM_TAXID: 12908; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLYCOSYL HYDROLASE, CHITOSANASE, VIRAL AUXILIARY METABOLIC GENE, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.A.SMITH,R.WU,G.W.BUCHKO,J.R.CORT,K.S.HOFMOCKEL,J.K.JANSSON REVDAT 2 22-MAY-24 7TVL 1 REMARK REVDAT 1 05-OCT-22 7TVL 0 JRNL AUTH R.WU,C.A.SMITH,G.W.BUCHKO,I.K.BLABY,D.PAEZ-ESPINO, JRNL AUTH 2 N.C.KYRPIDES,Y.YOSHIKUNI,J.E.MCDERMOTT,K.S.HOFMOCKEL, JRNL AUTH 3 J.R.CORT,J.K.JANSSON JRNL TITL STRUCTURAL CHARACTERIZATION OF A SOIL VIRAL AUXILIARY JRNL TITL 2 METABOLIC GENE PRODUCT - A FUNCTIONAL CHITOSANASE. JRNL REF NAT COMMUN V. 13 5485 2022 JRNL REFN ESSN 2041-1723 JRNL PMID 36123347 JRNL DOI 10.1038/S41467-022-32993-8 REMARK 2 REMARK 2 RESOLUTION. 0.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 0.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.18 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 174427 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.120 REMARK 3 R VALUE (WORKING SET) : 0.120 REMARK 3 FREE R VALUE : 0.131 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 8555 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 37.1800 - 2.7700 1.00 5745 303 0.1312 0.1294 REMARK 3 2 2.7700 - 2.1900 1.00 5599 305 0.1349 0.1508 REMARK 3 3 2.1900 - 1.9200 1.00 5628 304 0.1190 0.1338 REMARK 3 4 1.9200 - 1.7400 1.00 5603 287 0.1225 0.1391 REMARK 3 5 1.7400 - 1.6200 1.00 5616 290 0.1148 0.1281 REMARK 3 6 1.6200 - 1.5200 1.00 5591 276 0.1060 0.1183 REMARK 3 7 1.5200 - 1.4500 1.00 5620 274 0.1039 0.1106 REMARK 3 8 1.4500 - 1.3800 1.00 5589 280 0.1061 0.1336 REMARK 3 9 1.3800 - 1.3300 1.00 5583 313 0.1012 0.1047 REMARK 3 10 1.3300 - 1.2800 1.00 5551 294 0.0987 0.1114 REMARK 3 11 1.2800 - 1.2400 1.00 5608 275 0.0979 0.1032 REMARK 3 12 1.2400 - 1.2100 1.00 5610 253 0.0922 0.1024 REMARK 3 13 1.2100 - 1.1800 1.00 5541 302 0.0915 0.0971 REMARK 3 14 1.1800 - 1.1500 1.00 5542 279 0.0887 0.1066 REMARK 3 15 1.1500 - 1.1200 1.00 5587 266 0.0903 0.1082 REMARK 3 16 1.1200 - 1.1000 1.00 5561 298 0.0924 0.1032 REMARK 3 17 1.1000 - 1.0800 1.00 5576 268 0.0947 0.1042 REMARK 3 18 1.0800 - 1.0600 1.00 5547 279 0.1000 0.1054 REMARK 3 19 1.0600 - 1.0400 1.00 5568 278 0.1052 0.1129 REMARK 3 20 1.0400 - 1.0200 1.00 5556 308 0.1119 0.1198 REMARK 3 21 1.0200 - 1.0000 1.00 5550 295 0.1232 0.1429 REMARK 3 22 1.0000 - 0.9900 1.00 5527 270 0.1335 0.1468 REMARK 3 23 0.9900 - 0.9700 1.00 5512 305 0.1423 0.1620 REMARK 3 24 0.9700 - 0.9600 0.99 5562 277 0.1528 0.1547 REMARK 3 25 0.9600 - 0.9500 0.99 5490 266 0.1613 0.1912 REMARK 3 26 0.9500 - 0.9300 0.98 5459 306 0.1749 0.1740 REMARK 3 27 0.9300 - 0.9200 0.97 5407 282 0.1875 0.1993 REMARK 3 28 0.9200 - 0.9100 0.97 5364 284 0.1983 0.2071 REMARK 3 29 0.9100 - 0.9000 0.94 5248 269 0.2225 0.2257 REMARK 3 30 0.9000 - 0.8900 0.88 4932 269 0.2593 0.2828 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 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) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 11.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.12 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7TVL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-FEB-22. REMARK 100 THE DEPOSITION ID IS D_1000262930. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUN-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.72929 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 : 174574 REMARK 200 RESOLUTION RANGE HIGH (A) : 0.890 REMARK 200 RESOLUTION RANGE LOW (A) : 37.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 0.89 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 0.91 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: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 0.1 M SODIUM REMARK 280 ACETATE, PH 4.6, 30% PEG2000 MME, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 54.41800 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.81600 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 54.41800 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.81600 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 773 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 789 LIES ON A SPECIAL POSITION. 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 ALA A 174 2.68 -150.29 REMARK 500 VAL A 191 -63.98 -138.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 789 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH A 790 DISTANCE = 6.43 ANGSTROMS DBREF 7TVL A -2 224 PDB 7TVL 7TVL -2 224 SEQRES 1 A 227 GLY SER HIS MET SER GLU LEU SER GLU ILE ASP SER VAL SEQRES 2 A 227 ALA GLY VAL THR ILE TYR SER VAL ASP GLY GLU PRO LYS SEQRES 3 A 227 SER PHE VAL TYR LYS ALA GLY PHE ALA ILE ASP ALA ASP SEQRES 4 A 227 GLY ALA PRO ASN ALA TYR ALA PRO ASN ASN GLY GLY THR SEQRES 5 A 227 ASP PHE THR ALA ASN GLY GLY ASP ASP GLN GLY GLY ASP SEQRES 6 A 227 TRP TRP GLY GLY PRO VAL ASP ALA GLU GLY TYR PRO ILE SEQRES 7 A 227 LYS GLN LYS ILE PHE ASP PRO PHE PRO GLY TYR TYR VAL SEQRES 8 A 227 SER ALA THR ALA HIS PHE ASN PRO ALA TYR SER GLU ASP SEQRES 9 A 227 SER PRO TYR ARG TYR ILE ASP SER ASN SER ILE PRO PHE SEQRES 10 A 227 ILE VAL LEU PRO GLY ASN HIS SER ASN GLY ALA LYS LEU SEQRES 11 A 227 GLY ASP VAL ALA LEU VAL TYR ASN GLU LYS THR GLY ASP SEQRES 12 A 227 ASN CYS TYR ALA ILE TYR GLY ASP VAL GLY PRO SER SER SEQRES 13 A 227 LYS ILE GLY GLU GLY SER VAL ARG LEU ALA GLN ALA LEU SEQRES 14 A 227 LYS ILE ASP ASP ASN PRO LYS ALA GLY GLY THR GLU SER SEQRES 15 A 227 ARG ILE VAL VAL THR LEU VAL PHE PRO GLY SER VAL GLY SEQRES 16 A 227 LYS TRP GLU THR PRO LYS ARG TRP PHE SER HIS ALA ASN SEQRES 17 A 227 GLN LEU THR LYS ALA TRP GLY GLY LEU SER ARG LEU LYS SEQRES 18 A 227 THR LEU SER ASP GLN LEU HET GOL A 301 12 HET GOL A 302 6 HET GOL A 303 6 HET SO4 A 304 5 HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL 3(C3 H8 O3) FORMUL 5 SO4 O4 S 2- FORMUL 6 HOH *390(H2 O) HELIX 1 AA1 ALA A 43 GLY A 47 5 5 HELIX 2 AA2 PHE A 51 GLY A 56 5 6 HELIX 3 AA3 SER A 102 TYR A 106 5 5 HELIX 4 AA4 VAL A 160 LYS A 167 1 8 HELIX 5 AA5 THR A 196 GLY A 212 1 17 HELIX 6 AA6 GLY A 212 ASP A 222 1 11 SHEET 1 AA1 9 LEU A 4 VAL A 10 0 SHEET 2 AA1 9 VAL A 13 VAL A 18 -1 O SER A 17 N SER A 5 SHEET 3 AA1 9 PHE A 25 ASP A 34 -1 O VAL A 26 N TYR A 16 SHEET 4 AA1 9 THR A 177 VAL A 186 -1 O VAL A 186 N PHE A 25 SHEET 5 AA1 9 VAL A 130 ASN A 135 -1 N TYR A 134 O VAL A 183 SHEET 6 AA1 9 ASN A 141 GLY A 150 -1 O CYS A 142 N VAL A 133 SHEET 7 AA1 9 PHE A 114 PRO A 118 1 N ILE A 115 O ILE A 145 SHEET 8 AA1 9 GLU A 157 SER A 159 -1 O GLU A 157 N VAL A 116 SHEET 9 AA1 9 PHE A 25 ASP A 34 1 N ASP A 34 O GLY A 158 CISPEP 1 GLU A 21 PRO A 22 0 -9.21 CRYST1 108.836 47.632 45.546 90.00 97.82 90.00 C 1 2 1 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 0.009188 0.000000 0.001262 0.00000 SCALE2 0.000000 0.020994 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022162 0.00000