HEADER HYDROLASE 05-FEB-22 7TVP TITLE VIRAL AMG CHITOSANASE V-CSN, E157Q MUTANT, CHITOTRIOSE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: VIRAL CHITOSANASE V-CSN E157Q MUTANT CHITOTRIOSE COMPLEX; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES; COMPND 6 OTHER_DETAILS: N-TERMINAL H 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 MUTANT, CHITOSAN COMPLEX, 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 18-OCT-23 7TVP 1 REMARK REVDAT 1 05-OCT-22 7TVP 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. 1.30 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.13 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.380 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 55326 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.134 REMARK 3 R VALUE (WORKING SET) : 0.132 REMARK 3 FREE R VALUE : 0.164 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 2759 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 37.1300 - 3.5300 0.98 2748 134 0.1324 0.1272 REMARK 3 2 3.5300 - 2.8000 0.99 2693 131 0.1283 0.1620 REMARK 3 3 2.8000 - 2.4500 0.98 2650 138 0.1396 0.1742 REMARK 3 4 2.4500 - 2.2200 0.99 2677 135 0.1281 0.1709 REMARK 3 5 2.2200 - 2.0600 0.99 2628 141 0.1185 0.1278 REMARK 3 6 2.0600 - 1.9400 0.97 2644 136 0.1159 0.1624 REMARK 3 7 1.9400 - 1.8400 0.97 2624 118 0.1202 0.1411 REMARK 3 8 1.8400 - 1.7600 0.99 2635 141 0.1262 0.1862 REMARK 3 9 1.7600 - 1.7000 0.99 2613 160 0.1153 0.1684 REMARK 3 10 1.7000 - 1.6400 0.99 2695 132 0.1130 0.1638 REMARK 3 11 1.6400 - 1.5900 0.99 2648 150 0.1127 0.1576 REMARK 3 12 1.5900 - 1.5400 0.96 2560 131 0.1162 0.1714 REMARK 3 13 1.5400 - 1.5000 0.98 2611 149 0.1190 0.1741 REMARK 3 14 1.5000 - 1.4600 0.98 2603 135 0.1326 0.1668 REMARK 3 15 1.4600 - 1.4300 0.98 2626 140 0.1446 0.1945 REMARK 3 16 1.4300 - 1.4000 0.99 2639 143 0.1582 0.2055 REMARK 3 17 1.4000 - 1.3700 0.99 2646 128 0.1716 0.2484 REMARK 3 18 1.3700 - 1.3500 0.96 2555 130 0.1872 0.2376 REMARK 3 19 1.3500 - 1.3200 0.96 2545 160 0.2059 0.2545 REMARK 3 20 1.3200 - 1.3000 0.95 2527 127 0.2321 0.2335 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.20 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 7TVP 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_1000262987. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-NOV-21 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 : 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) : 0.97946 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 : 55448 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 37.130 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.9 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 : 1.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 7TVL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 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 54.46950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.71050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 54.46950 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.71050 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10160 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 721 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 726 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 VAL A 191 -63.23 -140.03 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 726 DISTANCE = 5.83 ANGSTROMS REMARK 525 HOH A 727 DISTANCE = 6.27 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7TVL RELATED DB: PDB REMARK 900 RELATED ID: 7TVM RELATED DB: PDB REMARK 900 RELATED ID: 7TVN RELATED DB: PDB REMARK 900 RELATED ID: 7TVO RELATED DB: PDB DBREF 7TVP A 0 224 PDB 7TVP 7TVP 0 224 SEQRES 1 A 225 HIS MET SER GLU LEU SER GLU ILE ASP SER VAL ALA GLY SEQRES 2 A 225 VAL THR ILE TYR SER VAL ASP GLY GLU PRO LYS SER PHE SEQRES 3 A 225 VAL TYR LYS ALA GLY PHE ALA ILE ASP ALA ASP GLY ALA SEQRES 4 A 225 PRO ASN ALA TYR ALA PRO ASN ASN GLY GLY THR ASP PHE SEQRES 5 A 225 THR ALA ASN GLY GLY ASP ASP GLN GLY GLY ASP TRP TRP SEQRES 6 A 225 GLY GLY PRO VAL ASP ALA GLU GLY TYR PRO ILE LYS GLN SEQRES 7 A 225 LYS ILE PHE ASP PRO PHE PRO GLY TYR TYR VAL SER ALA SEQRES 8 A 225 THR ALA HIS PHE ASN PRO ALA TYR SER GLU ASP SER PRO SEQRES 9 A 225 TYR ARG TYR ILE ASP SER ASN SER ILE PRO PHE ILE VAL SEQRES 10 A 225 LEU PRO GLY ASN HIS SER ASN GLY ALA LYS LEU GLY ASP SEQRES 11 A 225 VAL ALA LEU VAL TYR ASN GLU LYS THR GLY ASP ASN CYS SEQRES 12 A 225 TYR ALA ILE TYR GLY ASP VAL GLY PRO SER SER LYS ILE SEQRES 13 A 225 GLY GLN GLY SER VAL ARG LEU ALA GLN ALA LEU LYS ILE SEQRES 14 A 225 ASP ASP ASN PRO LYS ALA GLY GLY THR GLU SER ARG ILE SEQRES 15 A 225 VAL VAL THR LEU VAL PHE PRO GLY SER VAL GLY LYS TRP SEQRES 16 A 225 GLU THR PRO LYS ARG TRP PHE SER HIS ALA ASN GLN LEU SEQRES 17 A 225 THR LYS ALA TRP GLY GLY LEU SER ARG LEU LYS THR LEU SEQRES 18 A 225 SER ASP GLN LEU HET GCS B 1 12 HET GCS B 2 11 HET GCS B 3 11 HET GOL A 301 6 HET GOL A 302 6 HETNAM GCS 2-AMINO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM GOL GLYCEROL HETSYN GCS BETA-D-GLUCOSAMINE; 2-AMINO-2-DEOXY-BETA-D-GLUCOSE; 2- HETSYN 2 GCS AMINO-2-DEOXY-D-GLUCOSE; 2-AMINO-2-DEOXY-GLUCOSE; D- HETSYN 3 GCS GLUCOSAMINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GCS 3(C6 H13 N O5) FORMUL 3 GOL 2(C3 H8 O3) FORMUL 5 HOH *327(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 GLN A 157 SER A 159 -1 O GLN 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 LINK O4 GCS B 1 C1 GCS B 2 1555 1555 1.44 LINK O4 GCS B 2 C1 GCS B 3 1555 1555 1.44 CISPEP 1 GLU A 21 PRO A 22 0 -3.98 CRYST1 108.939 47.421 45.402 90.00 97.83 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 0.009179 0.000000 0.001262 0.00000 SCALE2 0.000000 0.021088 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022233 0.00000