HEADER HYDROLASE 23-NOV-19 6LDU TITLE CRYSTAL STRUCTURE OF CECHT1, A NEMATODE I FAMILY CHITINASE FROM C. TITLE 2 ELEGANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE ENDOCHITINASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.14; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_TAXID: 6239; SOURCE 4 GENE: CHT-1, C04F6.3; SOURCE 5 EXPRESSION_SYSTEM: KOMAGATAELLA PHAFFII GS115; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 644223 KEYWDS NEMATODE CHITINASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Q.CHEN,Q.YANG,Y.ZHOU REVDAT 3 30-OCT-24 6LDU 1 REMARK REVDAT 2 22-NOV-23 6LDU 1 REMARK REVDAT 1 26-MAY-21 6LDU 0 JRNL AUTH Q.CHEN,Q.YANG,Y.ZHOU JRNL TITL CRYSTAL STRUCTURE OF CECHT1, A NEMATODE I FAMILY CHITINASE JRNL TITL 2 FROM C. ELEGANS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.11.1_2575 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.93 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 38049 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.256 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 42.9266 - 4.0988 0.95 2545 142 0.1731 0.2129 REMARK 3 2 4.0988 - 3.2537 0.96 2535 140 0.1553 0.1867 REMARK 3 3 3.2537 - 2.8425 0.99 2575 142 0.1671 0.1856 REMARK 3 4 2.8425 - 2.5827 0.99 2599 145 0.1647 0.2015 REMARK 3 5 2.5827 - 2.3976 0.99 2602 145 0.1673 0.2136 REMARK 3 6 2.3976 - 2.2562 0.99 2594 143 0.1649 0.2104 REMARK 3 7 2.2562 - 2.1432 1.00 2579 143 0.1549 0.2160 REMARK 3 8 2.1432 - 2.0499 0.99 2600 145 0.1572 0.1936 REMARK 3 9 2.0499 - 1.9710 1.00 2592 144 0.1612 0.2403 REMARK 3 10 1.9710 - 1.9030 1.00 2589 143 0.1631 0.2232 REMARK 3 11 1.9030 - 1.8435 1.00 2590 144 0.1734 0.2299 REMARK 3 12 1.8435 - 1.7908 0.99 2582 143 0.1773 0.2266 REMARK 3 13 1.7908 - 1.7437 0.99 2587 143 0.1870 0.2589 REMARK 3 14 1.7437 - 1.7011 0.96 2480 138 0.1927 0.2264 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.163 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.199 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.55 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 3113 REMARK 3 ANGLE : 0.906 4240 REMARK 3 CHIRALITY : 0.059 435 REMARK 3 PLANARITY : 0.006 546 REMARK 3 DIHEDRAL : 16.327 1081 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 6LDU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 03-DEC-19. REMARK 100 THE DEPOSITION ID IS D_1300014539. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JAN-16 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 : SSRF REMARK 200 BEAMLINE : BL18U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9778 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 38049 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.08300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.1990 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.40100 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: 3W4R REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3.350, TRIS, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K 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 33.46750 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14750 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 KCAL/MOL 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 TYR A 76 -2.67 83.47 REMARK 500 ASP A 157 58.42 -119.13 REMARK 500 THR A 298 -163.95 -72.39 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 A1093 DISTANCE = 6.07 ANGSTROMS DBREF 6LDU A 32 413 UNP Q11174 CHIT_CAEEL 52 433 SEQADV 6LDU HIS A 414 UNP Q11174 EXPRESSION TAG SEQRES 1 A 383 SER TYR ILE ARG PRO CYS TYR PHE THR ASN TRP ALA GLN SEQRES 2 A 383 TYR ARG GLN GLY ARG ALA LYS PHE VAL PRO GLU ASP TYR SEQRES 3 A 383 THR PRO GLY LEU CYS THR HIS ILE LEU PHE ALA PHE GLY SEQRES 4 A 383 TRP MET ASN ALA ASP TYR THR VAL ARG ALA TYR ASP PRO SEQRES 5 A 383 ALA ASP LEU PRO ASN ASP TRP ALA GLY GLU GLY MET TYR SEQRES 6 A 383 ARG ARG VAL ASN LYS LEU LYS VAL THR ASP THR GLN LEU SEQRES 7 A 383 LYS THR LEU LEU SER PHE GLY GLY TRP SER PHE GLY THR SEQRES 8 A 383 ALA LEU PHE GLN GLY MET ALA ALA SER SER ALA SER ARG SEQRES 9 A 383 LYS VAL PHE ILE ASP SER ALA ILE THR PHE VAL ARG THR SEQRES 10 A 383 TRP GLY PHE ASP GLY ILE ASP ILE ASP TRP GLU TYR PRO SEQRES 11 A 383 SER GLY ALA THR ASP MET ALA ASN TYR VAL ALA LEU VAL SEQRES 12 A 383 LYS GLU LEU LYS ALA ALA CYS GLU SER GLU ALA GLY SER SEQRES 13 A 383 THR GLY LYS ASP ARG LEU LEU VAL THR ALA ALA VAL ALA SEQRES 14 A 383 ALA GLY PRO ALA THR ILE ASP ALA GLY TYR ASP ILE PRO SEQRES 15 A 383 ASN LEU ALA PRO ASN PHE ASP PHE ILE LEU LEU MET SER SEQRES 16 A 383 TYR ASP PHE PHE GLY ALA TRP ALA SER LEU VAL GLY PHE SEQRES 17 A 383 ASN SER PRO LEU TYR ALA THR THR GLU LEU PRO ALA GLU SEQRES 18 A 383 TRP ASN GLY TRP ASN VAL ASP SER SER ALA ARG TYR TRP SEQRES 19 A 383 ASN GLN LYS GLY MET PRO LYS GLU LYS ILE ILE VAL GLY SEQRES 20 A 383 MET PRO THR TYR GLY ARG GLY TRP THR LEU ASN ASN ALA SEQRES 21 A 383 SER ALA ILE ASN PRO GLY THR SER GLY SER PRO ALA LYS SEQRES 22 A 383 ILE THR GLN TYR VAL GLN GLU ALA GLY VAL GLY ALA TYR SEQRES 23 A 383 PHE GLU PHE CYS GLU MET LEU ALA ASN GLY ALA THR ARG SEQRES 24 A 383 TYR TRP ASP SER GLN SER GLN VAL PRO TYR LEU VAL GLN SEQRES 25 A 383 GLY ASN GLN TRP TRP SER TYR ASP ASP GLU GLU SER PHE SEQRES 26 A 383 ALA ASN LYS MET ALA TYR VAL LYS ARG GLU GLY TYR GLY SEQRES 27 A 383 GLY ALA PHE VAL TRP THR LEU ASP PHE ASP ASP PHE ASN SEQRES 28 A 383 ALA GLY CYS SER ASN SER ASN GLY GLN LEU TYR PRO LEU SEQRES 29 A 383 ILE SER VAL ILE ALA LYS GLU LEU GLY GLY VAL ILE ILE SEQRES 30 A 383 PRO LYS LYS GLY GLY HIS HET NAG A 501 14 HET GOL A 502 6 HET GOL A 503 6 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM GOL GLYCEROL HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NAG C8 H15 N O6 FORMUL 3 GOL 2(C3 H8 O3) FORMUL 5 HOH *493(H2 O) HELIX 1 AA1 TRP A 42 ARG A 46 5 5 HELIX 2 AA2 GLN A 47 LYS A 51 5 5 HELIX 3 AA3 VAL A 53 TYR A 57 5 5 HELIX 4 AA4 ASP A 82 LEU A 86 5 5 HELIX 5 AA5 GLY A 94 LYS A 101 1 8 HELIX 6 AA6 LYS A 101 ASP A 106 1 6 HELIX 7 AA7 THR A 122 ALA A 129 1 8 HELIX 8 AA8 SER A 131 GLY A 150 1 20 HELIX 9 AA9 GLY A 163 GLY A 189 1 27 HELIX 10 AB1 GLY A 202 TYR A 210 1 9 HELIX 11 AB2 ASP A 211 ALA A 216 1 6 HELIX 12 AB3 PRO A 217 PHE A 219 5 3 HELIX 13 AB4 PRO A 250 ASN A 254 5 5 HELIX 14 AB5 ASN A 257 LYS A 268 1 12 HELIX 15 AB6 PRO A 271 GLU A 273 5 3 HELIX 16 AB7 TYR A 317 ASN A 326 1 10 HELIX 17 AB8 ASP A 352 GLY A 367 1 16 HELIX 18 AB9 THR A 375 ASP A 379 5 5 HELIX 19 AC1 LEU A 395 GLY A 405 1 11 SHEET 1 AA110 VAL A 78 ALA A 80 0 SHEET 2 AA110 HIS A 64 MET A 72 -1 N TRP A 71 O ARG A 79 SHEET 3 AA110 LYS A 110 GLY A 116 1 O SER A 114 N GLY A 70 SHEET 4 AA110 GLY A 153 ASP A 157 1 O ASP A 157 N PHE A 115 SHEET 5 AA110 LEU A 194 VAL A 199 1 O LEU A 194 N ILE A 154 SHEET 6 AA110 PHE A 221 LEU A 224 1 O LEU A 223 N ALA A 197 SHEET 7 AA110 ILE A 275 PRO A 280 1 O ILE A 276 N LEU A 224 SHEET 8 AA110 GLY A 370 TRP A 374 1 O PHE A 372 N MET A 279 SHEET 9 AA110 PRO A 36 THR A 40 1 N TYR A 38 O VAL A 373 SHEET 10 AA110 HIS A 64 MET A 72 1 O ALA A 68 N PHE A 39 SHEET 1 AA2 3 GLY A 300 PRO A 302 0 SHEET 2 AA2 3 TYR A 282 LEU A 288 -1 N THR A 287 O SER A 301 SHEET 3 AA2 3 VAL A 314 ALA A 316 -1 O GLY A 315 N GLY A 283 SHEET 1 AA3 5 GLY A 300 PRO A 302 0 SHEET 2 AA3 5 TYR A 282 LEU A 288 -1 N THR A 287 O SER A 301 SHEET 3 AA3 5 GLN A 346 SER A 349 -1 O SER A 349 N ARG A 284 SHEET 4 AA3 5 VAL A 338 GLN A 343 -1 N GLN A 343 O GLN A 346 SHEET 5 AA3 5 THR A 329 ASP A 333 -1 N TYR A 331 O TYR A 340 SSBOND 1 CYS A 37 CYS A 62 1555 1555 2.02 SSBOND 2 CYS A 321 CYS A 385 1555 1555 2.05 LINK ND2 ASN A 290 C1 NAG A 501 1555 1555 1.43 CISPEP 1 ALA A 68 PHE A 69 0 1.86 CISPEP 2 GLU A 159 TYR A 160 0 5.35 CISPEP 3 TRP A 374 THR A 375 0 2.66 CRYST1 47.571 66.935 57.352 90.00 102.71 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 0.021021 0.000000 0.004741 0.00000 SCALE2 0.000000 0.014940 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017874 0.00000