HEADER HYDROLASE 21-DEC-12 4IJ4 TITLE CRYSTAL STRUCTURE OF A FAMILY GH19 CHITINASE FROM BRYUM CORONATUM IN TITLE 2 COMPLEX WITH (GLCNAC)4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHITINASE A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 25-228; COMPND 5 SYNONYM: FAMILY GH19 CHITINASE; COMPND 6 EC: 3.2.1.14; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BRYUM CORONATUM; SOURCE 3 ORGANISM_TAXID: 216087; SOURCE 4 GENE: BCCHIA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-22B KEYWDS CHITINASE, HYDROLASE, CARBOHYDRATE EXPDTA X-RAY DIFFRACTION AUTHOR T.NUMATA,N.UMEMOTO,T.OHNUMA,T.FUKAMIZO REVDAT 3 24-AUG-22 4IJ4 1 JRNL HETSYN REVDAT 2 29-JUL-20 4IJ4 1 COMPND REMARK SEQADV HETNAM REVDAT 2 2 1 LINK SITE ATOM REVDAT 1 26-MAR-14 4IJ4 0 JRNL AUTH T.OHNUMA,N.UMEMOTO,T.NAGATA,S.SHINYA,T.NUMATA,T.TAIRA, JRNL AUTH 2 T.FUKAMIZO JRNL TITL CRYSTAL STRUCTURE OF A "LOOPLESS" GH19 CHITINASE IN COMPLEX JRNL TITL 2 WITH CHITIN TETRASACCHARIDE SPANNING THE CATALYTIC CENTER. JRNL REF BIOCHIM.BIOPHYS.ACTA V.1844 793 2014 JRNL REFN ISSN 0006-3002 JRNL PMID 24582745 JRNL DOI 10.1016/J.BBAPAP.2014.02.013 REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.09 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1496373.830 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 25437 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1272 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.58 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.68 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.90 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3959 REMARK 3 BIN R VALUE (WORKING SET) : 0.1550 REMARK 3 BIN FREE R VALUE : 0.1850 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 183 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.014 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1575 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 73 REMARK 3 SOLVENT ATOMS : 257 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 10.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.38000 REMARK 3 B22 (A**2) : -1.27000 REMARK 3 B33 (A**2) : -2.11000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.62000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.13 REMARK 3 ESD FROM SIGMAA (A) : -0.0 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.400 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.970 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 39.77 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 4 : EDO.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 4 : EDO.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 4IJ4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JAN-13. REMARK 100 THE DEPOSITION ID IS D_1000076816. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUL-11 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97932 REMARK 200 MONOCHROMATOR : NUMERICAL LINK TYPE SI(111) REMARK 200 DOUBLE CRYSTAL MONOCHROMATER, REMARK 200 LIQUID NITROGEN COOLING REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25456 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 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 (%) : 99.7 REMARK 200 DATA REDUNDANCY : 13.50 REMARK 200 R MERGE (I) : 0.11900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 43.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.7 REMARK 200 DATA REDUNDANCY IN SHELL : 10.00 REMARK 200 R MERGE FOR SHELL (I) : 0.28100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SNB REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.09M TRIS-HCL(PH8.5), 1.35M DI REMARK 280 -AMMONIUM HYDROGEN PHOSPHATE, 0.001 M COBALT(II) CHRORIDE, 0.01M REMARK 280 SODIUM ACETATE(PH4.6), 0.1M 1,6-HEXANEDIOL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K 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 37.27300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.20000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 37.27300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.20000 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 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 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 MSE A 1 REMARK 465 GLN A 74 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 O4 NAG B 2 O5 NAG B 3 2.16 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 TRP A 103 141.62 80.68 REMARK 500 ASP A 117 44.94 -79.43 REMARK 500 ASP A 144 33.50 71.05 REMARK 500 ASN A 164 38.91 -161.03 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3WH1 RELATED DB: PDB DBREF 4IJ4 A 2 205 UNP A9ZSX9 A9ZSX9_9BRYO 25 228 SEQADV 4IJ4 MSE A 1 UNP A9ZSX9 EXPRESSION TAG SEQADV 4IJ4 ALA A 61 UNP A9ZSX9 GLU 84 ENGINEERED MUTATION SEQRES 1 A 205 MSE SER TRP THR SER PHE VAL THR PRO ALA VAL PHE GLU SEQRES 2 A 205 GLY TRP PHE PRO ASN ARG ASN PRO PHE TYR THR TYR ASP SEQRES 3 A 205 GLY LEU VAL SER ALA SER ASN GLY TYR PRO GLU PHE GLY SEQRES 4 A 205 THR THR GLY SER LEU ASP ASP GLN LYS ARG GLU LEU ALA SEQRES 5 A 205 ALA PHE LEU GLY ASN ILE ASN GLN ALA SER GLY GLY LEU SEQRES 6 A 205 GLN PHE ILE GLN GLU GLN ASN PRO GLN SER ASP TYR CYS SEQRES 7 A 205 ASP THR SER SER THR GLN TYR PRO CYS ALA ALA GLY LYS SEQRES 8 A 205 GLN TYR TYR GLY ARG GLY PRO ILE GLN LEU SER TRP ASN SEQRES 9 A 205 TYR ASN TYR GLY GLU ALA GLY ALA ASP LEU GLY LEU ASP SEQRES 10 A 205 LEU LEU ASN ASN PRO ASP LEU VAL ALA GLN ASP SER THR SEQRES 11 A 205 VAL ALA TRP ARG THR ALA LEU TRP PHE TRP MSE LYS ARG SEQRES 12 A 205 ASP CYS HIS GLY ALA ILE THR ALA SER PRO PRO SER PHE SEQRES 13 A 205 SER GLY THR ILE ARG ILE ILE ASN GLY GLY LEU GLU CYS SEQRES 14 A 205 ASN GLN PRO ALA GLY SER ILE GLY ASN MSE GLN MSE GLU SEQRES 15 A 205 ASN ARG VAL THR TYR TYR THR GLN PHE CYS GLN THR LEU SEQRES 16 A 205 GLY VAL ASP PRO GLY THR ASP LEU ARG CYS MODRES 4IJ4 MSE A 141 MET SELENOMETHIONINE MODRES 4IJ4 MSE A 179 MET SELENOMETHIONINE MODRES 4IJ4 MSE A 181 MET SELENOMETHIONINE HET MSE A 141 8 HET MSE A 179 8 HET MSE A 181 8 HET NAG B 1 15 HET NAG B 2 14 HET NAG B 3 14 HET NAG B 4 14 HET EDO A 305 4 HET EDO A 306 4 HET EDO A 307 4 HET EDO A 308 4 HETNAM MSE SELENOMETHIONINE HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM EDO 1,2-ETHANEDIOL 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 EDO ETHYLENE GLYCOL FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 NAG 4(C8 H15 N O6) FORMUL 3 EDO 4(C2 H6 O2) FORMUL 7 HOH *257(H2 O) HELIX 1 1 SER A 2 PHE A 6 5 5 HELIX 2 2 THR A 8 PHE A 16 1 9 HELIX 3 3 THR A 24 ASN A 33 1 10 HELIX 4 4 SER A 43 GLY A 63 1 21 HELIX 5 5 TRP A 103 GLY A 115 1 13 HELIX 6 6 ASP A 123 ASP A 128 1 6 HELIX 7 7 ASP A 128 ARG A 143 1 16 HELIX 8 8 ASP A 144 ALA A 151 1 8 HELIX 9 9 SER A 155 CYS A 169 1 15 HELIX 10 10 SER A 175 GLY A 196 1 22 SSBOND 1 CYS A 78 CYS A 87 1555 1555 2.05 SSBOND 2 CYS A 169 CYS A 205 1555 1555 2.04 LINK C TRP A 140 N MSE A 141 1555 1555 1.33 LINK C MSE A 141 N LYS A 142 1555 1555 1.33 LINK C ASN A 178 N MSE A 179 1555 1555 1.33 LINK C MSE A 179 N GLN A 180 1555 1555 1.33 LINK C GLN A 180 N MSE A 181 1555 1555 1.33 LINK C MSE A 181 N GLU A 182 1555 1555 1.33 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.37 LINK O4 NAG B 2 C1 NAG B 3 1555 1555 1.38 LINK O4 NAG B 3 C1 NAG B 4 1555 1555 1.37 CISPEP 1 SER A 152 PRO A 153 0 0.34 CRYST1 74.546 58.400 48.066 90.00 115.62 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 0.013415 0.000000 0.006432 0.00000 SCALE2 0.000000 0.017123 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023073 0.00000