HEADER HYDROLASE 25-JUL-05 2D05 TITLE CHITOSANASE FROM BACILLUS CIRCULANS MUTANT K218P COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHITOSANASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.132; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS CIRCULANS; SOURCE 3 ORGANISM_TAXID: 1397; SOURCE 4 STRAIN: MH-K1; SOURCE 5 EXPRESSION_SYSTEM: BREVIBACILLUS CHOSHINENSIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 54911; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: HPD31 KEYWDS HYDROLASE, CHITOSAN DEGRADATION EXPDTA X-RAY DIFFRACTION AUTHOR T.FUKAMIZO,S.AMANO,K.YAMAGUCHI,T.YOSHIKAWA,T.KATSUMI,J.SAITO, AUTHOR 2 M.SUZUKI,K.MIKI,Y.NAGATA,A.ANDO REVDAT 3 10-NOV-21 2D05 1 REMARK SEQADV REVDAT 2 24-FEB-09 2D05 1 VERSN REVDAT 1 06-DEC-05 2D05 0 JRNL AUTH T.FUKAMIZO,S.AMANO,K.YAMAGUCHI,T.YOSHIKAWA,T.KATSUMI, JRNL AUTH 2 J.SAITO,M.SUZUKI,K.MIKI,Y.NAGATA,A.ANDO JRNL TITL BACILLUS CIRCULANS MH-K1 CHITOSANASE: AMINO ACID RESIDUES JRNL TITL 2 RESPONSIBLE FOR SUBSTRATE BINDING JRNL REF J.BIOCHEM.(TOKYO) V. 138 563 2005 JRNL REFN ISSN 0021-924X JRNL PMID 16272568 JRNL DOI 10.1093/JB/MVI156 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH J.SAITO,A.KITA,Y.HIGUCHI,Y.NAGATA,A.ANDO,K.MIKI REMARK 1 TITL CRYSTAL STRUCTURE OF CHITOSANASE FROM BACILLUS CIRCULANS REMARK 1 TITL 2 MH-K1 AT 1.6-A RESOLUTION AND ITS SUBSTRATE RECOGNITION REMARK 1 TITL 3 MECHANISM REMARK 1 REF J.BIOL.CHEM. V. 274 30818 1999 REMARK 1 REFN ISSN 0021-9258 REMARK 1 PMID 10521473 REMARK 1 DOI 10.1074/JBC.274.43.30818 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.I.SAITO,Y.NAGATA,A.ANDO,A.KITA,K.MIKI REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY CRYSTALLOGRAPHIC REMARK 1 TITL 2 ANALYSIS OF CHITOSANASE FROM BACILLUS CIRCULANS MH-K1 REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 51 856 1995 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 15299827 REMARK 1 DOI 10.1107/S090744499500268X REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 19435 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1036 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2035 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 200 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL 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 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2D05 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-JUL-05. REMARK 100 THE DEPOSITION ID IS D_1000024822. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19983 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 88.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 79.1 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.77 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, TRIS-HCL, PH 7.2, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 21.65000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 64.05000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.65000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 64.05000 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 S SO4 A2001 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1501 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 SER A 2 -155.12 44.06 REMARK 500 PHE A 7 -133.72 -120.00 REMARK 500 LYS A 240 51.71 -98.22 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 2001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1QGI RELATED DB: PDB DBREF 2D05 A 1 259 UNP P33673 CHIS_BACCI 43 301 SEQADV 2D05 PRO A 218 UNP P33673 LYS 260 ENGINEERED MUTATION SEQRES 1 A 259 ALA SER PRO ASP ASP ASN PHE SER PRO GLU THR LEU GLN SEQRES 2 A 259 PHE LEU ARG ASN ASN THR GLY LEU ASP GLY GLU GLN TRP SEQRES 3 A 259 ASN ASN ILE MET LYS LEU ILE ASN LYS PRO GLU GLN ASP SEQRES 4 A 259 ASP LEU ASN TRP ILE LYS TYR TYR GLY TYR CYS GLU ASP SEQRES 5 A 259 ILE GLU ASP GLU ARG GLY TYR THR ILE GLY LEU PHE GLY SEQRES 6 A 259 ALA THR THR GLY GLY SER ARG ASP THR HIS PRO ASP GLY SEQRES 7 A 259 PRO ASP LEU PHE LYS ALA TYR ASP ALA ALA LYS GLY ALA SEQRES 8 A 259 SER ASN PRO SER ALA ASP GLY ALA LEU LYS ARG LEU GLY SEQRES 9 A 259 ILE ASN GLY LYS MET LYS GLY SER ILE LEU GLU ILE LYS SEQRES 10 A 259 ASP SER GLU LYS VAL PHE CYS GLY LYS ILE LYS LYS LEU SEQRES 11 A 259 GLN ASN ASP ALA ALA TRP ARG LYS ALA MET TRP GLU THR SEQRES 12 A 259 PHE TYR ASN VAL TYR ILE ARG TYR SER VAL GLU GLN ALA SEQRES 13 A 259 ARG GLN ARG GLY PHE THR SER ALA VAL THR ILE GLY SER SEQRES 14 A 259 PHE VAL ASP THR ALA LEU ASN GLN GLY ALA THR GLY GLY SEQRES 15 A 259 SER ASP THR LEU GLN GLY LEU LEU ALA ARG SER GLY SER SEQRES 16 A 259 SER SER ASN GLU LYS THR PHE MET LYS ASN PHE HIS ALA SEQRES 17 A 259 LYS ARG THR LEU VAL VAL ASP THR ASN PRO TYR ASN LYS SEQRES 18 A 259 PRO PRO ASN GLY LYS ASN ARG VAL LYS GLN TRP ASP THR SEQRES 19 A 259 LEU VAL ASP MET GLY LYS MET ASN LEU LYS ASN VAL ASP SEQRES 20 A 259 SER GLU ILE ALA GLN VAL THR ASP TRP GLU MET LYS HET SO4 A2001 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *200(H2 O) HELIX 1 1 SER A 2 PHE A 7 5 6 HELIX 2 2 SER A 8 GLY A 20 1 13 HELIX 3 3 ASP A 22 ASP A 39 1 18 HELIX 4 4 ASN A 42 GLY A 48 5 7 HELIX 5 5 ASP A 77 LYS A 89 1 13 HELIX 6 6 SER A 95 GLY A 104 1 10 HELIX 7 7 SER A 119 LYS A 129 1 11 HELIX 8 8 ASP A 133 TYR A 148 1 16 HELIX 9 9 TYR A 148 ARG A 159 1 12 HELIX 10 10 SER A 163 GLY A 178 1 16 HELIX 11 11 THR A 185 ARG A 192 1 8 HELIX 12 12 ASN A 198 VAL A 214 1 17 HELIX 13 13 PRO A 223 MET A 238 1 16 HELIX 14 14 VAL A 246 THR A 254 1 9 SHEET 1 A 3 CYS A 50 GLU A 51 0 SHEET 2 A 3 THR A 60 ILE A 61 -1 O THR A 60 N GLU A 51 SHEET 3 A 3 ALA A 66 THR A 67 -1 O ALA A 66 N ILE A 61 SHEET 1 B 2 GLY A 107 LYS A 110 0 SHEET 2 B 2 ILE A 113 ILE A 116 -1 O GLU A 115 N LYS A 108 SSBOND 1 CYS A 50 CYS A 124 1555 1555 2.04 CISPEP 1 ASN A 217 PRO A 218 0 -0.15 CISPEP 2 PRO A 222 PRO A 223 0 -0.05 SITE 1 AC1 5 SER A 119 GLU A 120 HOH A1142 HOH A1145 SITE 2 AC1 5 HOH A1185 CRYST1 43.300 128.100 57.800 90.00 90.00 90.00 P 21 21 2 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 0.023095 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007806 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017301 0.00000