HEADER HYDROLASE 10-JAN-00 1DXJ TITLE STRUCTURE OF THE CHITINASE FROM JACK BEAN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CLASS II CHITINASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.14 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CANAVALIA ENSIFORMIS; SOURCE 3 ORGANISM_COMMON: JACK BEAN; SOURCE 4 ORGANISM_TAXID: 3823; SOURCE 5 ORGAN: SEED KEYWDS HYDROLASE, FAMILY 19 GLYCOSIDASE, ALPHA HELICAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.HAHN,M.HENNIG,B.SCHLESIER,W.HOHNE REVDAT 5 16-OCT-24 1DXJ 1 REMARK REVDAT 4 06-DEC-23 1DXJ 1 REMARK REVDAT 3 08-MAY-19 1DXJ 1 REMARK REVDAT 2 24-FEB-09 1DXJ 1 VERSN REVDAT 1 29-AUG-00 1DXJ 0 JRNL AUTH M.HAHN,M.HENNIG,B.SCHLESIER,W.HOHNE JRNL TITL STRUCTURE OF JACK BEAN CHITINASE JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 56 1096 2000 JRNL REFN ISSN 0907-4449 JRNL PMID 10957628 JRNL DOI 10.1107/S090744490000857X REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.SONG REMARK 1 TITL REFINED STRUCTURE OF THE CHITINASE FROM BARLEY SEEDS AT 2.0 REMARK 1 TITL 2 A RESOLUTION REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 52 289 1996 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 15299702 REMARK 1 DOI 10.1107/S0907444995009061 REMARK 1 REFERENCE 2 REMARK 1 AUTH E.J.HARTMONZINGOREADY REMARK 1 TITL CRYSTAL STRUCTURE OF AN ENDOCHITINASE FROM HORDEUM VULGARE REMARK 1 TITL 2 L. SEEDS REMARK 1 REF J.MOL.BIOL. V. 229 189 1993 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 8421299 REMARK 1 DOI 10.1006/JMBI.1993.1017 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.30 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.2 REMARK 3 NUMBER OF REFLECTIONS : 24446 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : ALL, EXCEPT FINAL CYCLES REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2410 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 : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.60 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 : 1842 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 156 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.20 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 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) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.449 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.41 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.443 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 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DXJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 10-JAN-00. REMARK 100 THE DEPOSITION ID IS D_1290004197. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 297.0 REMARK 200 PH : 9.50 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 : NULL 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 : ENRAF NONIUS FR591 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24446 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 12.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05900 REMARK 200 FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.26800 REMARK 200 FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.1 REMARK 200 STARTING MODEL: 1CNS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.89 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN CONCENTRATION: 15 MG/ML REMARK 280 PROTEIN BUFFER: 0.1 M TRIS, PH 9.5, PRECIPITANT: 1.6 M AMMONIUM REMARK 280 SULFATE MIXING EQUAL VOLUMES IN SITTING DROPS, AT ROOM REMARK 280 TEMPERATURE, PH 9.50, VAPOR DIFFUSION, SITTING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 36.73667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 73.47333 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 55.10500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 91.84167 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 18.36833 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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 LEU A 16 57.27 -102.69 REMARK 500 HIS A 120 136.08 82.03 REMARK 500 ASN A 198 38.23 -153.45 REMARK 500 CYS A 235 28.24 -142.71 REMARK 500 PHE A 241 102.40 -49.53 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 A1244 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CNS RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CHITINASE AT 1.91A RESOLUTION (ENDOCHITINASE 2, REMARK 900 EC 3.2.1.14) REMARK 900 RELATED ID: 1CTN RELATED DB: PDB REMARK 900 CHITINASE A (E.C.3.2.1.14) (PH 5.5, 4 DEGREES C) FROM SERRATIA REMARK 900 MARCESCENS REMARK 900 RELATED ID: 1D2K RELATED DB: PDB REMARK 900 C. IMMITIS CHITINASE 1 AT 2. 2 ANGSTROMS RESOLUTION DBREF 1DXJ A 2 243 UNP O81934 O81934 29 270 SEQRES 1 A 242 ASP VAL GLY SER VAL ILE ASP ALA SER LEU PHE ASP GLN SEQRES 2 A 242 LEU LEU LYS HIS ARG ASN ASP PRO ALA CYS GLU GLY LYS SEQRES 3 A 242 GLY PHE TYR SER TYR ASN ALA PHE VAL THR ALA ALA ARG SEQRES 4 A 242 SER PHE GLY GLY PHE GLY THR THR GLY ASP THR ASN THR SEQRES 5 A 242 ARG LYS ARG GLU VAL ALA ALA PHE LEU ALA GLN THR SER SEQRES 6 A 242 HIS GLU THR THR GLY GLY ALA ALA GLY SER PRO ASP GLY SEQRES 7 A 242 PRO TYR ALA TRP GLY TYR CYS PHE VAL THR GLU ARG ASP SEQRES 8 A 242 LYS SER ASN LYS TYR CYS ASP PRO GLY THR PRO CYS PRO SEQRES 9 A 242 ALA GLY LYS SER TYR TYR GLY ARG GLY PRO ILE GLN LEU SEQRES 10 A 242 THR HIS ASN TYR ASN TYR ALA GLN ALA GLY ARG ALA LEU SEQRES 11 A 242 GLY VAL ASP LEU ILE ASN ASN PRO ASP LEU VAL ALA ARG SEQRES 12 A 242 ASP ALA VAL ILE SER PHE LYS THR ALA ILE TRP PHE TRP SEQRES 13 A 242 MET THR PRO GLN GLY ASN LYS PRO SER CYS HIS ASP VAL SEQRES 14 A 242 ILE THR ASN ARG TRP THR PRO SER ALA ALA ASP VAL ALA SEQRES 15 A 242 ALA ASN ARG THR PRO GLY PHE GLY VAL ILE THR ASN ILE SEQRES 16 A 242 ILE ASN GLY GLY ILE GLU CYS GLY ARG GLY PRO SER PRO SEQRES 17 A 242 ALA SER GLY ASP ARG ILE GLY PHE TYR LYS ARG TYR CYS SEQRES 18 A 242 ASP VAL LEU HIS LEU SER TYR GLY PRO ASN LEU ASN CYS SEQRES 19 A 242 ARG ASP GLN ARG PRO PHE GLY GLY HET SO4 A1244 5 HETNAM SO4 SULFATE ION FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *156(H2 O) HELIX 1 1 ASP A 2 VAL A 6 5 5 HELIX 2 2 ASP A 8 LEU A 16 1 9 HELIX 3 3 SER A 31 ARG A 40 1 10 HELIX 4 4 ASP A 50 THR A 69 1 20 HELIX 5 5 GLY A 79 TRP A 83 5 5 HELIX 6 6 HIS A 120 GLY A 132 1 13 HELIX 7 7 ASP A 140 ASP A 145 1 6 HELIX 8 8 ASP A 145 THR A 159 1 15 HELIX 9 9 SER A 166 THR A 172 1 7 HELIX 10 10 SER A 178 ALA A 184 1 7 HELIX 11 11 GLY A 189 GLY A 199 1 11 HELIX 12 12 ASN A 198 CYS A 203 1 6 HELIX 13 13 SER A 208 HIS A 226 1 19 SSBOND 1 CYS A 24 CYS A 86 1555 1555 2.03 SSBOND 2 CYS A 98 CYS A 104 1555 1555 2.30 SSBOND 3 CYS A 203 CYS A 235 1555 1555 2.23 SITE 1 AC1 7 ARG A 19 SER A 31 TYR A 32 ASN A 52 SITE 2 AC1 7 HOH A2026 HOH A2155 HOH A2166 CRYST1 67.690 67.690 110.210 90.00 90.00 120.00 P 61 6 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 0.014773 0.008529 0.000000 0.00000 SCALE2 0.000000 0.017059 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009074 0.00000