HEADER HYDROLASE 13-OCT-94 1HVM OBSLTE 11-JAN-97 1HVM 2HVM TITLE CRYSTAL STRUCTURES OF HEVAMINE, A PLANT DEFENCE PROTEIN TITLE 2 WITH CHITINASE AND LYSOZYME ACTIVITY, AND ITS COMPLEX WITH TITLE 3 AN INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEVAMINE A; COMPND 3 CHAIN: NULL; COMPND 4 EC: 3.2.1.14, 3.2.1.17; COMPND 5 OTHER_DETAILS: PLANT ENDOCHITINASE/LYSOZYME SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HEVEA BRASILIENSIS; SOURCE 3 ORGANISM_COMMON: RUBBER TREE; SOURCE 4 TISSUE: LATEX KEYWDS GLYCOSIDASE, CHITIN DEGRADATION, MULTIFUNCTIONAL ENZYME EXPDTA X-RAY DIFFRACTION AUTHOR A.C.TERWISSCHA VAN SCHELTINGA,K.H.KALK,J.J.BEINTEMA, AUTHOR 2 B.W.DIJKSTRA REVDAT 1 02-DEC-95 1HVM 0 JRNL AUTH A.C.TERWISSCHA VAN SCHELTINGA,K.H.KALK, JRNL AUTH 2 J.J.BEINTEMA,B.W.DIJKSTRA JRNL TITL CRYSTAL STRUCTURES OF HEVAMINE, A PLANT DEFENCE JRNL TITL 2 PROTEIN WITH CHITINASE AND LYSOZYME ACTIVITY, AND JRNL TITL 3 ITS COMPLEX WITH AN INHIBITOR JRNL REF STRUCTURE (LONDON) V. 2 1181 1994 JRNL REFN ASTM STRUE6 UK ISSN 0969-2126 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH H.J.ROZEBOOM,A.BUDIANI,J.J.BEINTEMA,B.W.DIJKSTRA REMARK 1 TITL CRYSTALLIZATION OF HEVAMINE, AN ENZYME WITH REMARK 1 TITL 2 LYSOZYME(SLASH)CHITINASE ACTIVITY FROM HEVEA REMARK 1 TITL 3 BRASILIENSIS LATEX REMARK 1 REF J.MOL.BIOL. V. 212 441 1990 REMARK 1 REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 1HVM REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 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) (%) : 87.8 REMARK 3 NUMBER OF REFLECTIONS : 11241 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.169 REMARK 3 FREE R VALUE : 0.261 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL 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 : 2087 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 249 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.42 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) : 0.25 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 1HVM COMPLIES WITH FORMAT V. 2.3, 09-JULY-1998 REMARK 18 REMARK 18 1HVM EXPERIMENTAL DETAILS. 1HVM DATE OF DATA COLLECTION : REMARK 18 08-12-89 1HVM MONOCHROMATIC (Y/N) : Y 1HVM LAUE (Y/N) : N REMARK 18 1HVM WAVELENGTH OR RANGE (A) : 1.54 1HVM DETECTOR TYPE : REMARK 18 FAST AREA DETECTOR 1HVM DETECTOR MANUFACTURER : ENRAF- REMARK 18 NONIUS 1HVM INTENSITY-INTEGRATION SOFTWARE : MADNES 1HVM REMARK 18 DATA REDUNDANCY : 3.6 1HVM MERGING R VALUE (INTENSITY) : REMARK 18 0.052 1HVM REMARK 19 REMARK 19 1HVM SOLVENT CONTENT (VS) : 42. % 1HVM MATTHEWS COEFFICIENT REMARK 19 (VM) : 2.14 ANGSTROMS**3/DA 1HVM REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-12-89 REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : N 1HVM REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : FAST AREA DETECTOR 1HVM REMARK 200 DETECTOR MANUFACTURER : ENRAF-NONIUS 1HVM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MADNES 1HVM REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11778 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.0 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.05200 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) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 1/2-X,-Y,1/2+Z REMARK 290 3555 -X,1/2+Y,1/2-Z REMARK 290 4555 1/2+X,1/2-Y,-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 26.15000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.02500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.86000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.02500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.15000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.86000 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 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES: ENGH AND HUBER, 1991 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PHE 32 N - CA - C ANGL. DEV. = 23.5 DEGREES REMARK 500 ALA 31 CA - C - N ANGL. DEV. =-24.4 DEGREES REMARK 500 PHE 32 C - N - CA ANGL. DEV. = 19.8 DEGREES 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 M RES CSSEQI PSI PHI REMARK 500 PHE 32 120.95 78.41 REMARK 500 SER 256 123.89 74.80 REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH 35 DISTANCE = 5.31 ANGSTROMS REMARK 525 HOH 66 DISTANCE = 6.61 ANGSTROMS REMARK 525 HOH 99 DISTANCE = 6.82 ANGSTROMS REMARK 525 HOH 110 DISTANCE = 7.98 ANGSTROMS REMARK 525 HOH 151 DISTANCE = 5.96 ANGSTROMS REMARK 525 HOH 159 DISTANCE = 6.66 ANGSTROMS REMARK 525 HOH 169 DISTANCE = 5.17 ANGSTROMS REMARK 525 HOH 179 DISTANCE = 8.37 ANGSTROMS REMARK 525 HOH 193 DISTANCE = 5.57 ANGSTROMS REMARK 525 HOH 195 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH 213 DISTANCE = 9.21 ANGSTROMS REMARK 525 HOH 215 DISTANCE = 10.41 ANGSTROMS REMARK 525 HOH 222 DISTANCE = 6.23 ANGSTROMS REMARK 525 HOH 226 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH 228 DISTANCE = 5.65 ANGSTROMS REMARK 525 HOH 233 DISTANCE = 5.24 ANGSTROMS DBREF 1HVM 1 273 UNP P23472 CHLY_HEVBR 1 273 SEQRES 1 273 GLY GLY ILE ALA ILE TYR TRP GLY GLN ASN GLY ASN GLU SEQRES 2 273 GLY THR LEU THR GLN THR CYS SER THR ARG LYS TYR SER SEQRES 3 273 TYR VAL ASN ILE ALA PHE LEU ASN LYS PHE GLY ASN GLY SEQRES 4 273 GLN THR PRO GLN ILE ASN LEU ALA GLY HIS CYS ASN PRO SEQRES 5 273 ALA ALA GLY GLY CYS THR ILE VAL SER ASN GLY ILE ARG SEQRES 6 273 SER CYS GLN ILE GLN GLY ILE LYS VAL MET LEU SER LEU SEQRES 7 273 GLY GLY GLY ILE GLY SER TYR THR LEU ALA SER GLN ALA SEQRES 8 273 ASP ALA LYS ASN VAL ALA ASP TYR LEU TRP ASN ASN PHE SEQRES 9 273 LEU GLY GLY LYS SER SER SER ARG PRO LEU GLY ASP ALA SEQRES 10 273 VAL LEU ASP GLY ILE ASP PHE ASP ILE GLU HIS GLY SER SEQRES 11 273 THR LEU TYR TRP ASP ASP LEU ALA ARG TYR LEU SER ALA SEQRES 12 273 TYR SER LYS GLN GLY LYS LYS VAL TYR LEU THR ALA ALA SEQRES 13 273 PRO GLN CYS PRO PHE PRO ASP ARG TYR LEU GLY THR ALA SEQRES 14 273 LEU ASN THR GLY LEU PHE ASP TYR VAL TRP VAL GLN PHE SEQRES 15 273 TYR ASN ASN PRO PRO CYS GLN TYR SER SER GLY ASN ILE SEQRES 16 273 ASN ASN ILE ILE ASN SER TRP ASN ARG TRP THR THR SER SEQRES 17 273 ILE ASN ALA GLY LYS ILE PHE LEU GLY LEU PRO ALA ALA SEQRES 18 273 PRO GLU ALA ALA GLY SER GLY TYR VAL PRO PRO ASP VAL SEQRES 19 273 LEU ILE SER ARG ILE LEU PRO GLU ILE LYS LYS SER PRO SEQRES 20 273 LYS TYR GLY GLY VAL MET LEU TRP SER LYS PHE TYR ASP SEQRES 21 273 ASP LYS ASN GLY TYR SER SER SER ILE LEU ASP SER VAL FTNOTE 1 CIS PROLINE - PRO 162 FORMUL 2 HOH *249(H2 O1) HELIX 1 1 ASN 10 GLY 14 5 5 HELIX 2 2 THR 15 THR 22 1 8 HELIX 3 3 LEU 46 CYS 50 5 5 HELIX 4 4 PRO 52 GLY 56 5 5 HELIX 5 5 CYS 57 THR 58 5 2 HELIX 6 6 ILE 59 GLN 70 1 12 HELIX 7 7 SER 89 LEU 105 1 17 HELIX 8 8 TYR 133 TYR 144 1 12 HELIX 9 9 SER 145 GLY 148 5 4 HELIX 10 10 LEU 166 ASN 171 1 6 HELIX 11 11 ASN 185 GLN 189 5 5 HELIX 12 12 ILE 195 ILE 209 1 15 HELIX 13 13 ALA 221 ALA 225 5 5 HELIX 14 14 PRO 231 ILE 239 1 9 HELIX 15 15 ILE 239 LYS 244 1 6 HELIX 16 16 SER 256 GLY 264 1 9 HELIX 17 17 GLY 264 LEU 270 1 7 HELIX 18 18 ASP 271 VAL 273 5 3 SHEET 1 A10 GLN 43 ILE 44 0 SHEET 2 A10 TYR 27 LYS 35 -1 N LYS 35 O GLN 43 SHEET 3 A10 LYS 73 GLY 79 1 O MET 75 N ILE 30 SHEET 4 A10 GLY 121 ASP 125 1 O ASP 123 N LEU 78 SHEET 5 A10 TYR 152 ALA 155 1 O THR 154 N ILE 122 SHEET 6 A10 TYR 177 GLN 181 1 O TRP 179 N ALA 155 SHEET 7 A10 LYS 213 PRO 219 1 O PHE 215 N VAL 178 SHEET 8 A10 TYR 249 TRP 255 1 O MET 253 N LEU 218 SHEET 9 A10 GLY 2 TRP 7 1 N ALA 4 O VAL 252 SHEET 10 A10 TYR 27 LYS 35 1 O ALA 31 N TRP 7 SSBOND 1 CYS 20 CYS 67 SSBOND 2 CYS 50 CYS 57 SSBOND 3 CYS 159 CYS 188 CISPEP 1 PHE 161 PRO 162 0 -11.70 CRYST1 52.300 57.720 82.050 90.00 90.00 90.00 P 21 21 21 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 0.019120 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017325 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012188 0.00000