HEADER HYDROLASE 02-JUL-96 2HVM TITLE HEVAMINE A AT 1.8 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HEVAMINE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CHITINASE/LYSOZYME; COMPND 5 EC: 3.2.1.14, 3.2.1.17 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HEVEA BRASILIENSIS; SOURCE 3 ORGANISM_TAXID: 3981; SOURCE 4 TISSUE: LATEX KEYWDS HYDROLASE, CHITINASE/LYSOZYME EXPDTA X-RAY DIFFRACTION AUTHOR A.C.TERWISSCHA VAN SCHELTINGA,M.HENNIG,B.W.DIJKSTRA REVDAT 3 24-FEB-09 2HVM 1 VERSN REVDAT 2 01-APR-03 2HVM 1 JRNL REVDAT 1 11-JAN-97 2HVM 0 SPRSDE 11-JAN-97 2HVM 1HVM JRNL AUTH A.C.TERWISSCHA VAN SCHELTINGA,M.HENNIG,B.W.DIJKSTRA JRNL TITL THE 1.8 A RESOLUTION STRUCTURE OF HEVAMINE, A JRNL TITL 2 PLANT CHITINASE/LYSOZYME, AND ANALYSIS OF THE JRNL TITL 3 CONSERVED SEQUENCE AND STRUCTURE MOTIFS OF JRNL TITL 4 GLYCOSYL HYDROLASE FAMILY 18. JRNL REF J.MOL.BIOL. V. 262 243 1996 JRNL REFN ISSN 0022-2836 JRNL PMID 8831791 JRNL DOI 10.1006/JMBI.1996.0510 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH A.C.TERWISSCHA VAN SCHELTINGA,S.ARMAND,K.H.KALK, REMARK 1 AUTH 2 A.ISOGAI,B.HENRISSAT,B.W.DIJKSTRA REMARK 1 TITL STEREOCHEMISTRY OF CHITIN HYDROLYSIS BY A PLANT REMARK 1 TITL 2 CHITINASE/LYSOZYME AND X-RAY STRUCTURE OF A REMARK 1 TITL 3 COMPLEX WITH ALLOSAMIDIN. EVIDENCE FOR SUBSTRATE REMARK 1 TITL 4 ASSISTED CATALYSIS REMARK 1 REF BIOCHEMISTRY V. 34 15619 1995 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH A.C.TERWISSCHA VAN SCHELTINGA,K.H.KALK, REMARK 1 AUTH 2 J.J.BEINTEMA,B.W.DIJKSTRA REMARK 1 TITL CRYSTAL STRUCTURES OF HEVAMINE, A PLANT DEFENCE REMARK 1 TITL 2 PROTEIN WITH CHITINASE AND LYSOZYME ACTIVITY, AND REMARK 1 TITL 3 ITS COMPLEX WITH AN INHIBITOR REMARK 1 REF STRUCTURE V. 2 1181 1994 REMARK 1 REFN ISSN 0969-2126 REMARK 1 REFERENCE 3 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/CHITINASE ACTIVITY FROM HEVEA REMARK 1 TITL 3 BRASILIENSIS LATEX REMARK 1 REF J.MOL.BIOL. V. 212 441 1990 REMARK 1 REFN ISSN 0022-2836 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TNT REMARK 3 AUTHORS : TRONRUD,TEN EYCK,MATTHEWS REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 8.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 88.0 REMARK 3 NUMBER OF REFLECTIONS : 20520 REMARK 3 REMARK 3 USING DATA ABOVE SIGMA CUTOFF. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : 0.149 REMARK 3 R VALUE (WORKING SET) : 0.149 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 USING ALL DATA, NO SIGMA CUTOFF. REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.1480 REMARK 3 FREE R VALUE (NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 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 : 206 REMARK 3 REMARK 3 WILSON B VALUE (FROM FCALC, A**2) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. RMS WEIGHT COUNT REMARK 3 BOND LENGTHS (A) : 0.010 ; 1.300 ; 4296 REMARK 3 BOND ANGLES (DEGREES) : 1.290 ; 1.200 ; 5826 REMARK 3 TORSION ANGLES (DEGREES) : 22.900; 0.000 ; 2492 REMARK 3 PSEUDOROTATION ANGLES (DEGREES) : NULL ; NULL ; NULL REMARK 3 TRIGONAL CARBON PLANES (A) : 0.010 ; 2.000 ; 102 REMARK 3 GENERAL PLANES (A) : 0.030 ; 0.000 ; 628 REMARK 3 ISOTROPIC THERMAL FACTORS (A**2) : 2.680 ; 60.000; 2148 REMARK 3 NON-BONDED CONTACTS (A) : 0.010 ; 40.000; 57 REMARK 3 REMARK 3 INCORRECT CHIRAL-CENTERS (COUNT) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 RESTRAINT LIBRARIES. REMARK 3 STEREOCHEMISTRY : NULL REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2HVM COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : JUL-93 REMARK 200 TEMPERATURE (KELVIN) : 279 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X11 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.92 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 23188 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 4.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.05000 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 (%): 42.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.0 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 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 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 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 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 ALA A 47 -124.17 54.58 REMARK 500 SER A 84 48.30 -103.49 REMARK 500 LEU A 105 -141.78 -105.09 REMARK 500 ASP A 125 62.73 -113.50 REMARK 500 TYR A 133 -7.54 79.37 REMARK 500 PHE A 182 54.82 -90.33 REMARK 500 SER A 192 114.93 -36.46 REMARK 500 REMARK 500 REMARK: NULL DBREF 2HVM A 1 273 UNP P23472 CHLY_HEVBR 1 273 SEQRES 1 A 273 GLY GLY ILE ALA ILE TYR TRP GLY GLN ASN GLY ASN GLU SEQRES 2 A 273 GLY THR LEU THR GLN THR CYS SER THR ARG LYS TYR SER SEQRES 3 A 273 TYR VAL ASN ILE ALA PHE LEU ASN LYS PHE GLY ASN GLY SEQRES 4 A 273 GLN THR PRO GLN ILE ASN LEU ALA GLY HIS CYS ASN PRO SEQRES 5 A 273 ALA ALA GLY GLY CYS THR ILE VAL SER ASN GLY ILE ARG SEQRES 6 A 273 SER CYS GLN ILE GLN GLY ILE LYS VAL MET LEU SER LEU SEQRES 7 A 273 GLY GLY GLY ILE GLY SER TYR THR LEU ALA SER GLN ALA SEQRES 8 A 273 ASP ALA LYS ASN VAL ALA ASP TYR LEU TRP ASN ASN PHE SEQRES 9 A 273 LEU GLY GLY LYS SER SER SER ARG PRO LEU GLY ASP ALA SEQRES 10 A 273 VAL LEU ASP GLY ILE ASP PHE ASP ILE GLU HIS GLY SER SEQRES 11 A 273 THR LEU TYR TRP ASP ASP LEU ALA ARG TYR LEU SER ALA SEQRES 12 A 273 TYR SER LYS GLN GLY LYS LYS VAL TYR LEU THR ALA ALA SEQRES 13 A 273 PRO GLN CYS PRO PHE PRO ASP ARG TYR LEU GLY THR ALA SEQRES 14 A 273 LEU ASN THR GLY LEU PHE ASP TYR VAL TRP VAL GLN PHE SEQRES 15 A 273 TYR ASN ASN PRO PRO CYS GLN TYR SER SER GLY ASN ILE SEQRES 16 A 273 ASN ASN ILE ILE ASN SER TRP ASN ARG TRP THR THR SER SEQRES 17 A 273 ILE ASN ALA GLY LYS ILE PHE LEU GLY LEU PRO ALA ALA SEQRES 18 A 273 PRO GLU ALA ALA GLY SER GLY TYR VAL PRO PRO ASP VAL SEQRES 19 A 273 LEU ILE SER ARG ILE LEU PRO GLU ILE LYS LYS SER PRO SEQRES 20 A 273 LYS TYR GLY GLY VAL MET LEU TRP SER LYS PHE TYR ASP SEQRES 21 A 273 ASP LYS ASN GLY TYR SER SER SER ILE LEU ASP SER VAL FORMUL 2 HOH *206(H2 O) HELIX 1 1 GLY A 11 GLU A 13 5 3 HELIX 2 2 LEU A 16 THR A 22 1 7 HELIX 3 3 ALA A 47 HIS A 49 5 3 HELIX 4 4 ALA A 53 GLY A 55 5 3 HELIX 5 5 THR A 58 GLN A 70 5 13 HELIX 6 6 GLN A 90 ASN A 103 1 14 HELIX 7 7 TRP A 134 GLN A 147 1 14 HELIX 8 8 GLY A 167 THR A 172 1 6 HELIX 9 9 PRO A 186 CYS A 188 5 3 HELIX 10 10 ASN A 196 SER A 208 1 13 HELIX 11 11 PRO A 222 ALA A 224 5 3 HELIX 12 12 PRO A 232 SER A 237 1 6 HELIX 13 13 LEU A 240 LYS A 245 1 6 HELIX 14 14 LYS A 257 ASN A 263 1 7 HELIX 15 15 TYR A 265 ILE A 269 1 5 SHEET 1 A 8 TYR A 152 ALA A 155 0 SHEET 2 A 8 GLY A 121 ASP A 125 1 N ILE A 122 O TYR A 152 SHEET 3 A 8 LYS A 73 GLY A 79 1 N LEU A 76 O GLY A 121 SHEET 4 A 8 TYR A 27 ILE A 30 1 N VAL A 28 O LYS A 73 SHEET 5 A 8 GLY A 2 TRP A 7 1 N ILE A 5 O TYR A 27 SHEET 6 A 8 TYR A 249 TRP A 255 1 N VAL A 252 O GLY A 2 SHEET 7 A 8 LYS A 213 PRO A 219 1 N ILE A 214 O GLY A 250 SHEET 8 A 8 TYR A 177 GLN A 181 1 N VAL A 178 O LYS A 213 SSBOND 1 CYS A 20 CYS A 67 1555 1555 2.03 SSBOND 2 CYS A 50 CYS A 57 1555 1555 2.03 SSBOND 3 CYS A 159 CYS A 188 1555 1555 2.03 CISPEP 1 ALA A 31 PHE A 32 0 12.40 CISPEP 2 PHE A 161 PRO A 162 0 -5.06 CISPEP 3 TRP A 255 SER A 256 0 -0.05 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