HEADER HYDROLASE 02-MAY-02 1IWD TITLE PROPOSED AMINO ACID SEQUENCE AND THE 1.63 ANGSTROM X-RAY CRYSTAL TITLE 2 STRUCTURE OF A PLANT CYSTEINE PROTEASE ERVATAMIN B: INSIGHT INTO THE TITLE 3 STRUCTURAL BASIS OF ITS STABILITY AND SUBSTRATE SPECIFICITY. COMPND MOL_ID: 1; COMPND 2 MOLECULE: ERVATAMIN B; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TABERNAEMONTANA DIVARICATA; SOURCE 3 ORGANISM_TAXID: 52861 KEYWDS CYSTEINE PROTEASE, ALPHA-BETA PROTEIN, CATALYTIC DYAD, L-DOMAIN, R- KEYWDS 2 DOMAIN., HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.CHAKRABARTI,S.BISWAS,J.K.DATTAGUPTA REVDAT 7 20-NOV-24 1IWD 1 REMARK REVDAT 6 25-OCT-23 1IWD 1 REMARK LINK REVDAT 5 27-JUN-18 1IWD 1 JRNL REVDAT 4 13-JUL-11 1IWD 1 VERSN REVDAT 3 07-APR-09 1IWD 1 HETNAM REVDAT 2 24-FEB-09 1IWD 1 VERSN REVDAT 1 06-MAY-03 1IWD 0 JRNL AUTH S.BISWAS,C.CHAKRABARTI,S.KUNDU,M.V.JAGANNADHAM, JRNL AUTH 2 J.K.DATTAGUPTA JRNL TITL PROPOSED AMINO ACID SEQUENCE AND THE 1.63 A X-RAY CRYSTAL JRNL TITL 2 STRUCTURE OF A PLANT CYSTEINE PROTEASE, ERVATAMIN B: SOME JRNL TITL 3 INSIGHTS INTO THE STRUCTURAL BASIS OF ITS STABILITY AND JRNL TITL 4 SUBSTRATE SPECIFICITY JRNL REF PROTEINS V. 51 489 2003 JRNL REFN ISSN 0887-3585 JRNL PMID 12784208 JRNL DOI 10.1002/PROT.10319 REMARK 2 REMARK 2 RESOLUTION. 1.63 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 1.63 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 14.94 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) (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 24993 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) : 0.161 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1213 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) : 1.63 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.73 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3749 REMARK 3 BIN R VALUE (WORKING SET) : 0.2560 REMARK 3 BIN FREE R VALUE : 0.2620 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 203 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.018 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1632 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 5 REMARK 3 SOLVENT ATOMS : 208 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.72000 REMARK 3 B22 (A**2) : -1.07000 REMARK 3 B33 (A**2) : -0.65000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 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) : 0.17 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.12 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.740 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) : 1.310 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.990 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.110 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.740 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.36 REMARK 3 BSOL : 47.35 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 : THJ.PARAM REMARK 3 PARAMETER FILE 4 : PEPTIDE.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1IWD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 08-MAY-02. REMARK 100 THE DEPOSITION ID IS D_1000005337. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-MAR-99 REMARK 200 TEMPERATURE (KELVIN) : 293 REMARK 200 PH : 8.5 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : OSMIC MAX-FLUX OPTIC SYSTEM REMARK 200 OPTICS : OSMIC MAX-FLUX CONFOCAL OPTICS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25048 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.630 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 (%) : 99.1 REMARK 200 DATA REDUNDANCY : 5.600 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 24.0600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.63 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.67 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.28100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000 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: PDB ENTRY 2ACT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, TRIS HCL, MAGNESIUM CHLORIDE, REMARK 280 PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 292K 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 24.10000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 34.67500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.38000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 34.67500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.10000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 29.38000 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 LYS A 20 -143.81 57.20 REMARK 500 GLN A 21 48.39 -86.07 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 THJ A 601 DBREF 1IWD A 1 215 UNP P60994 ERVB_TABDI 1 215 SEQRES 1 A 215 LEU PRO SER PHE VAL ASP TRP ARG SER LYS GLY ALA VAL SEQRES 2 A 215 ASN SER ILE LYS ASN GLN LYS GLN CYS GLY SER CYS TRP SEQRES 3 A 215 ALA PHE SER ALA VAL ALA ALA VAL GLU SER ILE ASN LYS SEQRES 4 A 215 ILE ARG THR GLY GLN LEU ILE SER LEU SER GLU GLN GLU SEQRES 5 A 215 LEU VAL ASP CYS ASP THR ALA SER HIS GLY CYS ASN GLY SEQRES 6 A 215 GLY TRP MET ASN ASN ALA PHE GLN TYR ILE ILE THR ASN SEQRES 7 A 215 GLY GLY ILE ASP THR GLN GLN ASN TYR PRO TYR SER ALA SEQRES 8 A 215 VAL GLN GLY SER CYS LYS PRO TYR ARG LEU ARG VAL VAL SEQRES 9 A 215 SER ILE ASN GLY PHE GLN ARG VAL THR ARG ASN ASN GLU SEQRES 10 A 215 SER ALA LEU GLN SER ALA VAL ALA SER GLN PRO VAL SER SEQRES 11 A 215 VAL THR VAL GLU ALA ALA GLY ALA PRO PHE GLN HIS TYR SEQRES 12 A 215 SER SER GLY ILE PHE THR GLY PRO CYS GLY THR ALA GLN SEQRES 13 A 215 ASN HIS GLY VAL VAL ILE VAL GLY TYR GLY THR GLN SER SEQRES 14 A 215 GLY LYS ASN TYR TRP ILE VAL ARG ASN SER TRP GLY GLN SEQRES 15 A 215 ASN TRP GLY ASN GLN GLY TYR ILE TRP MET GLU ARG ASN SEQRES 16 A 215 VAL ALA SER SER ALA GLY LEU CYS GLY ILE ALA GLN LEU SEQRES 17 A 215 PRO SER TYR PRO THR LYS ALA HET THJ A 601 5 HETNAM THJ THIOSULFATE FORMUL 2 THJ O3 S2 2- FORMUL 3 HOH *208(H2 O) HELIX 1 1 ARG A 8 GLY A 11 5 4 HELIX 2 2 SER A 24 GLY A 43 1 20 HELIX 3 3 SER A 49 ASP A 57 1 9 HELIX 4 4 HIS A 61 GLY A 65 5 5 HELIX 5 5 TRP A 67 GLY A 79 1 13 HELIX 6 6 ASN A 116 GLN A 127 1 12 HELIX 7 7 GLY A 137 HIS A 142 1 6 HELIX 8 8 GLY A 201 ILE A 205 5 5 SHEET 1 A 5 ILE A 147 PHE A 148 0 SHEET 2 A 5 TYR A 189 GLU A 193 1 O TRP A 191 N PHE A 148 SHEET 3 A 5 LYS A 171 ARG A 177 -1 N VAL A 176 O ILE A 190 SHEET 4 A 5 HIS A 158 GLN A 168 -1 N VAL A 161 O ARG A 177 SHEET 5 A 5 VAL A 5 ASP A 6 -1 N VAL A 5 O TYR A 165 SHEET 1 B 5 ILE A 147 PHE A 148 0 SHEET 2 B 5 TYR A 189 GLU A 193 1 O TRP A 191 N PHE A 148 SHEET 3 B 5 LYS A 171 ARG A 177 -1 N VAL A 176 O ILE A 190 SHEET 4 B 5 HIS A 158 GLN A 168 -1 N VAL A 161 O ARG A 177 SHEET 5 B 5 VAL A 129 VAL A 133 -1 N VAL A 129 O ILE A 162 SHEET 1 C 2 GLY A 108 ARG A 111 0 SHEET 2 C 2 SER A 210 THR A 213 -1 O THR A 213 N GLY A 108 SSBOND 1 CYS A 22 CYS A 63 1555 1555 2.03 SSBOND 2 CYS A 56 CYS A 96 1555 1555 2.03 SSBOND 3 CYS A 152 CYS A 203 1555 1555 2.04 LINK SG CYS A 25 S2 THJ A 601 1555 1555 1.96 CISPEP 1 GLY A 150 PRO A 151 0 0.27 SITE 1 AC1 9 GLN A 19 GLY A 23 SER A 24 CYS A 25 SITE 2 AC1 9 GLY A 65 ASN A 157 HIS A 158 HOH A 374 SITE 3 AC1 9 HOH A 445 CRYST1 48.200 58.760 69.350 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 0.020747 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017018 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014420 0.00000