HEADER HYDROLASE 04-MAR-03 1OP0 TITLE CRYSTAL STRUCTURE OF AAV-SP-I, A GLYCOSYLATED SNAKE VENOM SERINE TITLE 2 PROTEINASE FROM AGKISTRODON ACUTUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: VENOM SERINE PROTEINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SNAKE VENOM SERINE PROTEINASE, AAV-SP-I; COMPND 5 EC: 3.4.21.- SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DEINAGKISTRODON ACUTUS; SOURCE 3 ORGANISM_COMMON: CHINESE MOCCASIN; SOURCE 4 ORGANISM_TAXID: 36307; SOURCE 5 SECRETION: VENOM GLAND KEYWDS SNAKE VENOM, SERINE PROTEINASE, GLYCOPROTEIN, AGKISTRODON ACUTUS, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Z.ZHU,M.TENG,L.NIU REVDAT 6 25-OCT-23 1OP0 1 HETSYN REVDAT 5 29-JUL-20 1OP0 1 COMPND REMARK SEQADV HETNAM REVDAT 5 2 1 LINK SITE ATOM REVDAT 4 13-JUL-11 1OP0 1 VERSN REVDAT 3 24-FEB-09 1OP0 1 VERSN REVDAT 2 29-MAR-05 1OP0 1 JRNL REVDAT 1 25-MAY-04 1OP0 0 JRNL AUTH Z.ZHU,Z.LIANG,T.ZHANG,Z.ZHU,W.XU,M.TENG,L.NIU JRNL TITL CRYSTAL STRUCTURES AND AMIDOLYTIC ACTIVITIES OF TWO JRNL TITL 2 GLYCOSYLATED SNAKE VENOM SERINE PROTEINASES JRNL REF J.BIOL.CHEM. V. 280 10524 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15632114 JRNL DOI 10.1074/JBC.M412900200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Z.ZHU,P.GONG,M.TENG,L.NIU REMARK 1 TITL PURIFICATION, N-TERMINAL SEQUENCING, PARTIAL REMARK 1 TITL 2 CHARACTERIZATION, CRYSTALLIZATION AND PRELIMINARY REMARK 1 TITL 3 CRYSTALLOGRAPHIC ANALYSIS OF TWO GLYCOSYLATED SERINE REMARK 1 TITL 4 PROTEINASES FROM AGKISTRODON ACUTUS VENOM REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 59 547 2003 REMARK 1 REFN ISSN 0907-4449 REMARK 1 PMID 12595722 REMARK 1 DOI 10.1107/S0907444902023375 REMARK 2 REMARK 2 RESOLUTION. 2.00 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.07 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 268424.980 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.5 REMARK 3 NUMBER OF REFLECTIONS : 19629 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) : 0.181 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1935 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) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2472 REMARK 3 BIN R VALUE (WORKING SET) : 0.2800 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 259 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1776 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 142 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.10 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.77000 REMARK 3 B22 (A**2) : -2.74000 REMARK 3 B33 (A**2) : -0.03000 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) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.25 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.23 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.830 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) : 1.340 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.120 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.150 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.290 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 43.42 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 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1OP0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-MAR-03. REMARK 100 THE DEPOSITION ID IS D_1000018523. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUL-99 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 6.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE 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 : GRAPHITE REMARK 200 OPTICS : NULL 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 : 20865 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.12300 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) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.4 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: PDB ENTRY 1BQY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: LITHIUM SULFATE, SODIUM CACODYLATE, PH REMARK 280 6.3, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 24.70750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 41.20950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 37.29650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 41.20950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.70750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 37.29650 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, B 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 PHE A 41 -8.16 -140.08 REMARK 500 HIS A 71 -76.89 -128.93 REMARK 500 ASN A 93 39.69 -95.88 REMARK 500 VAL A 147 -61.62 -101.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1OP2 RELATED DB: PDB REMARK 900 THE CRYSTAL STRUCTURE OF AAV-SP-II DBREF 1OP0 A 16 245G UNP Q9I8X1 VSP2_AGKAC 25 258 SEQADV 1OP0 ASP A 63 UNP Q9I8X1 ASN 70 CONFLICT SEQRES 1 A 234 VAL ILE GLY GLY ASN GLU CYS ASP ILE ASN GLU HIS ARG SEQRES 2 A 234 PHE LEU VAL ALA PHE PHE ASN THR THR GLY PHE PHE CYS SEQRES 3 A 234 GLY GLY THR LEU ILE ASN PRO GLU TRP VAL VAL THR ALA SEQRES 4 A 234 ALA HIS CYS ASP SER THR ASP PHE GLN MET GLN LEU GLY SEQRES 5 A 234 VAL HIS SER LYS LYS VAL LEU ASN GLU ASP GLU GLN THR SEQRES 6 A 234 ARG ASN PRO LYS GLU LYS PHE ILE CYS PRO ASN LYS ASN SEQRES 7 A 234 ASN ASN GLU VAL LEU ASP LYS ASP ILE MET LEU ILE LYS SEQRES 8 A 234 LEU ASP LYS PRO ILE SER ASN SER LYS HIS ILE ALA PRO SEQRES 9 A 234 LEU SER LEU PRO SER SER PRO PRO SER VAL GLY SER VAL SEQRES 10 A 234 CYS ARG ILE MET GLY TRP GLY SER ILE THR PRO VAL LYS SEQRES 11 A 234 GLU THR PHE PRO ASP VAL PRO TYR CYS ALA ASN ILE ASN SEQRES 12 A 234 LEU LEU ASP HIS ALA VAL CYS GLN ALA GLY TYR PRO GLU SEQRES 13 A 234 LEU LEU ALA GLU TYR ARG THR LEU CYS ALA GLY ILE VAL SEQRES 14 A 234 GLN GLY GLY LYS ASP THR CYS GLY GLY ASP SER GLY GLY SEQRES 15 A 234 PRO LEU ILE CYS ASN GLY GLN PHE GLN GLY ILE VAL SER SEQRES 16 A 234 TYR GLY ALA HIS PRO CYS GLY GLN GLY PRO LYS PRO GLY SEQRES 17 A 234 ILE TYR THR ASN VAL PHE ASP TYR THR ASP TRP ILE GLN SEQRES 18 A 234 ARG ASN ILE ALA GLY ASN THR ASP ALA THR CYS PRO PRO MODRES 1OP0 ASN A 35 ASN GLYCOSYLATION SITE HET NAG B 1 14 HET NAG B 2 14 HET FUC B 3 10 HET SO4 A 901 5 HET SO4 A 501 5 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM SO4 SULFATE ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE FORMUL 2 NAG 2(C8 H15 N O6) FORMUL 2 FUC C6 H12 O5 FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *142(H2 O) HELIX 1 1 ALA A 55 ASP A 59 5 5 HELIX 2 2 ASP A 164 TYR A 172 1 9 HELIX 3 3 TYR A 234 GLY A 244 1 11 SHEET 1 A 8 ASN A 20 GLU A 21 0 SHEET 2 A 8 TYR A 156 LEU A 163 -1 N CYS A 157 O ASN A 20 SHEET 3 A 8 VAL A 135 GLY A 140 -1 N CYS A 136 O ILE A 160 SHEET 4 A 8 PRO A 198 CYS A 201 -1 O ILE A 200 N ARG A 137 SHEET 5 A 8 GLN A 208 TYR A 215 -1 N GLN A 208 O CYS A 201 SHEET 6 A 8 GLY A 226 ASN A 230 -1 N ILE A 227 O TYR A 215 SHEET 7 A 8 THR A 180 GLY A 184 -1 N LEU A 181 O TYR A 228 SHEET 8 A 8 TYR A 156 LEU A 163 -1 N ASN A 161 O GLY A 184 SHEET 1 B 7 GLN A 81 ARG A 83 0 SHEET 2 B 7 GLN A 65 LEU A 68 -1 O MET A 66 N ARG A 83 SHEET 3 B 7 LEU A 30 ASN A 35 -1 O ALA A 32 N GLN A 67 SHEET 4 B 7 GLY A 39 ASN A 48 -1 O GLY A 39 N ASN A 35 SHEET 5 B 7 TRP A 51 THR A 54 -1 O TRP A 51 N ILE A 47 SHEET 6 B 7 MET A 104 LEU A 108 -1 N MET A 104 O THR A 54 SHEET 7 B 7 PRO A 85 ILE A 90 -1 N LYS A 86 O LYS A 107 SSBOND 1 CYS A 22 CYS A 157 1555 1555 2.03 SSBOND 2 CYS A 42 CYS A 58 1555 1555 2.03 SSBOND 3 CYS A 91 CYS A 245E 1555 1555 2.03 SSBOND 4 CYS A 136 CYS A 201 1555 1555 2.03 SSBOND 5 CYS A 168 CYS A 182 1555 1555 2.03 SSBOND 6 CYS A 191 CYS A 220 1555 1555 2.03 LINK ND2 ASN A 35 C1 NAG B 1 1555 1555 1.45 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.38 LINK O6 NAG B 1 C1 FUC B 3 1555 1555 1.40 CISPEP 1 HIS A 218 PRO A 219 0 -0.03 CRYST1 49.415 74.593 82.419 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 0.020237 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013406 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012133 0.00000