HEADER HYDROLASE INHIBITOR 04-AUG-10 3O9N TITLE CRYSTAL STRUCTURE OF A NEW FORM OF XYLANASE-A-AMYLASE INHIBITOR TITLE 2 PROTEIN(XAIP-III) AT 2.4 A RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: HAEMENTHIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCADOXUS MULTIFLORUS; SOURCE 3 ORGANISM_TAXID: 82246 KEYWDS XAIP-III, TIM BARREL, INHIBITORY PROTEIN, AMYLASE, XYLANASE, KEYWDS 2 HYDROLASE INHIBITOR EXPDTA X-RAY DIFFRACTION AUTHOR A.SINGH,S.KUMAR,M.SINHA,S.SHARMA,T.P.SINGH REVDAT 2 01-NOV-23 3O9N 1 REMARK REVDAT 1 22-SEP-10 3O9N 0 JRNL AUTH A.SINGH,S.KUMAR,M.SINHA,S.SHARMA,T.P.SINGH JRNL TITL CRYSTAL STRUCTURE OF A NEW FORM OF XYLANASE-A-AMYLASE JRNL TITL 2 INHIBITOR PROTEIN(XAIP-III) AT 2.4 A RESOLUTION JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 0.9 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.92 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 830251.580 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 10258 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 : 0.206 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 543 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1615 REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE : 0.2630 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 102 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.026 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2094 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 183 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 47.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.38000 REMARK 3 B22 (A**2) : 1.56000 REMARK 3 B33 (A**2) : -0.18000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 2.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.25 REMARK 3 ESD FROM SIGMAA (A) : 0.27 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) : 0.30 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.29 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.080 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) : 1.150 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.060 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.410 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.150 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.33 REMARK 3 BSOL : 52.68 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 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 5 : ACET.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : ION.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 5 : ACET.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3O9N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 31-AUG-10. REMARK 100 THE DEPOSITION ID IS D_1000060839. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.2 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 RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.514 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRROR 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 : 10519 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 48.300 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07100 REMARK 200 FOR THE DATA SET : 8.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.31700 REMARK 200 FOR SHELL : 1.700 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: 3D5H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.06 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM ACETATE, 20% PEG 6000, PH REMARK 280 7.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 32.68150 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 PHE A 100 -35.68 -135.21 REMARK 500 GLU A 108 -138.99 -170.38 REMARK 500 ASN A 109 113.34 166.89 REMARK 500 HIS A 123 56.81 -117.28 REMARK 500 SER A 130 -121.93 39.02 REMARK 500 THR A 147 76.58 -112.03 REMARK 500 PHE A 180 56.39 -90.86 REMARK 500 ASN A 183 99.15 -160.20 REMARK 500 SER A 190 75.11 -153.04 REMARK 500 ASP A 270 94.77 42.15 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 ACT A 1209 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 273 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3D5H RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY REMARK 999 EXIST. THE NEW SEQUENCE DATA OF XAIP-III WILL BE RELEASED SOON DBREF 3O9N A 1 272 PDB 3O9N 3O9N 1 272 SEQRES 1 A 272 GLY ASN LEU ASP ILE ALA VAL TYR TRP GLY GLN ASN PHE SEQRES 2 A 272 ASP GLU ARG SER LEU GLU ALA THR CYS ASP SER GLY ASN SEQRES 3 A 272 TYR ALA TYR VAL ILE ILE GLY PHE LEU ASN THR PHE GLY SEQRES 4 A 272 GLY GLY GLN THR PRO ALA LEU ASP ILE SER GLY HIS SER SEQRES 5 A 272 PRO SER GLY LEU GLU PRO GLN ILE LYS HIS CYS GLN SER SEQRES 6 A 272 LYS ASN VAL LYS VAL LEU LEU SER ILE GLY GLY PRO ALA SEQRES 7 A 272 GLY PRO TYR SER LEU ASP SER ARG SER ASP ALA ASN ASP SEQRES 8 A 272 LEU ALA VAL TYR LEU PHE ASN ASN PHE LEU LEU PRO PRO SEQRES 9 A 272 GLY HIS SER GLU ASN ASN PRO PHE GLY ASN ALA VAL LEU SEQRES 10 A 272 ASP GLY ILE ASP PHE HIS ILE GLU HIS GLY GLY PRO SER SEQRES 11 A 272 GLN TYR GLN LEU LEU ALA ASN ILE LEU SER SER PHE ARG SEQRES 12 A 272 LEU LYS GLY THR GLU PHE ALA LEU THR ALA ALA PRO GLN SEQRES 13 A 272 CYS VAL TYR PRO ASP PRO ASN LEU GLY THR VAL ILE ASN SEQRES 14 A 272 SER ALA THR PHE ASP ALA ILE TRP VAL GLN PHE TYR ASN SEQRES 15 A 272 ASN PRO GLN CYS SER TYR SER SER GLY ASN ALA GLU ALA SEQRES 16 A 272 LEU MET ASN ALA TRP ARG GLU TRP SER MET LYS ALA ARG SEQRES 17 A 272 THR LYS LYS VAL PHE LEU GLY PHE PRO ALA HIS PRO ASP SEQRES 18 A 272 ALA ALA GLY SER GLY TYR MET PRO PRO ALA LYS VAL LYS SEQRES 19 A 272 PHE HIS VAL PHE PRO ALA ALA LYS LYS SER TYR LYS PHE SEQRES 20 A 272 GLY GLY ILE MET LEU TRP ASP SER TYR TRP ASP THR VAL SEQRES 21 A 272 SER GLN PHE SER ASN LYS ILE LEU GLY ASP GLY VAL HET ACT A1209 4 HET PO4 A 273 5 HETNAM ACT ACETATE ION HETNAM PO4 PHOSPHATE ION FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 PO4 O4 P 3- FORMUL 4 HOH *183(H2 O) HELIX 1 1 SER A 17 SER A 24 1 8 HELIX 2 2 PRO A 53 GLY A 55 5 3 HELIX 3 3 LEU A 56 LYS A 66 1 11 HELIX 4 4 SER A 85 PHE A 100 1 16 HELIX 5 5 GLN A 131 LEU A 144 1 14 HELIX 6 6 LEU A 164 ASN A 169 1 6 HELIX 7 7 ALA A 193 ALA A 207 1 15 HELIX 8 8 HIS A 219 ALA A 223 5 5 HELIX 9 9 PRO A 229 VAL A 237 1 9 HELIX 10 10 VAL A 237 LYS A 243 1 7 HELIX 11 11 ASP A 254 GLN A 262 1 9 HELIX 12 12 GLN A 262 GLY A 269 1 8 SHEET 1 A10 GLN A 42 LEU A 46 0 SHEET 2 A10 TYR A 29 GLY A 39 -1 N THR A 37 O ALA A 45 SHEET 3 A10 LYS A 69 GLY A 76 1 O LEU A 71 N ILE A 32 SHEET 4 A10 GLY A 119 ILE A 124 1 O ASP A 121 N LEU A 72 SHEET 5 A10 ALA A 150 ALA A 153 1 O THR A 152 N PHE A 122 SHEET 6 A10 ALA A 175 GLN A 179 1 O TRP A 177 N ALA A 153 SHEET 7 A10 LYS A 211 PRO A 217 1 O PHE A 213 N ILE A 176 SHEET 8 A10 PHE A 247 TRP A 253 1 O TRP A 253 N PHE A 216 SHEET 9 A10 ILE A 5 TRP A 9 1 N ALA A 6 O LEU A 252 SHEET 10 A10 TYR A 29 GLY A 39 1 O ILE A 31 N TRP A 9 SSBOND 1 CYS A 22 CYS A 63 1555 1555 2.03 SSBOND 2 CYS A 157 CYS A 186 1555 1555 2.03 CISPEP 1 GLY A 33 PHE A 34 0 10.38 CISPEP 2 TYR A 159 PRO A 160 0 0.30 CISPEP 3 TRP A 253 ASP A 254 0 0.90 SITE 1 AC1 2 TYR A 188 LYS A 232 SITE 1 AC2 6 HIS A 51 SER A 52 HOH A 304 HOH A 328 SITE 2 AC2 6 HOH A 395 HOH A 399 CRYST1 42.792 65.363 49.418 90.00 102.13 90.00 P 1 21 1 2 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 0.023369 0.000000 0.005024 0.00000 SCALE2 0.000000 0.015299 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020698 0.00000