HEADER HYDROLASE 02-JAN-01 1HI2 TITLE EOSINOPHIL-DERIVED NEUROTOXIN (EDN) - SULPHATE COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: EOSINOPHIL-DERIVED NEUROTOXIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RNASE-2, RNASE-US, EDN; COMPND 5 EC: 3.1.27.5; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 TISSUE: BLOOD; SOURCE 6 CELL: EOSINOPHIL; SOURCE 7 ORGANELLE: GRANULE; SOURCE 8 CELLULAR_LOCATION: SECRETORY GRANULES; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS HYDROLASE, RNASE-2, RNASE US, RIBONUCLEASE EXPDTA X-RAY DIFFRACTION AUTHOR D.D.LEONIDAS,E.BOIX,R.PRILL,M.SUZUKI,R.TURTON,K.MINSON, AUTHOR 2 G.J.SWAMINATHAN,R.J.YOULE,K.R.ACHARYA REVDAT 2 24-FEB-09 1HI2 1 VERSN REVDAT 1 31-MAY-01 1HI2 0 JRNL AUTH D.D.LEONIDAS,E.BOIX,R.PRILL,M.SUZUKI,R.TURTON, JRNL AUTH 2 K.MINSON,G.J.SWAMINATHAN,R.J.YOULE,K.R.ACHARYA JRNL TITL MAPPING THE RIBONUCLEOLYTIC ACTIVE SITE OF JRNL TITL 2 EOSINOPHIL-DERIVED NEUROTOXIN (EDN): HIGH JRNL TITL 3 RESOLUTION CRYSTAL STRUCTURES OF EDN COMPLEXES JRNL TITL 4 WITH ADENYLIC NUCLEOTIDE INHIBITORS JRNL REF J.BIOL.CHEM. V. 276 15009 2001 JRNL REFN ISSN 0021-9258 JRNL PMID 11154698 JRNL DOI 10.1074/JBC.M010585200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.C.MOSIMANN,D.L.NEWTON,R.J.YOULE,M.N.JAMES REMARK 1 TITL X-RAY CRYSTALLOGRAPHIC STRUCTURE OF RECOMBINANT REMARK 1 TITL 2 EOSINOPHIL-DERIVED NEUROTOXIN AT 1.83 A RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 260 540 1996 REMARK 1 REFN ISSN 0022-2836 REMARK 1 PMID 8759319 REMARK 1 DOI 10.1006/JMBI.1996.0420 REMARK 2 REMARK 2 RESOLUTION. 1.6 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.0 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.00 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.001000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 96.7 REMARK 3 NUMBER OF REFLECTIONS : 17059 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) : 0.177 REMARK 3 FREE R VALUE : 0.219 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.9 REMARK 3 FREE R VALUE TEST SET COUNT : 836 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 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) : 1.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.70 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.5 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2640 REMARK 3 BIN R VALUE (WORKING SET) : 0.218 REMARK 3 BIN FREE R VALUE : 0.218 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.1 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 141 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 : 1089 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.1 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.3 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00 REMARK 3 B22 (A**2) : 0.00 REMARK 3 B33 (A**2) : 0.00 REMARK 3 B12 (A**2) : 0.00 REMARK 3 B13 (A**2) : 0.00 REMARK 3 B23 (A**2) : 0.00 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.15 REMARK 3 ESD FROM SIGMAA (A) : 0.12 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) : 0.17 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.06 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 BOND ANGLES (DEGREES) : 1.3 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.1 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.70 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) : 1.25 ; 1.50 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.06 ; 2.00 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.43 ; 2.00 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.99 ; 2.50 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 REMARK 3 PARAMETER FILE 2 : PAR REMARK 3 PARAMETER FILE 3 : SO4 REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PR REMARK 3 TOPOLOGY FILE 2 : TOP REMARK 3 TOPOLOGY FILE 3 : SO4 REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1HI2 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-JAN-01. REMARK 100 THE PDBE ID CODE IS EBI-5745. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-NOV-98 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.5 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS 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 : 17303 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.600 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.6 REMARK 200 DATA REDUNDANCY : 8.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06500 REMARK 200 FOR THE DATA SET : 25.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.66 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.06500 REMARK 200 FOR SHELL : 28.000 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5M AMMONIUM SULFATE, REMARK 280 0.1M SODIUM CACODYLATE PH 6.5, 5% ETHANOL 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 26.70000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 21.11000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.61500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 21.11000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.70000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.61500 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 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 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PQS 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 REMARK 500 O HOH A 2044 O HOH A 2069 2555 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 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 66 -6.81 -53.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 957 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 958 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HI3 RELATED DB: PDB REMARK 900 EOSINOPHIL-DERIVED NEUROTOXIN (EDN) - REMARK 900 ADENOSINE-2'-5'-DIPHOSPHATE COMPLEX REMARK 900 RELATED ID: 1HI4 RELATED DB: PDB REMARK 900 EOSINOPHIL-DERIVED NEUROTOXIN (EDN) - REMARK 900 ADENOSINE-3'-5'-DIPHOSPHATE COMPLEX REMARK 900 RELATED ID: 1HI5 RELATED DB: PDB REMARK 900 EOSINOPHIL-DERIVED NEUROTOXIN (EDN) - REMARK 900 ADENOSINE-5'-DIPHOSPHATE COMPLEX DBREF 1HI2 A 0 134 UNP P10153 RNKD_HUMAN 27 161 SEQADV 1HI2 MET A 0 UNP P10153 CLONING ARTIFACT SEQRES 1 A 135 MET LYS PRO PRO GLN PHE THR TRP ALA GLN TRP PHE GLU SEQRES 2 A 135 THR GLN HIS ILE ASN MET THR SER GLN GLN CYS THR ASN SEQRES 3 A 135 ALA MET GLN VAL ILE ASN ASN TYR GLN ARG ARG CYS LYS SEQRES 4 A 135 ASN GLN ASN THR PHE LEU LEU THR THR PHE ALA ASN VAL SEQRES 5 A 135 VAL ASN VAL CYS GLY ASN PRO ASN MET THR CYS PRO SER SEQRES 6 A 135 ASN LYS THR ARG LYS ASN CYS HIS HIS SER GLY SER GLN SEQRES 7 A 135 VAL PRO LEU ILE HIS CYS ASN LEU THR THR PRO SER PRO SEQRES 8 A 135 GLN ASN ILE SER ASN CYS ARG TYR ALA GLN THR PRO ALA SEQRES 9 A 135 ASN MET PHE TYR ILE VAL ALA CYS ASP ASN ARG ASP GLN SEQRES 10 A 135 ARG ARG ASP PRO PRO GLN TYR PRO VAL VAL PRO VAL HIS SEQRES 11 A 135 LEU ASP ARG ILE ILE HET SO4 A 957 5 HET SO4 A 958 5 HETNAM SO4 SULFATE ION HETSYN SO4 SULPHATE FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 HOH *110(H2 O1) HELIX 1 1 THR A 6 ILE A 16 1 11 HELIX 2 2 GLN A 22 ARG A 35 1 14 HELIX 3 3 THR A 47 CYS A 55 1 9 HELIX 4 4 ASN A 92 CYS A 96 5 5 SHEET 1 AA 3 GLN A 40 LEU A 44 0 SHEET 2 AA 3 VAL A 78 THR A 87 -1 O ILE A 81 N PHE A 43 SHEET 3 AA 3 ARG A 97 MET A 105 -1 O ARG A 97 N THR A 86 SHEET 1 AB 3 CYS A 71 HIS A 73 0 SHEET 2 AB 3 TYR A 107 ASN A 113 -1 O VAL A 109 N HIS A 72 SHEET 3 AB 3 VAL A 125 ILE A 133 -1 O VAL A 126 N ASP A 112 SSBOND 1 CYS A 23 CYS A 83 1555 1555 2.03 SSBOND 2 CYS A 37 CYS A 96 1555 1555 2.03 SSBOND 3 CYS A 55 CYS A 111 1555 1555 2.03 SSBOND 4 CYS A 62 CYS A 71 1555 1555 2.03 SITE 1 AC1 6 GLN A 14 HIS A 15 HIS A 129 LEU A 130 SITE 2 AC1 6 HOH A2015 HOH A2110 SITE 1 AC2 4 ARG A 36 LYS A 38 ASN A 39 GLN A 40 CRYST1 53.400 57.230 42.220 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 0.018726 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017473 0.000000 0.00000 SCALE3 0.000000 0.000000 0.023685 0.00000