HEADER HYDROLASE 02-JAN-01 1HI5
TITLE EOSINOPHIL-DERIVED NEUROTOXIN (EDN) - ADENOSINE-5'-DIPHOSPHATE 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 3 30-MAY-18 1HI5 1 TITLE
REVDAT 2 24-FEB-09 1HI5 1 VERSN
REVDAT 1 31-MAY-01 1HI5 0
JRNL AUTH D.D.LEONIDAS,E.BOIX,R.PRILL,M.SUZUKI,R.TURTON,K.MINSON,
JRNL AUTH 2 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 RESOLUTION CRYSTAL
JRNL TITL 3 STRUCTURES OF EDN COMPLEXES WITH ADENYLIC NUCLEOTIDE
JRNL TITL 4 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. 1.80 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) : 1.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.000
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0010
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.7
REMARK 3 NUMBER OF REFLECTIONS : 11720
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) : 0.193
REMARK 3 FREE R VALUE : 0.253
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200
REMARK 3 FREE R VALUE TEST SET COUNT : 604
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010
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) : 1.80
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.90
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1674
REMARK 3 BIN R VALUE (WORKING SET) : 0.2810
REMARK 3 BIN FREE R VALUE : 0.3280
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.30
REMARK 3 BIN FREE R VALUE TEST SET COUNT : 76
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.038
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 : 27
REMARK 3 SOLVENT ATOMS : 132
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 14.10
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.30
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : 0.00000
REMARK 3 B22 (A**2) : 0.00000
REMARK 3 B33 (A**2) : 0.00000
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) : 0.19
REMARK 3 ESD FROM SIGMAA (A) : 0.19
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) : 0.26
REMARK 3 ESD FROM C-V SIGMAA (A) : 0.24
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : 0.009
REMARK 3 BOND ANGLES (DEGREES) : 1.500
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.70
REMARK 3 IMPROPER ANGLES (DEGREES) : 0.790
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) : 1.400 ; 1.500
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.090 ; 2.000
REMARK 3 SIDE-CHAIN BOND (A**2) : 2.540 ; 2.000
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.830 ; 2.500
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 : LIG
REMARK 3 PARAMETER FILE 4 : NULL
REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PR
REMARK 3 TOPOLOGY FILE 2 : TOP
REMARK 3 TOPOLOGY FILE 3 : LIG
REMARK 3 TOPOLOGY FILE 4 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED
REMARK 4
REMARK 4 1HI5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-JAN-01.
REMARK 100 THE DEPOSITION ID IS D_1290005748.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 15-MAR-99
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) : N
REMARK 200 RADIATION SOURCE : ROTATING ANODE
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418
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 : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11749
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
REMARK 200 RESOLUTION RANGE LOW (A) : 30.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4
REMARK 200 DATA REDUNDANCY : 5.000
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.06400
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86
REMARK 200 COMPLETENESS FOR SHELL (%) : 82.9
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.26300
REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.200
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 (%): 44.00
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.34
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 1.5M AMMONIUM SULFATE, 0.1M SODIUM
REMARK 280 CACODYLATE PH 6.5, 5% ETHANOL, PH 6.50
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 26.32300
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 20.88550
REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.15900
REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 20.88550
REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 26.32300
REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.15900
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 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: 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 ARG A 36 146.04 175.57
REMARK 500 LYS A 66 -18.68 -48.86
REMARK 500 ASN A 92 103.74 -178.37
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 ADP A 999
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1HI2 RELATED DB: PDB
REMARK 900 EOSINOPHIL-DERIVED NEUROTOXIN (EDN) - SULPHATE COMPLEX
REMARK 900 RELATED ID: 1HI3 RELATED DB: PDB
REMARK 900 EOSINOPHIL-DERIVED NEUROTOXIN (EDN) - ADENOSINE-2'-5'-DIPHOSPHATE
REMARK 900 COMPLEX
REMARK 900 RELATED ID: 1HI4 RELATED DB: PDB
REMARK 900 EOSINOPHIL-DERIVED NEUROTOXIN (EDN) - ADENOSINE-3'-5'-DIPHOSPHATE
REMARK 900 COMPLEX
DBREF 1HI5 A 0 134 UNP P10153 RNKD_HUMAN 27 161
SEQADV 1HI5 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 ADP A 999 27
HETNAM ADP ADENOSINE-5'-DIPHOSPHATE
FORMUL 2 ADP C10 H15 N5 O10 P2
FORMUL 3 HOH *132(H2 O)
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 4 ASN A 59 MET A 60 0
SHEET 2 AB 4 CYS A 71 HIS A 73 0
SHEET 3 AB 4 TYR A 107 ASN A 113 -1 O VAL A 109 N HIS A 72
SHEET 4 AB 4 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 2.04
SSBOND 4 CYS A 62 CYS A 71 1555 1555 2.03
SITE 1 AC1 12 GLN A 14 HIS A 15 LYS A 38 GLN A 40
SITE 2 AC1 12 HIS A 82 HIS A 129 LEU A 130 HOH A2016
SITE 3 AC1 12 HOH A2052 HOH A2123 HOH A2128 HOH A2131
CRYST1 52.646 56.318 41.771 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 0.018995 0.000000 0.000000 0.00000
SCALE2 0.000000 0.017756 0.000000 0.00000
SCALE3 0.000000 0.000000 0.023940 0.00000
(ATOM LINES ARE NOT SHOWN.)
END