HEADER RIBONUCLEASE 06-OCT-99 1QMT TITLE RECOMBINANT HUMAN EOSINOPHIL CATIONIC PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: EOSINOPHIL CATIONIC PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: RIBONUCLEASE 3, RNASE 3; COMPND 5 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 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS EOSINOPHIL, RIBONUCLEASE, CYTOTOXICITY EXPDTA X-RAY DIFFRACTION AUTHOR E.BOIX,D.D.LEONIDAS,K.R.ACHARYA REVDAT 3 01-MAY-24 1QMT 1 REMARK REVDAT 2 24-FEB-09 1QMT 1 VERSN REVDAT 1 04-FEB-00 1QMT 0 JRNL AUTH E.BOIX,D.D.LEONIDAS,Z.NIKOLOVSKI,M.V.NOGUES,C.M.CUCHILLO, JRNL AUTH 2 K.R.ACHARYA JRNL TITL THE CRYSTAL STRUCTURE OF EOSINOPHIL CATIONIC PROTEIN AT 2.4 JRNL TITL 2 A RESOLUTION JRNL REF BIOCHEMISTRY V. 38 16794 1999 JRNL REFN ISSN 0006-2960 JRNL PMID 10606511 JRNL DOI 10.1021/BI9919145 REMARK 2 REMARK 2 RESOLUTION. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 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) (%) : 95.4 REMARK 3 NUMBER OF REFLECTIONS : 6907 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) : 0.176 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.000 REMARK 3 FREE R VALUE TEST SET COUNT : 552 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 74.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 810 REMARK 3 BIN R VALUE (WORKING SET) : 0.3180 REMARK 3 BIN FREE R VALUE : 0.2960 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.20 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 63 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.037 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1102 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 27 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 41.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.80 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) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.38 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) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.34 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 28.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.780 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.280 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.750 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.150 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.380 ; 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.PARAM REMARK 3 PARAMETER FILE 2 : PARAM.WATER REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : TOPOW.WATER REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 1QMT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-OCT-99. REMARK 100 THE DEPOSITION ID IS D_1290004188. 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) : 293.0 REMARK 200 PH : 8.00 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 : 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 : 6916 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 4.930 REMARK 200 R MERGE (I) : 0.10700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.7000 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 (%) : 65.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.28700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: X-PLOR 3.851 REMARK 200 STARTING MODEL: EOSINOPHIL DERIVED NEUROTOXIN STRUCTURE AT 1.8 REMARK 200 ANGSTROMS (COORDINATES NOT SUBMITTED) WAS PROVIDED BY S.MOSIMANN REMARK 200 AND M.N.G.JAMES AND USED FOR MOLECULAR REPLACEMENT. REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8.00 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 15.64050 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 15.64050 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 15.64050 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 300 REMARK: BIOLOGICAL_UNIT: MONOMER 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: 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 SER A 17 113.87 -167.54 REMARK 500 GLN A 58 142.48 -38.64 REMARK 500 ASN A 65 75.85 -155.60 REMARK 500 ALA A 90 -103.02 -129.04 REMARK 500 ASN A 92 128.00 -29.56 REMARK 500 ILE A 93 38.75 -73.45 REMARK 500 ASN A 95 64.86 -115.33 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 SEQUENCE FOR 1QMT PDB CORRESPONDS TO RECOMBINANT HUMAN REMARK 999 ECP. IT INCLUDES THE COMPLETE NATIVE PROTEIN AND AN REMARK 999 ADDITIONAL MET AT THE N-TERMINAL. THE NATIVE ECP REMARK 999 (RESIDUES 1 -133) CORRESPONDS TO RESIDUES 28-160 OF THE ECP REMARK 999 PRECURSOR (SWS P12724). REMARK 999 RESIDUES 1-27 OF P12724 ARE THE SIGNAL PEPTIDE. DBREF 1QMT A 1 133 UNP P12724 ECP_HUMAN 28 160 SEQADV 1QMT MET A 0 UNP P12724 CLONING ARTIFACT SEQRES 1 A 134 MET ARG PRO PRO GLN PHE THR ARG ALA GLN TRP PHE ALA SEQRES 2 A 134 ILE GLN HIS ILE SER LEU ASN PRO PRO ARG CYS THR ILE SEQRES 3 A 134 ALA MET ARG ALA ILE ASN ASN TYR ARG TRP ARG CYS LYS SEQRES 4 A 134 ASN GLN ASN THR PHE LEU ARG THR THR PHE ALA ASN VAL SEQRES 5 A 134 VAL ASN VAL CYS GLY ASN GLN SER ILE ARG CYS PRO HIS SEQRES 6 A 134 ASN ARG THR LEU ASN ASN CYS HIS ARG SER ARG PHE ARG SEQRES 7 A 134 VAL PRO LEU LEU HIS CYS ASP LEU ILE ASN PRO GLY ALA SEQRES 8 A 134 GLN ASN ILE SER ASN CYS ARG TYR ALA ASP ARG PRO GLY SEQRES 9 A 134 ARG ARG PHE TYR VAL VAL ALA CYS ASP ASN ARG ASP PRO SEQRES 10 A 134 ARG ASP SER PRO ARG TYR PRO VAL VAL PRO VAL HIS LEU SEQRES 11 A 134 ASP THR THR ILE FORMUL 2 HOH *27(H2 O) HELIX 1 1 THR A 6 ILE A 16 1 11 HELIX 2 2 ARG A 22 MET A 27 1 6 HELIX 3 3 MET A 27 ASN A 32 1 6 HELIX 4 4 THR A 47 GLY A 56 1 10 HELIX 5 5 PRO A 63 ASN A 65 5 3 SHEET 1 A 3 GLN A 40 LEU A 44 0 SHEET 2 A 3 VAL A 78 LEU A 85 -1 N CYS A 83 O ASN A 41 SHEET 3 A 3 TYR A 98 ARG A 105 -1 N ARG A 105 O VAL A 78 SHEET 1 B 3 CYS A 71 ARG A 73 0 SHEET 2 B 3 TYR A 107 ALA A 110 -1 N VAL A 109 O HIS A 72 SHEET 3 B 3 HIS A 128 THR A 132 -1 N THR A 131 O VAL A 108 SHEET 1 C 2 CYS A 111 ASN A 113 0 SHEET 2 C 2 VAL A 124 PRO A 126 -1 N VAL A 125 O ASP A 112 SSBOND 1 CYS A 23 CYS A 83 1555 1555 2.02 SSBOND 2 CYS A 37 CYS A 96 1555 1555 2.00 SSBOND 3 CYS A 55 CYS A 111 1555 1555 2.03 SSBOND 4 CYS A 62 CYS A 71 1555 1555 2.02 CRYST1 100.159 100.159 31.281 90.00 90.00 120.00 P 63 6 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 0.009984 0.005764 0.000000 0.00000 SCALE2 0.000000 0.011529 0.000000 0.00000 SCALE3 0.000000 0.000000 0.031968 0.00000