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 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,
JRNL AUTH 2 C.M.CUCHILLO,K.R.ACHARYA
JRNL TITL THE CRYSTAL STRUCTURE OF EOSINOPHIL CATIONIC
JRNL TITL 2 PROTEIN AT 2.4 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. 2.4 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)) : 0.0
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 10000000.00
REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.001000
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 (%) : 8.0
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) (%) : 74.4
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 810
REMARK 3 BIN R VALUE (WORKING SET) : 0.318
REMARK 3 BIN FREE R VALUE : 0.296
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.2
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) : 41.2
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 38.8
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) : 0.27
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) : 1.5
REMARK 3 DIHEDRAL ANGLES (DEGREES) : 28.1
REMARK 3 IMPROPER ANGLES (DEGREES) : 0.78
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) : 2.28 ; 1.50
REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.75 ; 2.00
REMARK 3 SIDE-CHAIN BOND (A**2) : 4.15 ; 2.00
REMARK 3 SIDE-CHAIN ANGLE (A**2) : 6.38 ; 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.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. 3.15, 01-DEC-08
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-OCT-99.
REMARK 100 THE PDBE ID CODE IS EBI-4188.
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 <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) : 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 <I/SIGMA(I)> 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
REMARK 200 S.MOSIMANN 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 (%): 53.2
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.3
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
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 300 DETAILS:BIOLOGICAL_UNIT: MONOMER
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 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 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 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 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 O1)
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
(ATOM LINES ARE NOT SHOWN.)
END
