HEADER CYTOKINE 19-DEC-94 1NAP
TITLE THE CRYSTAL STRUCTURE OF RECOMBINANT HUMAN NEUTROPHIL-ACTIVATING
TITLE 2 PEPTIDE-2 (M6L) AT 1.9-ANGSTROMS RESOLUTION
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: NEUTROPHIL ACTIVATING PEPTIDE-2;
COMPND 3 CHAIN: A, B, C, D;
COMPND 4 SYNONYM: NAP-2;
COMPND 5 ENGINEERED: YES;
COMPND 6 MUTATION: YES
SOURCE MOL_ID: 1;
SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS;
SOURCE 3 ORGANISM_COMMON: HUMAN;
SOURCE 4 ORGANISM_TAXID: 9606;
SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562;
SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PBR-CRM-CTAP-MET20,LEU26
KEYWDS CYTOKINE
EXPDTA X-RAY DIFFRACTION
AUTHOR M.G.MALKOWSKI,B.F.P.EDWARDS
REVDAT 5 14-AUG-19 1NAP 1 REMARK
REVDAT 4 17-JUL-19 1NAP 1 REMARK
REVDAT 3 24-FEB-09 1NAP 1 VERSN
REVDAT 2 01-APR-03 1NAP 1 JRNL
REVDAT 1 19-DEC-95 1NAP 0
JRNL AUTH M.G.MALKOWSKI,J.Y.WU,J.B.LAZAR,P.H.JOHNSON,B.F.EDWARDS
JRNL TITL THE CRYSTAL STRUCTURE OF RECOMBINANT HUMAN
JRNL TITL 2 NEUTROPHIL-ACTIVATING PEPTIDE-2 (M6L) AT 1.9-A RESOLUTION.
JRNL REF J.BIOL.CHEM. V. 270 7077 1995
JRNL REFN ISSN 0021-9258
JRNL PMID 7706245
JRNL DOI 10.1074/JBC.270.13.7077
REMARK 1
REMARK 1 REFERENCE 1
REMARK 1 AUTH R.ST.CHARLES,D.A.WALZ,B.F.P.EDWARDS
REMARK 1 TITL THE THREE DIMENSIONAL STRUCTURE OF BOVINE PLATELET FACTOR 4
REMARK 1 TITL 2 AT 3.0 ANGSTROMS RESOLUTION
REMARK 1 REF J.BIOL.CHEM. V. 264 2092 1989
REMARK 1 REFN ISSN 0021-9258
REMARK 1 REFERENCE 2
REMARK 1 AUTH E.T.BALDWIN,I.T.WEBER,R.ST.CHARLES,J.C.XUAN,E.APPELLA,
REMARK 1 AUTH 2 M.YAMADA,K.MATSUSHIMA,B.F.P.EDWARDS,G.M.CLORE,
REMARK 1 AUTH 3 A.M.GRONENBORN,A.WLODAWER
REMARK 1 TITL CRYSTAL STRUCTURE OF INTERLEUKIN 8: SYMBIOSIS OF NMR AND
REMARK 1 TITL 2 CRYSTALLOGRAPHY
REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 88 502 1991
REMARK 1 REFN ISSN 0027-8424
REMARK 1 REFERENCE 3
REMARK 1 AUTH G.M.CLORE,E.APPELLA,M.YAMADA,K.MATSUSHIMA,A.M.GRONENBORN
REMARK 1 TITL THREE DIMENSIONAL STRUCTURE OF INTERLEUKIN 8 IN SOLUTION
REMARK 1 REF BIOCHEMISTRY V. 29 1689 1990
REMARK 1 REFN ISSN 0006-2960
REMARK 2
REMARK 2 RESOLUTION. 1.90 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : GPRLSA
REMARK 3 AUTHORS : FUREY
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL
REMARK 3 COMPLETENESS FOR RANGE (%) : NULL
REMARK 3 NUMBER OF REFLECTIONS : 17475
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3 R VALUE (WORKING + TEST SET) : 0.202
REMARK 3 R VALUE (WORKING SET) : 0.202
REMARK 3 FREE R VALUE : 0.230
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : NULL
REMARK 3
REMARK 3 FIT/AGREEMENT OF MODEL WITH ALL DATA.
REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL
REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE (NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : NULL
REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 1982
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 0
REMARK 3 SOLVENT ATOMS : 265
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : NULL
REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA
REMARK 3 BOND LENGTH (A) : NULL ; NULL
REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL
REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL
REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL
REMARK 3
REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL
REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL
REMARK 3
REMARK 3 NON-BONDED CONTACT RESTRAINTS.
REMARK 3 SINGLE TORSION (A) : NULL ; NULL
REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL
REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL
REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL
REMARK 3
REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS.
REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL
REMARK 3 PLANAR (DEGREES) : NULL ; NULL
REMARK 3 STAGGERED (DEGREES) : NULL ; NULL
REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS:
REMARK 3 THE MUTATION M26L IS DESCRIBED AS M6L IN THE JRNL
REMARK 3 REFERENCE.
REMARK 4
REMARK 4 1NAP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL.
REMARK 100 THE DEPOSITION ID IS D_1000175210.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
REMARK 200 TEMPERATURE (KELVIN) : NULL
REMARK 200 PH : NULL
REMARK 200 NUMBER OF CRYSTALS USED : NULL
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : NULL
REMARK 200 RADIATION SOURCE : NULL
REMARK 200 BEAMLINE : NULL
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL
REMARK 200 WAVELENGTH OR RANGE (A) : NULL
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : NULL
REMARK 200 DETECTOR MANUFACTURER : NULL
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : NULL
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : NULL
REMARK 200 RESOLUTION RANGE HIGH (A) : NULL
REMARK 200 RESOLUTION RANGE LOW (A) : NULL
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : NULL
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL
REMARK 200 COMPLETENESS FOR SHELL (%) : NULL
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: NULL
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL
REMARK 200 SOFTWARE USED: X-PLOR
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 44.36
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: NULL
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,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
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: TETRAMERIC
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 6170 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 12830 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D
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 465
REMARK 465 MISSING RESIDUES
REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE
REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN
REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.)
REMARK 465
REMARK 465 M RES C SSSEQI
REMARK 465 GLU A 87
REMARK 465 SER A 88
REMARK 465 ALA A 89
REMARK 465 ASP A 90
REMARK 465 GLU B 87
REMARK 465 SER B 88
REMARK 465 ALA B 89
REMARK 465 ASP B 90
REMARK 465 ALA C 21
REMARK 465 GLU C 22
REMARK 465 LEU C 23
REMARK 465 GLU C 87
REMARK 465 SER C 88
REMARK 465 ALA C 89
REMARK 465 ASP C 90
REMARK 465 GLU D 87
REMARK 465 SER D 88
REMARK 465 ALA D 89
REMARK 465 ASP D 90
REMARK 999
REMARK 999 SEQUENCE
REMARK 999 THE NUMBERING SCHEME FOR NAP-2 FOLLOWS HOMOLOGY ALIGNMENT
REMARK 999 WITH THE FIRST PAIR OF CYSTEINE RESIDUES IN BOVINE PLATELET
REMARK 999 FACTOR FOUR. THE NUMBERING SCHEME IS SEQUENTIAL BEGINNING
REMARK 999 WITH RESIDUE 21 AND ENDING WITH RESIDUE 90. SEE FIGURE 1
REMARK 999 IN THE JRNL REFERENCE LISTED ABOVE.
DBREF 1NAP A 21 90 UNP P02775 SCYB7_HUMAN 522 591
DBREF 1NAP B 21 90 UNP P02775 SCYB7_HUMAN 522 591
DBREF 1NAP C 21 90 UNP P02775 SCYB7_HUMAN 522 591
DBREF 1NAP D 21 90 UNP P02775 SCYB7_HUMAN 522 591
SEQRES 1 A 70 ALA GLU LEU ARG CYS LEU CYS ILE LYS THR THR SER GLY
SEQRES 2 A 70 ILE HIS PRO LYS ASN ILE GLN SER LEU GLU VAL ILE GLY
SEQRES 3 A 70 LYS GLY THR HIS CYS ASN GLN VAL GLU VAL ILE ALA THR
SEQRES 4 A 70 LEU LYS ASP GLY ARG LYS ILE CYS LEU ASP PRO ASP ALA
SEQRES 5 A 70 PRO ARG ILE LYS LYS ILE VAL GLN LYS LYS LEU ALA GLY
SEQRES 6 A 70 ASP GLU SER ALA ASP
SEQRES 1 B 70 ALA GLU LEU ARG CYS LEU CYS ILE LYS THR THR SER GLY
SEQRES 2 B 70 ILE HIS PRO LYS ASN ILE GLN SER LEU GLU VAL ILE GLY
SEQRES 3 B 70 LYS GLY THR HIS CYS ASN GLN VAL GLU VAL ILE ALA THR
SEQRES 4 B 70 LEU LYS ASP GLY ARG LYS ILE CYS LEU ASP PRO ASP ALA
SEQRES 5 B 70 PRO ARG ILE LYS LYS ILE VAL GLN LYS LYS LEU ALA GLY
SEQRES 6 B 70 ASP GLU SER ALA ASP
SEQRES 1 C 70 ALA GLU LEU ARG CYS LEU CYS ILE LYS THR THR SER GLY
SEQRES 2 C 70 ILE HIS PRO LYS ASN ILE GLN SER LEU GLU VAL ILE GLY
SEQRES 3 C 70 LYS GLY THR HIS CYS ASN GLN VAL GLU VAL ILE ALA THR
SEQRES 4 C 70 LEU LYS ASP GLY ARG LYS ILE CYS LEU ASP PRO ASP ALA
SEQRES 5 C 70 PRO ARG ILE LYS LYS ILE VAL GLN LYS LYS LEU ALA GLY
SEQRES 6 C 70 ASP GLU SER ALA ASP
SEQRES 1 D 70 ALA GLU LEU ARG CYS LEU CYS ILE LYS THR THR SER GLY
SEQRES 2 D 70 ILE HIS PRO LYS ASN ILE GLN SER LEU GLU VAL ILE GLY
SEQRES 3 D 70 LYS GLY THR HIS CYS ASN GLN VAL GLU VAL ILE ALA THR
SEQRES 4 D 70 LEU LYS ASP GLY ARG LYS ILE CYS LEU ASP PRO ASP ALA
SEQRES 5 D 70 PRO ARG ILE LYS LYS ILE VAL GLN LYS LYS LEU ALA GLY
SEQRES 6 D 70 ASP GLU SER ALA ASP
FORMUL 5 HOH *265(H2 O)
HELIX 1 1 PRO A 36 ASN A 38 5 3
HELIX 2 2 PRO A 73 LEU A 83 1 11
HELIX 3 3 PRO B 36 ASN B 38 5 3
HELIX 4 4 PRO B 73 LEU B 83 1 11
HELIX 5 5 PRO C 36 ASN C 38 5 3
HELIX 6 6 PRO C 73 LYS C 82 1 10
HELIX 7 7 PRO D 36 ASN D 38 5 3
HELIX 8 8 PRO D 73 ALA D 84 1 12
SHEET 1 A 6 LYS A 65 LEU A 68 0
SHEET 2 A 6 GLU A 55 LEU A 60 -1 N ALA A 58 O ILE A 66
SHEET 3 A 6 ILE A 39 ILE A 45 -1 N ILE A 45 O GLU A 55
SHEET 4 A 6 ILE B 39 ILE B 45 -1 N VAL B 44 O LEU A 42
SHEET 5 A 6 GLU B 55 LEU B 60 -1 N THR B 59 O GLN B 40
SHEET 6 A 6 LYS B 65 LEU B 68 -1 N LEU B 68 O VAL B 56
SHEET 1 B 6 LYS C 65 LEU C 68 0
SHEET 2 B 6 GLU C 55 LEU C 60 -1 N ALA C 58 O ILE C 66
SHEET 3 B 6 ILE C 39 ILE C 45 -1 N ILE C 45 O GLU C 55
SHEET 4 B 6 ILE D 39 ILE D 45 -1 N VAL D 44 O LEU C 42
SHEET 5 B 6 GLU D 55 LEU D 60 -1 N THR D 59 O GLN D 40
SHEET 6 B 6 LYS D 65 LEU D 68 -1 N LEU D 68 O VAL D 56
SSBOND 1 CYS A 25 CYS A 51 1555 1555 2.04
SSBOND 2 CYS A 27 CYS A 67 1555 1555 2.00
SSBOND 3 CYS B 25 CYS B 51 1555 1555 2.01
SSBOND 4 CYS B 27 CYS B 67 1555 1555 2.02
SSBOND 5 CYS C 25 CYS C 51 1555 1555 1.95
SSBOND 6 CYS C 27 CYS C 67 1555 1555 2.00
SSBOND 7 CYS D 25 CYS D 51 1555 1555 1.97
SSBOND 8 CYS D 27 CYS D 67 1555 1555 1.92
CRYST1 40.770 43.810 44.650 98.37 120.28 92.78 P 1 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 0.024528 0.001191 0.014847 0.00000
SCALE2 0.000000 0.022853 0.004595 0.00000
SCALE3 0.000000 0.000000 0.026454 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
