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 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 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