HEADER CYTOKINE 08-NOV-10 3PIV TITLE ZEBRAFISH INTERFERON 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERFERON; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: LEOPARD DANIO,ZEBRA DANIO,ZEBRA FISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: IFNPHI1, IFN1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS INTERFERON, ZEBRAFISH, CYTOKINE EXPDTA X-RAY DIFFRACTION AUTHOR O.J.HAMMING,R.HARTMANN,G.LUTFALLA,J.-P.LEVRAUD REVDAT 3 07-MAR-18 3PIV 1 REMARK REVDAT 2 03-AUG-11 3PIV 1 JRNL REVDAT 1 20-JUL-11 3PIV 0 JRNL AUTH O.J.HAMMING,G.LUTFALLA,J.P.LEVRAUD,R.HARTMANN JRNL TITL CRYSTAL STRUCTURE OF ZEBRAFISH INTERFERONS I AND II REVEALS JRNL TITL 2 CONSERVATION OF TYPE I INTERFERON STRUCTURE IN VERTEBRATES. JRNL REF J.VIROL. V. 85 8181 2011 JRNL REFN ISSN 0022-538X JRNL PMID 21653665 JRNL DOI 10.1128/JVI.00521-11 REMARK 2 REMARK 2 RESOLUTION. 2.09 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.09 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.82 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.140 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.0 REMARK 3 NUMBER OF REFLECTIONS : 16604 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.235 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.080 REMARK 3 FREE R VALUE TEST SET COUNT : 843 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 48.8323 - 3.7907 0.98 2897 178 0.1685 0.1997 REMARK 3 2 3.7907 - 3.0089 0.98 2849 164 0.1765 0.2158 REMARK 3 3 3.0089 - 2.6286 0.96 2832 115 0.1918 0.2788 REMARK 3 4 2.6286 - 2.3883 0.93 2690 146 0.1871 0.2445 REMARK 3 5 2.3883 - 2.2171 0.86 2499 125 0.1989 0.3048 REMARK 3 6 2.2171 - 2.0864 0.69 1994 115 0.2026 0.2878 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 40.31 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 24.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.23130 REMARK 3 B22 (A**2) : 2.76700 REMARK 3 B33 (A**2) : -4.99830 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.98610 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 2647 REMARK 3 ANGLE : 1.026 3555 REMARK 3 CHIRALITY : 0.067 393 REMARK 3 PLANARITY : 0.004 443 REMARK 3 DIHEDRAL : 17.750 1005 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3PIV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1000062425. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUN-09 REMARK 200 TEMPERATURE (KELVIN) : 77 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I911-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8742 REMARK 200 MONOCHROMATOR : SI (111) DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18309 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.086 REMARK 200 RESOLUTION RANGE LOW (A) : 51.290 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.3 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.14000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.09 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.22 REMARK 200 COMPLETENESS FOR SHELL (%) : 69.0 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: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.67 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M NACL, 20% PEG3350, 0.1 M HEPES REMARK 280 PH 6.5, 3% (V/V) JEFFAMINE M-600, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 31.12350 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: PISA 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 GLY A 1 REMARK 465 SER A 2 REMARK 465 THR A 3 REMARK 465 VAL A 160 REMARK 465 ASN A 161 REMARK 465 PRO A 162 REMARK 465 ARG A 163 REMARK 465 VAL A 164 REMARK 465 GLY B 1 REMARK 465 SER B 2 REMARK 465 THR B 3 REMARK 465 ASN B 161 REMARK 465 PRO B 162 REMARK 465 ARG B 163 REMARK 465 VAL B 164 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ARG A 159 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 5 CG CD OE1 OE2 REMARK 470 ARG B 91 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 159 CG CD NE CZ NH1 NH2 REMARK 470 VAL B 160 CG1 CG2 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 ALA A 68 39.09 -142.64 REMARK 500 ALA B 68 41.06 -142.16 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 NI A 165 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 165 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3PIW RELATED DB: PDB REMARK 900 RELATED PROTEIN FROM SAME CITATION DBREF 3PIV A 2 164 UNP Q8AY12 Q8AY12_DANRE 23 185 DBREF 3PIV B 2 164 UNP Q8AY12 Q8AY12_DANRE 23 185 SEQADV 3PIV GLY A 1 UNP Q8AY12 EXPRESSION TAG SEQADV 3PIV GLY B 1 UNP Q8AY12 EXPRESSION TAG SEQRES 1 A 164 GLY SER THR CYS GLU TRP LEU GLY ARG TYR ARG ILE ILE SEQRES 2 A 164 THR THR GLU SER LEU ASN LEU LEU LYS ASN MET GLY GLY SEQRES 3 A 164 LYS TYR ALA ASP LEU GLU THR PRO PHE PRO SER ARG LEU SEQRES 4 A 164 TYR THR LEU MET ASP LYS SER LYS VAL GLU ASP GLN VAL SEQRES 5 A 164 LYS PHE LEU VAL LEU THR LEU ASP HIS ILE ILE HIS LEU SEQRES 6 A 164 MET ASP ALA ARG GLU HIS MET ASN SER VAL ASN TRP ASP SEQRES 7 A 164 GLN ASN THR VAL GLU ASP PHE LEU ASN ILE LEU HIS ARG SEQRES 8 A 164 LYS SER SER ASP LEU LYS GLU CYS VAL ALA ARG TYR ALA SEQRES 9 A 164 LYS PRO ALA HIS LYS GLU SER TYR GLU ILE ARG ILE LYS SEQRES 10 A 164 ARG HIS PHE ARG THR LEU LYS LYS ILE LEU LYS LYS LYS SEQRES 11 A 164 GLN TYR SER ALA GLU ALA TRP GLU GLN ILE ARG ARG VAL SEQRES 12 A 164 VAL LYS SER HIS LEU GLN ARG MET ASP ILE ILE ALA SER SEQRES 13 A 164 ASN ALA ARG VAL ASN PRO ARG VAL SEQRES 1 B 164 GLY SER THR CYS GLU TRP LEU GLY ARG TYR ARG ILE ILE SEQRES 2 B 164 THR THR GLU SER LEU ASN LEU LEU LYS ASN MET GLY GLY SEQRES 3 B 164 LYS TYR ALA ASP LEU GLU THR PRO PHE PRO SER ARG LEU SEQRES 4 B 164 TYR THR LEU MET ASP LYS SER LYS VAL GLU ASP GLN VAL SEQRES 5 B 164 LYS PHE LEU VAL LEU THR LEU ASP HIS ILE ILE HIS LEU SEQRES 6 B 164 MET ASP ALA ARG GLU HIS MET ASN SER VAL ASN TRP ASP SEQRES 7 B 164 GLN ASN THR VAL GLU ASP PHE LEU ASN ILE LEU HIS ARG SEQRES 8 B 164 LYS SER SER ASP LEU LYS GLU CYS VAL ALA ARG TYR ALA SEQRES 9 B 164 LYS PRO ALA HIS LYS GLU SER TYR GLU ILE ARG ILE LYS SEQRES 10 B 164 ARG HIS PHE ARG THR LEU LYS LYS ILE LEU LYS LYS LYS SEQRES 11 B 164 GLN TYR SER ALA GLU ALA TRP GLU GLN ILE ARG ARG VAL SEQRES 12 B 164 VAL LYS SER HIS LEU GLN ARG MET ASP ILE ILE ALA SER SEQRES 13 B 164 ASN ALA ARG VAL ASN PRO ARG VAL HET NI A 165 1 HET NI B 165 1 HETNAM NI NICKEL (II) ION FORMUL 3 NI 2(NI 2+) FORMUL 5 HOH *149(H2 O) HELIX 1 1 CYS A 4 GLY A 8 5 5 HELIX 2 2 ARG A 9 MET A 24 1 16 HELIX 3 3 PRO A 36 LYS A 45 1 10 HELIX 4 4 LYS A 47 ASP A 67 1 21 HELIX 5 5 ALA A 68 MET A 72 5 5 HELIX 6 6 ASP A 78 ARG A 102 1 25 HELIX 7 7 GLU A 110 LYS A 130 1 21 HELIX 8 8 SER A 133 ARG A 159 1 27 HELIX 9 9 CYS B 4 GLY B 8 5 5 HELIX 10 10 ARG B 9 MET B 24 1 16 HELIX 11 11 PRO B 36 LYS B 45 1 10 HELIX 12 12 LYS B 47 ASP B 67 1 21 HELIX 13 13 ALA B 68 MET B 72 5 5 HELIX 14 14 ASP B 78 ALA B 101 1 24 HELIX 15 15 GLU B 110 LYS B 130 1 21 HELIX 16 16 SER B 133 VAL B 160 1 28 SSBOND 1 CYS A 4 CYS A 99 1555 1555 2.04 SSBOND 2 CYS B 4 CYS B 99 1555 1555 2.07 SITE 1 AC1 2 HIS A 61 HIS A 64 SITE 1 AC2 2 HIS B 61 HIS B 64 CRYST1 48.834 62.247 51.306 90.00 91.42 90.00 P 1 21 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 0.020478 0.000000 0.000509 0.00000 SCALE2 0.000000 0.016065 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019497 0.00000