HEADER CYTOKINE 05-AUG-15 5D22 TITLE STRUCTURE OF OVINE GRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: GRANULOCYTE-MACROPHAGE COLONY-STIMULATING FACTOR; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: GM-CSF,COLONY-STIMULATING FACTOR,CSF; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: OVIS ARIES; SOURCE 3 ORGANISM_COMMON: SHEEP; SOURCE 4 ORGANISM_TAXID: 9940; SOURCE 5 GENE: CSF2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SIGNALING PROTEIN, RECOMBINANT PROTEINS, CYTOKINE IMMUNOLOGY, KEYWDS 2 CYTOKINE EXPDTA X-RAY DIFFRACTION AUTHOR J.FELIX,S.N.SAVVIDES REVDAT 4 06-NOV-24 5D22 1 REMARK REVDAT 3 10-JAN-24 5D22 1 REMARK REVDAT 2 07-MAR-18 5D22 1 REMARK REVDAT 1 16-NOV-16 5D22 0 JRNL AUTH J.FELIX,E.KANDIAH,S.DE MUNCK,Y.BLOCH,G.C.VAN ZUNDERT, JRNL AUTH 2 K.PAUWELS,A.DANSERCOER,K.NOVANSKA,R.J.READ,A.M.BONVIN, JRNL AUTH 3 B.VERGAUWEN,K.VERSTRAETE,I.GUTSCHE,S.N.SAVVIDES JRNL TITL STRUCTURAL BASIS OF GM-CSF AND IL-2 SEQUESTRATION BY THE JRNL TITL 2 VIRAL DECOY RECEPTOR GIF. JRNL REF NAT COMMUN V. 7 13228 2016 JRNL REFN ESSN 2041-1723 JRNL PMID 27819269 JRNL DOI 10.1038/NCOMMS13228 REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.51 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 NUMBER OF REFLECTIONS : 18017 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.188 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 900 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 38.5172 - 3.6231 0.97 2946 156 0.1525 0.1751 REMARK 3 2 3.6231 - 2.8760 0.98 2933 154 0.1769 0.2426 REMARK 3 3 2.8760 - 2.5126 0.98 2889 150 0.1961 0.2450 REMARK 3 4 2.5126 - 2.2829 0.95 2829 150 0.2160 0.2497 REMARK 3 5 2.2829 - 2.1192 0.96 2853 152 0.2473 0.2885 REMARK 3 6 2.1192 - 1.9943 0.91 2667 138 0.2881 0.3277 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.270 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.090 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 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 : 0.009 1981 REMARK 3 ANGLE : 1.068 2685 REMARK 3 CHIRALITY : 0.049 310 REMARK 3 PLANARITY : 0.006 343 REMARK 3 DIHEDRAL : 12.777 734 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 3.6389 -18.0912 -9.3264 REMARK 3 T TENSOR REMARK 3 T11: 0.2436 T22: 0.2360 REMARK 3 T33: 0.2640 T12: -0.0429 REMARK 3 T13: 0.0148 T23: -0.0164 REMARK 3 L TENSOR REMARK 3 L11: 0.7692 L22: 0.6854 REMARK 3 L33: 1.1407 L12: -0.4638 REMARK 3 L13: 0.4686 L23: -0.2923 REMARK 3 S TENSOR REMARK 3 S11: -0.0122 S12: -0.0032 S13: -0.0200 REMARK 3 S21: -0.0281 S22: 0.0123 S23: -0.0039 REMARK 3 S31: 0.0081 S32: -0.0134 S33: 0.0001 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 5D22 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-AUG-15. REMARK 100 THE DEPOSITION ID IS D_1000212558. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-NOV-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P14 (MX2) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.239 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18252 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 38.510 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 3.280 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12900 REMARK 200 FOR THE DATA SET : 8.1700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.14 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.73200 REMARK 200 FOR SHELL : 2.120 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: 2GMF REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM ACETATE TRIHYDRATE 0.1 M REMARK 280 TRIS HYDROCHLORIDE PH 8.5 30% W/V PEG 4000, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K 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 38.51000 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 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 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 ALA A 1 REMARK 465 PRO A 2 REMARK 465 THR A 3 REMARK 465 ARG A 4 REMARK 465 VAL A 125 REMARK 465 GLN A 126 REMARK 465 LYS A 127 REMARK 465 ALA B 1 REMARK 465 PRO B 2 REMARK 465 THR B 3 REMARK 465 ARG B 4 REMARK 465 GLN B 126 REMARK 465 LYS B 127 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 GLN A 5 CG CD OE1 NE2 REMARK 470 GLN B 5 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH B 308 O HOH B 351 1.73 REMARK 500 N ASP A 31 O HOH A 301 1.80 REMARK 500 OE1 GLU B 45 O HOH B 301 1.82 REMARK 500 CA THR A 30 O HOH A 301 1.87 REMARK 500 O MET B 46 O HOH B 302 1.89 REMARK 500 O HOH B 312 O HOH B 348 1.96 REMARK 500 O HOH A 360 O HOH A 361 2.07 REMARK 500 C THR A 30 O HOH A 301 2.12 REMARK 500 O HOH A 362 O HOH B 347 2.12 REMARK 500 REMARK 500 REMARK: NULL 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 TRP A 13 -7.18 -144.64 REMARK 500 GLU A 51 75.37 -119.62 REMARK 500 TRP B 13 -6.91 -144.82 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 ACT A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT B 201 DBREF 5D22 A 1 127 UNP P28773 CSF2_SHEEP 18 144 DBREF 5D22 B 1 127 UNP P28773 CSF2_SHEEP 18 144 SEQRES 1 A 127 ALA PRO THR ARG GLN PRO SER PRO VAL THR ARG PRO TRP SEQRES 2 A 127 GLN HIS VAL ASP ALA ILE LYS GLU ALA LEU SER LEU LEU SEQRES 3 A 127 ASN ASP SER THR ASP THR ALA ALA VAL MET ASP GLU THR SEQRES 4 A 127 VAL GLU VAL VAL SER GLU MET PHE ASP SER GLN GLU PRO SEQRES 5 A 127 THR CYS LEU GLN THR ARG LEU GLU LEU TYR LYS GLN GLY SEQRES 6 A 127 LEU ARG GLY SER LEU THR SER LEU THR GLY SER LEU THR SEQRES 7 A 127 MET MET ALA SER HIS TYR LYS LYS HIS CYS PRO PRO THR SEQRES 8 A 127 GLN GLU THR SER CYS GLU THR GLN ILE ILE THR PHE LYS SEQRES 9 A 127 SER PHE LYS GLU ASN LEU LYS ASP PHE LEU PHE ILE ILE SEQRES 10 A 127 PRO PHE ASP CYS TRP GLU PRO VAL GLN LYS SEQRES 1 B 127 ALA PRO THR ARG GLN PRO SER PRO VAL THR ARG PRO TRP SEQRES 2 B 127 GLN HIS VAL ASP ALA ILE LYS GLU ALA LEU SER LEU LEU SEQRES 3 B 127 ASN ASP SER THR ASP THR ALA ALA VAL MET ASP GLU THR SEQRES 4 B 127 VAL GLU VAL VAL SER GLU MET PHE ASP SER GLN GLU PRO SEQRES 5 B 127 THR CYS LEU GLN THR ARG LEU GLU LEU TYR LYS GLN GLY SEQRES 6 B 127 LEU ARG GLY SER LEU THR SER LEU THR GLY SER LEU THR SEQRES 7 B 127 MET MET ALA SER HIS TYR LYS LYS HIS CYS PRO PRO THR SEQRES 8 B 127 GLN GLU THR SER CYS GLU THR GLN ILE ILE THR PHE LYS SEQRES 9 B 127 SER PHE LYS GLU ASN LEU LYS ASP PHE LEU PHE ILE ILE SEQRES 10 B 127 PRO PHE ASP CYS TRP GLU PRO VAL GLN LYS HET ACT A 201 4 HET EDO A 202 4 HET ACT B 201 4 HETNAM ACT ACETATE ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 ACT 2(C2 H3 O2 1-) FORMUL 4 EDO C2 H6 O2 FORMUL 6 HOH *121(H2 O) HELIX 1 AA1 TRP A 13 ASP A 28 1 16 HELIX 2 AA2 THR A 32 ASP A 37 1 6 HELIX 3 AA3 CYS A 54 LEU A 66 1 13 HELIX 4 AA4 ARG A 67 SER A 72 5 6 HELIX 5 AA5 LEU A 73 CYS A 88 1 16 HELIX 6 AA6 PHE A 103 ILE A 117 1 15 HELIX 7 AA7 TRP B 13 SER B 29 1 17 HELIX 8 AA8 THR B 32 ASP B 37 1 6 HELIX 9 AA9 CYS B 54 GLY B 65 1 12 HELIX 10 AB1 ARG B 67 SER B 72 5 6 HELIX 11 AB2 LEU B 73 CYS B 88 1 16 HELIX 12 AB3 PHE B 103 ILE B 117 1 15 SHEET 1 AA1 2 THR A 39 VAL A 43 0 SHEET 2 AA1 2 THR A 98 THR A 102 -1 O ILE A 101 N VAL A 40 SHEET 1 AA2 2 THR B 39 VAL B 43 0 SHEET 2 AA2 2 THR B 98 THR B 102 -1 O ILE B 101 N VAL B 40 SSBOND 1 CYS A 54 CYS A 96 1555 1555 2.05 SSBOND 2 CYS A 88 CYS A 121 1555 1555 2.06 SSBOND 3 CYS B 54 CYS B 96 1555 1555 2.06 SSBOND 4 CYS B 88 CYS B 121 1555 1555 2.06 CISPEP 1 SER A 7 PRO A 8 0 -3.02 CISPEP 2 SER B 7 PRO B 8 0 -3.58 SITE 1 AC1 3 THR A 98 HOH A 317 HOH B 303 SITE 1 AC2 4 TRP A 13 VAL A 16 ASP A 17 LYS A 20 SITE 1 AC3 3 LYS A 86 HOH A 305 THR B 98 CRYST1 41.100 77.020 47.450 90.00 111.54 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 0.024331 0.000000 0.009603 0.00000 SCALE2 0.000000 0.012984 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022657 0.00000