HEADER IMMUNE SYSTEM 13-APR-14 4PBO TITLE CRYSTAL STRUCTURE OF ZEBRAFISH SHORT-CHAIN PENTRAXIN PROTEIN WITHOUT TITLE 2 CALCIUM IONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: C-REACTIVE PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: ZEBRAFISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: CRP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ACUTE PHASE PROTEIN, PENTRAXIN, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR R.CHEN,J.X.QI,F.G.GEORGE,C.XIA REVDAT 2 27-DEC-23 4PBO 1 SOURCE JRNL REMARK REVDAT 1 25-MAR-15 4PBO 0 JRNL AUTH R.CHEN,J.QI,H.YUAN,Y.WU,W.HU,C.XIA JRNL TITL CRYSTAL STRUCTURES FOR SHORT-CHAIN PENTRAXIN FROM ZEBRAFISH JRNL TITL 2 DEMONSTRATE A CYCLIC TRIMER WITH NEW RECOGNITION AND JRNL TITL 3 EFFECTOR FACES. JRNL REF J.STRUCT.BIOL. V. 189 259 2015 JRNL REFN ESSN 1095-8657 JRNL PMID 25592778 JRNL DOI 10.1016/J.JSB.2015.01.001 REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.090 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 30815 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.186 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 1554 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 26.0035 - 3.7785 0.93 2652 126 0.1801 0.1777 REMARK 3 2 3.7785 - 3.0005 0.99 2804 157 0.1602 0.1686 REMARK 3 3 3.0005 - 2.6216 0.99 2846 142 0.1707 0.1863 REMARK 3 4 2.6216 - 2.3821 0.99 2770 181 0.1692 0.1882 REMARK 3 5 2.3821 - 2.2115 0.98 2781 148 0.1667 0.2042 REMARK 3 6 2.2115 - 2.0812 0.98 2814 138 0.1628 0.1844 REMARK 3 7 2.0812 - 1.9770 0.95 2672 141 0.1564 0.1989 REMARK 3 8 1.9770 - 1.8909 0.93 2637 146 0.1612 0.1742 REMARK 3 9 1.8909 - 1.8182 0.90 2535 139 0.1734 0.2034 REMARK 3 10 1.8182 - 1.7554 0.86 2474 121 0.1765 0.1996 REMARK 3 11 1.7554 - 1.7010 0.80 2276 115 0.1827 0.1894 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 : 0.43 REMARK 3 B_SOL : 60.90 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.600 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) : -11.05150 REMARK 3 B22 (A**2) : -11.05150 REMARK 3 B33 (A**2) : 22.10290 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 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 : 0.006 1706 REMARK 3 ANGLE : 1.033 2322 REMARK 3 CHIRALITY : 0.072 256 REMARK 3 PLANARITY : 0.004 298 REMARK 3 DIHEDRAL : 14.693 599 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): -2.8936 -20.1554 -22.2289 REMARK 3 T TENSOR REMARK 3 T11: 0.2428 T22: 0.2228 REMARK 3 T33: 0.2246 T12: -0.0006 REMARK 3 T13: -0.0242 T23: -0.0053 REMARK 3 L TENSOR REMARK 3 L11: 0.8500 L22: 0.8266 REMARK 3 L33: 0.3021 L12: 0.5679 REMARK 3 L13: -0.1221 L23: -0.1542 REMARK 3 S TENSOR REMARK 3 S11: -0.0295 S12: 0.0340 S13: -0.2051 REMARK 3 S21: 0.0235 S22: 0.0388 S23: -0.0671 REMARK 3 S31: 0.0004 S32: 0.0119 S33: -0.0002 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 4PBO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-APR-14. REMARK 100 THE DEPOSITION ID IS D_1000201107. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NE3A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98048 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32265 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 26.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 10.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 31.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.0 REMARK 200 DATA REDUNDANCY IN SHELL : 9.70 REMARK 200 R MERGE FOR SHELL (I) : 0.27400 REMARK 200 R SYM FOR SHELL (I) : 0.27400 REMARK 200 FOR SHELL : 7.111 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.085M HEPES, 1.7% V/V POLYETHYLENE REMARK 280 GLYCOL 400, 1.7M AMMONIUM SULPHATE, 15% V/V GLYCEROL, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: H 3 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+2/3,Y+1/3,Z+1/3 REMARK 290 5555 -Y+2/3,X-Y+1/3,Z+1/3 REMARK 290 6555 -X+Y+2/3,-X+1/3,Z+1/3 REMARK 290 7555 X+1/3,Y+2/3,Z+2/3 REMARK 290 8555 -Y+1/3,X-Y+2/3,Z+2/3 REMARK 290 9555 -X+Y+1/3,-X+2/3,Z+2/3 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 57.37250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.12403 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 20.34100 REMARK 290 SMTRY1 5 -0.500000 -0.866025 0.000000 57.37250 REMARK 290 SMTRY2 5 0.866025 -0.500000 0.000000 33.12403 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 20.34100 REMARK 290 SMTRY1 6 -0.500000 0.866025 0.000000 57.37250 REMARK 290 SMTRY2 6 -0.866025 -0.500000 0.000000 33.12403 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 20.34100 REMARK 290 SMTRY1 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 66.24806 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 40.68200 REMARK 290 SMTRY1 8 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 8 0.866025 -0.500000 0.000000 66.24806 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 40.68200 REMARK 290 SMTRY1 9 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 -0.500000 0.000000 66.24806 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 40.68200 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: TRIMERIC 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 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 376 LIES ON A SPECIAL POSITION. 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 ASP A 58 12.60 58.70 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4PBP RELATED DB: PDB DBREF 4PBO A 1 207 UNP G9D324 G9D324_DANRE 18 224 SEQRES 1 A 207 PHE LYS ASN LEU SER GLY LYS VAL LEU GLN PHE LYS THR SEQRES 2 A 207 ALA THR ASP ASN SER TYR VAL LYS LEU TYR PRO GLU LYS SEQRES 3 A 207 PRO LEU SER LEU SER ALA PHE THR LEU CYS MET ARG VAL SEQRES 4 A 207 ALA THR GLU LEU PRO LEU ASP ARG GLU VAL ILE LEU PHE SEQRES 5 A 207 ALA TYR TYR THR PRO ASP VAL ASP GLU LEU ASN VAL TRP SEQRES 6 A 207 ARG GLU ARG ASP GLY ARG VAL SER LEU TYR ILE GLN SER SEQRES 7 A 207 SER LYS ASP ALA ALA PHE PHE ARG LEU PRO PRO LEU SER SEQRES 8 A 207 THR LEU GLN THR HIS LEU CYS VAL ALA TRP GLU SER ALA SEQRES 9 A 207 THR GLY LEU THR ALA PHE TRP MET ASP GLY ARG ARG SER SEQRES 10 A 207 LEU HIS GLN VAL TYR ARG LYS GLY TYR SER ILE ARG SER SEQRES 11 A 207 GLY GLY THR VAL VAL LEU GLY GLN ASP PRO ASP SER TYR SEQRES 12 A 207 VAL GLY SER PHE ASP VAL ASP GLN SER PHE VAL GLY GLU SEQRES 13 A 207 ILE ALA ASN LEU GLN MET TRP ASP TYR VAL LEU SER SER SEQRES 14 A 207 ALA GLN ILE LYS ALA VAL TYR TYR ASN GLN ASP ASN ARG SEQRES 15 A 207 VAL LYS GLY ASN VAL PHE ASP TRP ASP THR ILE GLU TYR SEQRES 16 A 207 ASP VAL THR GLY ASN VAL LEU VAL VAL PRO ASP ASN FORMUL 2 HOH *233(H2 O) HELIX 1 AA1 ASP A 139 TYR A 143 5 5 HELIX 2 AA2 ASP A 148 SER A 152 5 5 HELIX 3 AA3 SER A 168 TYR A 177 1 10 SHEET 1 AA1 6 ARG A 115 ARG A 116 0 SHEET 2 AA1 6 LEU A 107 MET A 112 -1 N MET A 112 O ARG A 115 SHEET 3 AA1 6 THR A 95 GLU A 102 -1 N CYS A 98 O TRP A 111 SHEET 4 AA1 6 ALA A 32 ALA A 40 -1 N MET A 37 O LEU A 97 SHEET 5 AA1 6 GLY A 155 TRP A 163 -1 O ALA A 158 N ARG A 38 SHEET 6 AA1 6 PHE A 188 ASP A 189 -1 O PHE A 188 N MET A 162 SHEET 1 AA2 7 GLN A 120 VAL A 121 0 SHEET 2 AA2 7 LEU A 107 MET A 112 -1 N THR A 108 O GLN A 120 SHEET 3 AA2 7 THR A 95 GLU A 102 -1 N CYS A 98 O TRP A 111 SHEET 4 AA2 7 ALA A 32 ALA A 40 -1 N MET A 37 O LEU A 97 SHEET 5 AA2 7 GLY A 155 TRP A 163 -1 O ALA A 158 N ARG A 38 SHEET 6 AA2 7 LYS A 7 PHE A 11 -1 N PHE A 11 O GLY A 155 SHEET 7 AA2 7 LEU A 202 PRO A 205 -1 O LEU A 202 N GLN A 10 SHEET 1 AA3 7 ALA A 83 PHE A 85 0 SHEET 2 AA3 7 VAL A 72 ILE A 76 -1 N VAL A 72 O PHE A 85 SHEET 3 AA3 7 VAL A 59 ARG A 66 -1 N ASN A 63 O TYR A 75 SHEET 4 AA3 7 VAL A 49 THR A 56 -1 N THR A 56 O VAL A 59 SHEET 5 AA3 7 THR A 133 LEU A 136 -1 O VAL A 135 N ALA A 53 SHEET 6 AA3 7 TYR A 19 TYR A 23 -1 N VAL A 20 O LEU A 136 SHEET 7 AA3 7 GLU A 194 THR A 198 -1 O THR A 198 N TYR A 19 SSBOND 1 CYS A 36 CYS A 98 1555 1555 2.07 CRYST1 114.745 114.745 61.023 90.00 90.00 120.00 H 3 9 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 0.008715 0.005032 0.000000 0.00000 SCALE2 0.000000 0.010063 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016387 0.00000