HEADER IMMUNE SYSTEM 05-JUN-17 5XPW TITLE STRUCTURE OF AMPHIOXUS IGVJ-C2 MOLECULE COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMPHIOXUS IGVJ-C2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 20-199; COMPND 5 SYNONYM: AMPHIOXUS IGVJ-C2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BRANCHIOSTOMA FLORIDAE; SOURCE 3 ORGANISM_COMMON: FLORIDA LANCELET; SOURCE 4 ORGANISM_TAXID: 7739; SOURCE 5 GENE: BRAFLDRAFT_122935; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI 042; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 216592; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: 042 KEYWDS IMMUNOGLOBULIN SUPERFAMILY, DIMMER, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR R.CHEN,J.QI,N.ZHANG,L.ZHANG,S.YAO,Y.WU,B.JIANG,Z.WANG,H.YUAN,Q.ZHANG, AUTHOR 2 C.XIA REVDAT 3 16-OCT-24 5XPW 1 REMARK REVDAT 2 25-APR-18 5XPW 1 JRNL REVDAT 1 18-APR-18 5XPW 0 JRNL AUTH R.CHEN,L.ZHANG,J.QI,N.ZHANG,L.ZHANG,S.YAO,Y.WU,B.JIANG, JRNL AUTH 2 Z.WANG,H.YUAN,Q.ZHANG,C.XIA JRNL TITL DISCOVERY AND ANALYSIS OF INVERTEBRATE IGVJ-C2 STRUCTURE JRNL TITL 2 FROM AMPHIOXUS PROVIDES INSIGHT INTO THE EVOLUTION OF THE IG JRNL TITL 3 SUPERFAMILY. JRNL REF J. IMMUNOL. V. 200 2869 2018 JRNL REFN ESSN 1550-6606 JRNL PMID 29514951 JRNL DOI 10.4049/JIMMUNOL.1700906 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.25 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.160 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 14607 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.266 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 734 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 34.2578 - 3.4240 0.95 2973 160 0.2353 0.2741 REMARK 3 2 3.4240 - 2.7181 1.00 2948 153 0.1870 0.2275 REMARK 3 3 2.7181 - 2.3746 0.98 2848 137 0.2317 0.2567 REMARK 3 4 2.3746 - 2.1575 0.94 2693 159 0.2305 0.2959 REMARK 3 5 2.1575 - 2.0029 0.85 2411 125 0.2467 0.2790 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 : 0.41 REMARK 3 B_SOL : 58.75 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.890 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) : 5.95170 REMARK 3 B22 (A**2) : 5.95170 REMARK 3 B33 (A**2) : -11.90340 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 1429 REMARK 3 ANGLE : 0.828 1948 REMARK 3 CHIRALITY : 0.056 214 REMARK 3 PLANARITY : 0.003 261 REMARK 3 DIHEDRAL : 18.159 499 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): 6.5601 4.4873 10.6224 REMARK 3 T TENSOR REMARK 3 T11: 0.3462 T22: 0.3263 REMARK 3 T33: 0.3387 T12: 0.0243 REMARK 3 T13: -0.0005 T23: 0.0213 REMARK 3 L TENSOR REMARK 3 L11: 0.1433 L22: 0.1927 REMARK 3 L33: 0.2233 L12: 0.0473 REMARK 3 L13: 0.0945 L23: 0.0077 REMARK 3 S TENSOR REMARK 3 S11: -0.0628 S12: -0.0275 S13: -0.0723 REMARK 3 S21: 0.0591 S22: 0.0020 S23: -0.0754 REMARK 3 S31: -0.0551 S32: 0.1397 S33: -0.0000 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 5XPW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 14-JUN-17. REMARK 100 THE DEPOSITION ID IS D_1300003966. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-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) : 0.98051 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15493 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 15.90 REMARK 200 R MERGE (I) : 0.09400 REMARK 200 R SYM (I) : 0.09400 REMARK 200 FOR THE DATA SET : 24.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.1 REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.43900 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: SAD 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 (%): 54.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M LITHIUM SULFATE MONOHYDRATE, 0.1M REMARK 280 BIS-TRIS (PH 5.5), 25% W/V POLYETHYLENE GLYCOL 3350, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 71.23967 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 142.47933 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 142.47933 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 71.23967 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: DIMERIC 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NH1 ARG A 124 O HOH A 262 4655 1.71 REMARK 500 O HOH A 221 O HOH A 262 4655 1.84 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 PRO A 16 97.27 -67.75 REMARK 500 GLU A 46 -126.44 55.41 REMARK 500 ARG A 60 -55.26 -141.05 REMARK 500 REMARK 500 REMARK: NULL DBREF 5XPW A 1 180 UNP C3ZN36 C3ZN36_BRAFL 20 199 SEQRES 1 A 180 VAL SER HIS GLN GLN GLY GLN SER HIS LEU PHE GLU CYS SEQRES 2 A 180 ASP TYR PRO ILE SER ALA ASP THR TYR VAL ILE ASN TRP SEQRES 3 A 180 TYR LYS ASP GLY THR SER VAL MET ASN TYR LEU SER GLY SEQRES 4 A 180 GLY GLU PRO ALA PHE THR GLU ASP LEU ASP ASP ARG THR SEQRES 5 A 180 ASP VAL GLN PHE VAL ASN ASN ARG ASN LEU GLU ILE THR SEQRES 6 A 180 ASN LEU ARG VAL SER ASP GLU GLY GLU TYR TYR CYS SER SEQRES 7 A 180 VAL ILE GLU ILE GLY ALA GLY GLY GLN SER GLY ASP GLY SEQRES 8 A 180 THR ARG TYR GLN LEU VAL VAL PHE VAL PRO PRO THR ILE SEQRES 9 A 180 THR LEU MET GLY GLY PRO TYR GLU VAL GLU VAL GLY GLU SEQRES 10 A 180 MET MET MET SER THR CYS ARG ALA ASN SER HIS PRO PRO SEQRES 11 A 180 SER ASN PHE THR TRP THR LEU PRO ASN GLY ASN VAL THR SEQRES 12 A 180 GLN GLY ALA VAL LEU GLU ILE THR ASN MET THR GLN ALA SEQRES 13 A 180 GLU ILE GLY THR TYR MET CYS THR ALA ASP ASN GLY TYR SEQRES 14 A 180 GLY THR ASP TYR GLU SER VAL ASP ILE THR MET FORMUL 2 HOH *72(H2 O) HELIX 1 AA1 GLU A 46 ASP A 49 5 4 HELIX 2 AA2 ARG A 68 GLU A 72 5 5 SHEET 1 AA1 4 SER A 2 GLN A 4 0 SHEET 2 AA1 4 TYR A 94 GLY A 109 1 O PHE A 99 N HIS A 3 SHEET 3 AA1 4 GLY A 73 GLU A 81 -1 N TYR A 75 O TYR A 94 SHEET 4 AA1 4 SER A 88 ASP A 90 -1 O GLY A 89 N VAL A 79 SHEET 1 AA2 7 ALA A 43 PHE A 44 0 SHEET 2 AA2 7 THR A 31 LEU A 37 -1 N ASN A 35 O ALA A 43 SHEET 3 AA2 7 TYR A 22 LYS A 28 -1 N TRP A 26 O VAL A 33 SHEET 4 AA2 7 GLY A 73 GLU A 81 -1 O TYR A 76 N TYR A 27 SHEET 5 AA2 7 TYR A 94 GLY A 109 -1 O TYR A 94 N TYR A 75 SHEET 6 AA2 7 MET A 119 HIS A 128 -1 O THR A 122 N MET A 107 SHEET 7 AA2 7 VAL A 147 ILE A 150 -1 O LEU A 148 N SER A 121 SHEET 1 AA3 3 HIS A 9 PHE A 11 0 SHEET 2 AA3 3 ASN A 61 ILE A 64 -1 O LEU A 62 N PHE A 11 SHEET 3 AA3 3 VAL A 54 VAL A 57 -1 N GLN A 55 O GLU A 63 SHEET 1 AA4 4 VAL A 142 GLN A 144 0 SHEET 2 AA4 4 ASN A 132 THR A 136 -1 N TRP A 135 O THR A 143 SHEET 3 AA4 4 GLY A 159 ASP A 166 -1 O MET A 162 N THR A 136 SHEET 4 AA4 4 THR A 171 ILE A 178 -1 O VAL A 176 N TYR A 161 SSBOND 1 CYS A 13 CYS A 77 1555 1555 2.04 SSBOND 2 CYS A 123 CYS A 163 1555 1555 2.02 CISPEP 1 GLY A 109 PRO A 110 0 -4.88 CISPEP 2 HIS A 128 PRO A 129 0 1.27 CRYST1 41.755 41.755 213.719 90.00 90.00 120.00 P 31 2 1 6 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 0.023949 0.013827 0.000000 0.00000 SCALE2 0.000000 0.027654 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004679 0.00000