HEADER IMMUNE SYSTEM 05-JUN-17 5XPV TITLE STRUCTURE OF THE V DOMAIN OF AMPHIOXUS IGVJ-C2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMPHIOXUS IGVJ-C2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: V DOMAIN, UNP RESIDUES 20-119; 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 4 23-OCT-24 5XPV 1 REMARK REVDAT 3 22-NOV-23 5XPV 1 REMARK REVDAT 2 25-APR-18 5XPV 1 JRNL REVDAT 1 18-APR-18 5XPV 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. 1.90 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 18730 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.207 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 966 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 23.3540 - 3.6287 1.00 2705 130 0.1728 0.1991 REMARK 3 2 3.6287 - 2.8819 1.00 2551 141 0.1811 0.1951 REMARK 3 3 2.8819 - 2.5181 1.00 2524 146 0.1885 0.2380 REMARK 3 4 2.5181 - 2.2881 1.00 2551 124 0.1847 0.1958 REMARK 3 5 2.2881 - 2.1242 1.00 2498 136 0.1738 0.2085 REMARK 3 6 2.1242 - 1.9991 1.00 2510 132 0.1759 0.1887 REMARK 3 7 1.9991 - 1.8990 0.99 2425 157 0.1953 0.2422 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.040 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 : 0.005 1614 REMARK 3 ANGLE : 0.819 2192 REMARK 3 CHIRALITY : 0.036 234 REMARK 3 PLANARITY : 0.004 296 REMARK 3 DIHEDRAL : 14.798 570 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): -11.3577 14.3008 -22.9049 REMARK 3 T TENSOR REMARK 3 T11: 0.1734 T22: 0.1645 REMARK 3 T33: 0.1778 T12: -0.0141 REMARK 3 T13: -0.0058 T23: -0.0024 REMARK 3 L TENSOR REMARK 3 L11: 0.3642 L22: 0.2117 REMARK 3 L33: 0.8937 L12: -0.0984 REMARK 3 L13: -0.3794 L23: -0.0989 REMARK 3 S TENSOR REMARK 3 S11: 0.0179 S12: 0.0200 S13: -0.0146 REMARK 3 S21: 0.0045 S22: 0.0024 S23: -0.0106 REMARK 3 S31: -0.0427 S32: -0.0168 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 5XPV 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_1300003967. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-JAN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18794 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.04900 REMARK 200 R SYM (I) : 0.04900 REMARK 200 FOR THE DATA SET : 35.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.18600 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: 5XPW REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5M AMMONIUM SULFATE, 0.1M SODIUM REMARK 280 CITRATE TRIBASIC DEHYDRATE, 1.0M LITHIUM SULFATE MONOHYDRATE (PH REMARK 280 5.6), VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 X,-Y,-Z REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.89250 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.31250 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.89250 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 37.31250 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1190 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 B 299 LIES ON A SPECIAL POSITION. 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 226 O HOH B 249 1.81 REMARK 500 O HOH A 202 O HOH A 281 1.94 REMARK 500 O HOH A 253 O HOH A 290 1.94 REMARK 500 O HOH B 293 O HOH B 297 2.14 REMARK 500 OD2 ASP B 49 O HOH B 201 2.14 REMARK 500 O HOH B 214 O HOH B 279 2.18 REMARK 500 NE2 GLN B 55 O HOH B 202 2.18 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 GLU A 46 -123.09 51.16 REMARK 500 ASP A 50 -0.69 65.30 REMARK 500 ARG A 60 -50.99 -152.45 REMARK 500 GLU B 46 -124.31 51.62 REMARK 500 ARG B 60 -34.38 -156.29 REMARK 500 REMARK 500 REMARK: NULL DBREF 5XPV A 1 100 UNP C3ZN36 C3ZN36_BRAFL 20 119 DBREF 5XPV B 1 100 UNP C3ZN36 C3ZN36_BRAFL 20 119 SEQRES 1 A 100 VAL SER HIS GLN GLN GLY GLN SER HIS LEU PHE GLU CYS SEQRES 2 A 100 ASP TYR PRO ILE SER ALA ASP THR TYR VAL ILE ASN TRP SEQRES 3 A 100 TYR LYS ASP GLY THR SER VAL MET ASN TYR LEU SER GLY SEQRES 4 A 100 GLY GLU PRO ALA PHE THR GLU ASP LEU ASP ASP ARG THR SEQRES 5 A 100 ASP VAL GLN PHE VAL ASN ASN ARG ASN LEU GLU ILE THR SEQRES 6 A 100 ASN LEU ARG VAL SER ASP GLU GLY GLU TYR TYR CYS SER SEQRES 7 A 100 VAL ILE GLU ILE GLY ALA GLY GLY GLN SER GLY ASP GLY SEQRES 8 A 100 THR ARG TYR GLN LEU VAL VAL PHE VAL SEQRES 1 B 100 VAL SER HIS GLN GLN GLY GLN SER HIS LEU PHE GLU CYS SEQRES 2 B 100 ASP TYR PRO ILE SER ALA ASP THR TYR VAL ILE ASN TRP SEQRES 3 B 100 TYR LYS ASP GLY THR SER VAL MET ASN TYR LEU SER GLY SEQRES 4 B 100 GLY GLU PRO ALA PHE THR GLU ASP LEU ASP ASP ARG THR SEQRES 5 B 100 ASP VAL GLN PHE VAL ASN ASN ARG ASN LEU GLU ILE THR SEQRES 6 B 100 ASN LEU ARG VAL SER ASP GLU GLY GLU TYR TYR CYS SER SEQRES 7 B 100 VAL ILE GLU ILE GLY ALA GLY GLY GLN SER GLY ASP GLY SEQRES 8 B 100 THR ARG TYR GLN LEU VAL VAL PHE VAL FORMUL 3 HOH *202(H2 O) HELIX 1 AA1 GLU A 46 ASP A 49 5 4 HELIX 2 AA2 ARG A 68 GLU A 72 5 5 HELIX 3 AA3 GLU B 46 ASP B 49 5 4 HELIX 4 AA4 ARG B 68 GLU B 72 5 5 SHEET 1 AA1 6 SER A 2 GLN A 4 0 SHEET 2 AA1 6 TYR A 94 PHE A 99 1 O PHE A 99 N HIS A 3 SHEET 3 AA1 6 GLY A 73 GLU A 81 -1 N GLY A 73 O LEU A 96 SHEET 4 AA1 6 TYR A 22 LYS A 28 -1 N TYR A 27 O TYR A 76 SHEET 5 AA1 6 THR A 31 LEU A 37 -1 O VAL A 33 N TRP A 26 SHEET 6 AA1 6 ALA A 43 PHE A 44 -1 O ALA A 43 N ASN A 35 SHEET 1 AA2 4 SER A 2 GLN A 4 0 SHEET 2 AA2 4 TYR A 94 PHE A 99 1 O PHE A 99 N HIS A 3 SHEET 3 AA2 4 GLY A 73 GLU A 81 -1 N GLY A 73 O LEU A 96 SHEET 4 AA2 4 SER A 88 ASP A 90 -1 O GLY A 89 N VAL A 79 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 VAL A 57 O ASN A 61 SHEET 1 AA4 6 SER B 2 GLN B 4 0 SHEET 2 AA4 6 TYR B 94 PHE B 99 1 O VAL B 97 N HIS B 3 SHEET 3 AA4 6 GLY B 73 GLU B 81 -1 N TYR B 75 O TYR B 94 SHEET 4 AA4 6 TYR B 22 LYS B 28 -1 N TYR B 27 O TYR B 76 SHEET 5 AA4 6 THR B 31 LEU B 37 -1 O VAL B 33 N TRP B 26 SHEET 6 AA4 6 ALA B 43 PHE B 44 -1 O ALA B 43 N ASN B 35 SHEET 1 AA5 4 SER B 2 GLN B 4 0 SHEET 2 AA5 4 TYR B 94 PHE B 99 1 O VAL B 97 N HIS B 3 SHEET 3 AA5 4 GLY B 73 GLU B 81 -1 N TYR B 75 O TYR B 94 SHEET 4 AA5 4 SER B 88 ASP B 90 -1 O GLY B 89 N VAL B 79 SHEET 1 AA6 3 HIS B 9 PHE B 11 0 SHEET 2 AA6 3 ASN B 61 ILE B 64 -1 O LEU B 62 N PHE B 11 SHEET 3 AA6 3 VAL B 54 VAL B 57 -1 N GLN B 55 O GLU B 63 SSBOND 1 CYS A 13 CYS A 77 1555 1555 2.04 SSBOND 2 CYS B 13 CYS B 77 1555 1555 2.06 CRYST1 45.412 67.785 74.625 90.00 90.00 90.00 P 2 21 21 8 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 0.022021 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014753 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013400 0.00000