HEADER CYTOKINE 05-AUG-20 7JNY TITLE CRYSTAL STRUCTURE OF CXCL13 COMPND MOL_ID: 1; COMPND 2 MOLECULE: C-X-C MOTIF CHEMOKINE 13; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ANGIE,B CELL-ATTRACTING CHEMOKINE 1,BCA-1,B LYMPHOCYTE COMPND 5 CHEMOATTRACTANT,CXC CHEMOKINE BLC,SMALL-INDUCIBLE CYTOKINE B13; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CXCL13, BCA1, BLC, SCYB13; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CHEMOKINE, CXCL13, CYTOKINE EXPDTA X-RAY DIFFRACTION AUTHOR E.M.ROSENBERG JR.,D.RAJASEKARAN,J.W.MURPHY,G.PANTOURIS,E.J.LOLIS REVDAT 3 18-OCT-23 7JNY 1 REMARK REVDAT 2 21-OCT-20 7JNY 1 JRNL REVDAT 1 07-OCT-20 7JNY 0 SPRSDE 07-OCT-20 7JNY 4ZAI JRNL AUTH E.M.ROSENBERG JR.,J.HERRINGTON,D.RAJASEKARAN,J.W.MURPHY, JRNL AUTH 2 G.PANTOURIS,E.J.LOLIS JRNL TITL THE N-TERMINAL LENGTH AND SIDE-CHAIN COMPOSITION OF CXCL13 JRNL TITL 2 AFFECT CRYSTALLIZATION, STRUCTURE AND FUNCTIONAL ACTIVITY. JRNL REF ACTA CRYSTALLOGR D STRUCT V. 76 1033 2020 JRNL REF 2 BIOL JRNL REFN ISSN 2059-7983 JRNL PMID 33021505 JRNL DOI 10.1107/S2059798320011687 REMARK 2 REMARK 2 RESOLUTION. 1.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_3946 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) : 1.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 42.41 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 9388 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.280 REMARK 3 FREE R VALUE TEST SET COUNT : 1756 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 42.4100 - 4.4300 0.99 1211 126 0.1553 0.2009 REMARK 3 2 4.4200 - 3.5100 1.00 1186 144 0.1504 0.1729 REMARK 3 3 3.5100 - 3.0700 1.00 1205 132 0.1685 0.2257 REMARK 3 4 3.0700 - 2.7900 1.00 1204 149 0.1984 0.2049 REMARK 3 5 2.7900 - 2.5900 1.00 1183 136 0.2036 0.2432 REMARK 3 6 2.5900 - 2.4400 1.00 1201 135 0.2075 0.2705 REMARK 3 7 2.4400 - 2.3100 0.99 1212 137 0.2136 0.2444 REMARK 3 8 2.3100 - 2.2100 0.98 1187 136 0.1934 0.2021 REMARK 3 9 2.2100 - 2.1300 0.99 1165 134 0.2025 0.2467 REMARK 3 10 2.1300 - 2.0600 0.98 1196 138 0.2337 0.2673 REMARK 3 11 2.0500 - 1.9900 0.98 1194 137 0.2506 0.2998 REMARK 3 12 1.9900 - 1.9300 0.95 1139 131 0.2653 0.3278 REMARK 3 13 1.9300 - 1.8800 0.90 1038 121 0.3101 0.3630 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.760 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 39.77 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 0 THROUGH 14 ) REMARK 3 ORIGIN FOR THE GROUP (A): 29.2790 3.3403 -4.5933 REMARK 3 T TENSOR REMARK 3 T11: 0.3105 T22: 0.1741 REMARK 3 T33: 0.2780 T12: -0.0635 REMARK 3 T13: -0.0235 T23: 0.0146 REMARK 3 L TENSOR REMARK 3 L11: 1.4287 L22: 1.4816 REMARK 3 L33: 5.9592 L12: 0.5630 REMARK 3 L13: 1.1010 L23: 2.5817 REMARK 3 S TENSOR REMARK 3 S11: 0.0419 S12: -0.0909 S13: -0.0564 REMARK 3 S21: 0.3342 S22: -0.1615 S23: -0.1653 REMARK 3 S31: 0.0193 S32: 0.3048 S33: 0.1300 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 15 THROUGH 22 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.4519 18.8980 -8.6927 REMARK 3 T TENSOR REMARK 3 T11: 0.8360 T22: 0.1716 REMARK 3 T33: 0.2837 T12: -0.0674 REMARK 3 T13: -0.0744 T23: 0.0315 REMARK 3 L TENSOR REMARK 3 L11: 3.2776 L22: 4.2169 REMARK 3 L33: 4.7097 L12: -0.2598 REMARK 3 L13: -0.9234 L23: -1.4094 REMARK 3 S TENSOR REMARK 3 S11: -0.2605 S12: -0.4275 S13: 0.1524 REMARK 3 S21: 0.6406 S22: -0.3094 S23: -0.2098 REMARK 3 S31: -0.2013 S32: 0.2962 S33: -0.4268 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 23 THROUGH 47 ) REMARK 3 ORIGIN FOR THE GROUP (A): 27.4631 8.5599 -7.9843 REMARK 3 T TENSOR REMARK 3 T11: 0.3424 T22: 0.1807 REMARK 3 T33: 0.2485 T12: -0.1141 REMARK 3 T13: -0.0156 T23: 0.0033 REMARK 3 L TENSOR REMARK 3 L11: 2.8580 L22: 2.2257 REMARK 3 L33: 5.9907 L12: 0.5361 REMARK 3 L13: -0.1571 L23: -1.5331 REMARK 3 S TENSOR REMARK 3 S11: 0.2221 S12: -0.0216 S13: -0.0515 REMARK 3 S21: 0.4723 S22: -0.2834 S23: -0.0548 REMARK 3 S31: -0.7571 S32: 0.5522 S33: 0.1292 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 48 THROUGH 59 ) REMARK 3 ORIGIN FOR THE GROUP (A): 28.8829 14.7952 -9.2420 REMARK 3 T TENSOR REMARK 3 T11: 0.6769 T22: 0.2408 REMARK 3 T33: 0.2423 T12: -0.2181 REMARK 3 T13: -0.0637 T23: 0.0261 REMARK 3 L TENSOR REMARK 3 L11: 1.7830 L22: 2.2237 REMARK 3 L33: 2.1062 L12: 0.3628 REMARK 3 L13: 1.8187 L23: -0.3942 REMARK 3 S TENSOR REMARK 3 S11: -0.4589 S12: 0.4250 S13: 0.3450 REMARK 3 S21: 0.4320 S22: -0.0022 S23: -0.0781 REMARK 3 S31: -0.9843 S32: 0.4720 S33: 0.0275 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 60 THROUGH 79 ) REMARK 3 ORIGIN FOR THE GROUP (A): 17.3476 7.7909 -18.6401 REMARK 3 T TENSOR REMARK 3 T11: 0.3479 T22: 0.1703 REMARK 3 T33: 0.2985 T12: 0.1181 REMARK 3 T13: -0.0240 T23: -0.0087 REMARK 3 L TENSOR REMARK 3 L11: 1.5604 L22: 5.5513 REMARK 3 L33: 4.7560 L12: -0.1977 REMARK 3 L13: -1.2536 L23: 4.6790 REMARK 3 S TENSOR REMARK 3 S11: -0.0835 S12: 0.0846 S13: -0.0753 REMARK 3 S21: 0.1823 S22: -0.3537 S23: 0.4804 REMARK 3 S31: -0.6650 S32: -0.6794 S33: 0.3509 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 7JNY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-AUG-20. REMARK 100 THE DEPOSITION ID IS D_1000251097. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 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) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9412 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.880 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.1200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL 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: 4ZAI REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.65 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CHLORIDE 0.1 M BIS-TRIS REMARK 280 PROPANE PH 9.0, 25% W/V POLYETHYLENE GLYCOL 1,500. CRYSTALS REMARK 280 FORMED WITHIN A COUPLE DAYS, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 295K 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 26.75933 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 53.51867 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 53.51867 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 26.75933 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: 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 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 PRO A 80 REMARK 465 VAL A 81 REMARK 465 PHE A 82 REMARK 465 LYS A 83 REMARK 465 ARG A 84 REMARK 465 LYS A 85 REMARK 465 ILE A 86 REMARK 465 PRO A 87 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4ZAI RELATED DB: PDB DBREF 7JNY A 1 87 UNP O43927 CXL13_HUMAN 23 109 SEQADV 7JNY MET A 0 UNP O43927 INITIATING METHIONINE SEQRES 1 A 88 MET VAL LEU GLU VAL TYR TYR THR SER LEU ARG CYS ARG SEQRES 2 A 88 CYS VAL GLN GLU SER SER VAL PHE ILE PRO ARG ARG PHE SEQRES 3 A 88 ILE ASP ARG ILE GLN ILE LEU PRO ARG GLY ASN GLY CYS SEQRES 4 A 88 PRO ARG LYS GLU ILE ILE VAL TRP LYS LYS ASN LYS SER SEQRES 5 A 88 ILE VAL CYS VAL ASP PRO GLN ALA GLU TRP ILE GLN ARG SEQRES 6 A 88 MET MET GLU VAL LEU ARG LYS ARG SER SER SER THR LEU SEQRES 7 A 88 PRO VAL PRO VAL PHE LYS ARG LYS ILE PRO FORMUL 2 HOH *75(H2 O) HELIX 1 AA1 PRO A 22 ARG A 24 5 3 HELIX 2 AA2 ALA A 59 ARG A 72 1 14 SHEET 1 AA1 4 VAL A 1 VAL A 4 0 SHEET 2 AA1 4 ILE A 26 LEU A 32 1 O ILE A 31 N GLU A 3 SHEET 3 AA1 4 GLU A 42 LYS A 47 -1 O TRP A 46 N ARG A 28 SHEET 4 AA1 4 ILE A 52 VAL A 55 -1 O VAL A 55 N ILE A 43 SSBOND 1 CYS A 11 CYS A 38 1555 1555 2.04 SSBOND 2 CYS A 13 CYS A 54 1555 1555 2.05 CRYST1 48.967 48.967 80.278 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 0.020422 0.011791 0.000000 0.00000 SCALE2 0.000000 0.023581 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012457 0.00000