HEADER SIGNALING PROTEIN 03-OCT-12 4HED TITLE ZEBRAFISH CHEMOKINE CXL1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DANIO RERIO; SOURCE 3 ORGANISM_COMMON: LEOPARD DANIO,ZEBRA DANIO,ZEBRA FISH; SOURCE 4 ORGANISM_TAXID: 7955; SOURCE 5 GENE: CXL-CHR24A, SI:DKEY-25O1.2; SOURCE 6 EXPRESSION_SYSTEM: PICHIA; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4919 KEYWDS CHEMOKINE FOLD, CHEMOTAXIS, NEW CHEMOKINE FAMILY, ZEBRAFISH FISH KEYWDS 2 CHEMOKINE STRUCTURE, CXCL1A, SULFUR-SAD, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.RAJASEKARAN,C.FAN,W.MENG,J.W.PFLUGRATH,E.J.LOLIS REVDAT 5 06-NOV-24 4HED 1 REMARK REVDAT 4 23-APR-14 4HED 1 JRNL REVDAT 3 30-OCT-13 4HED 1 JRNL REVDAT 2 28-AUG-13 4HED 1 JRNL REVDAT 1 21-AUG-13 4HED 0 JRNL AUTH D.RAJASEKARAN,C.FAN,W.MENG,J.W.PFLUGRATH,E.J.LOLIS JRNL TITL STRUCTURAL INSIGHT INTO THE EVOLUTION OF A NEW CHEMOKINE JRNL TITL 2 FAMILY FROM ZEBRAFISH. JRNL REF PROTEINS V. 82 708 2014 JRNL REFN ISSN 0887-3585 JRNL PMID 23900850 JRNL DOI 10.1002/PROT.24380 REMARK 2 REMARK 2 RESOLUTION. 1.62 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) 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) : 1.62 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.39 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.070 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 9709 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.182 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.770 REMARK 3 FREE R VALUE TEST SET COUNT : 851 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 28.3893 - 2.9430 0.99 2845 125 0.1579 0.2121 REMARK 3 2 2.9430 - 2.3363 1.00 2814 153 0.2032 0.2500 REMARK 3 3 2.3363 - 2.0411 1.00 2804 178 0.1769 0.2402 REMARK 3 4 2.0411 - 1.8545 1.00 2878 124 0.2076 0.2220 REMARK 3 5 1.8545 - 1.7216 1.00 2831 138 0.2219 0.2560 REMARK 3 6 1.7216 - 1.6200 0.99 2835 133 0.2166 0.2406 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) : 0.160 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.070 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 : 0.009 564 REMARK 3 ANGLE : 1.327 753 REMARK 3 CHIRALITY : 0.099 85 REMARK 3 PLANARITY : 0.005 94 REMARK 3 DIHEDRAL : 11.422 220 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A AND (RESID 12:27) REMARK 3 ORIGIN FOR THE GROUP (A): -6.8044 15.0449 -7.7890 REMARK 3 T TENSOR REMARK 3 T11: 0.1864 T22: 0.1907 REMARK 3 T33: 0.1943 T12: 0.0278 REMARK 3 T13: -0.0422 T23: -0.0098 REMARK 3 L TENSOR REMARK 3 L11: 2.8206 L22: 5.0922 REMARK 3 L33: 2.5298 L12: 0.1119 REMARK 3 L13: -0.9552 L23: 0.6518 REMARK 3 S TENSOR REMARK 3 S11: 0.0648 S12: 0.4761 S13: -0.3023 REMARK 3 S21: -0.7165 S22: 0.0865 S23: 0.7157 REMARK 3 S31: 0.0416 S32: -0.3997 S33: 0.0098 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN A AND (RESID 28:42) REMARK 3 ORIGIN FOR THE GROUP (A): -5.9078 6.7221 -4.7006 REMARK 3 T TENSOR REMARK 3 T11: 0.2642 T22: 0.1925 REMARK 3 T33: 0.2829 T12: -0.0113 REMARK 3 T13: -0.0486 T23: -0.0137 REMARK 3 L TENSOR REMARK 3 L11: 1.8685 L22: 1.5191 REMARK 3 L33: 1.9477 L12: 0.2268 REMARK 3 L13: -0.1799 L23: 0.2258 REMARK 3 S TENSOR REMARK 3 S11: 0.1754 S12: 0.0409 S13: -0.6610 REMARK 3 S21: -0.4420 S22: -0.1209 S23: 0.1580 REMARK 3 S31: 0.3540 S32: 0.0572 S33: 0.0572 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN A AND (RESID 43:56) REMARK 3 ORIGIN FOR THE GROUP (A): -9.8526 15.3410 -1.9129 REMARK 3 T TENSOR REMARK 3 T11: -0.0154 T22: 0.0904 REMARK 3 T33: 0.1665 T12: 0.0396 REMARK 3 T13: 0.0087 T23: 0.0258 REMARK 3 L TENSOR REMARK 3 L11: 5.3148 L22: 3.6642 REMARK 3 L33: 2.2314 L12: -2.2366 REMARK 3 L13: -3.0360 L23: 1.6055 REMARK 3 S TENSOR REMARK 3 S11: 0.2408 S12: 0.7760 S13: 0.0230 REMARK 3 S21: -0.9264 S22: -0.1757 S23: 0.5122 REMARK 3 S31: -0.3040 S32: -0.6350 S33: 0.3599 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN A AND (RESID 57:62) REMARK 3 ORIGIN FOR THE GROUP (A): 3.8039 15.0315 -8.3799 REMARK 3 T TENSOR REMARK 3 T11: 0.1666 T22: 0.1919 REMARK 3 T33: 0.1072 T12: 0.0194 REMARK 3 T13: 0.0529 T23: -0.0240 REMARK 3 L TENSOR REMARK 3 L11: 3.8076 L22: 7.3252 REMARK 3 L33: 3.6752 L12: 3.1200 REMARK 3 L13: 1.5161 L23: -0.9910 REMARK 3 S TENSOR REMARK 3 S11: 0.1457 S12: 0.4349 S13: 0.0411 REMARK 3 S21: -0.7485 S22: 0.1241 S23: -0.6540 REMARK 3 S31: -0.4191 S32: 0.4230 S33: -0.2435 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN A AND (RESID 63:73) REMARK 3 ORIGIN FOR THE GROUP (A): 3.1378 18.7345 4.6182 REMARK 3 T TENSOR REMARK 3 T11: 0.0490 T22: 0.2382 REMARK 3 T33: 0.1167 T12: -0.0823 REMARK 3 T13: 0.0104 T23: -0.0597 REMARK 3 L TENSOR REMARK 3 L11: 3.5390 L22: 6.6454 REMARK 3 L33: 4.2397 L12: 1.2946 REMARK 3 L13: -2.6182 L23: -0.1486 REMARK 3 S TENSOR REMARK 3 S11: 0.7566 S12: -1.0932 S13: 0.3009 REMARK 3 S21: 0.8642 S22: -0.0782 S23: -0.7355 REMARK 3 S31: -0.6101 S32: 0.9355 S33: 0.5293 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN A AND (RESID 74:81) REMARK 3 ORIGIN FOR THE GROUP (A): -1.7295 7.9527 5.3644 REMARK 3 T TENSOR REMARK 3 T11: 0.3356 T22: 0.2173 REMARK 3 T33: 0.3547 T12: -0.0624 REMARK 3 T13: 0.0076 T23: 0.0719 REMARK 3 L TENSOR REMARK 3 L11: 9.2449 L22: 0.5078 REMARK 3 L33: 7.1949 L12: 1.0749 REMARK 3 L13: 0.3893 L23: 1.6747 REMARK 3 S TENSOR REMARK 3 S11: -0.1128 S12: -0.0280 S13: -1.4630 REMARK 3 S21: 0.3597 S22: -0.2248 S23: -0.2004 REMARK 3 S31: 0.9658 S32: 0.2166 S33: 0.0845 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 4HED COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000075360. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : 7.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9709 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.620 REMARK 200 RESOLUTION RANGE LOW (A) : 46.310 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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 <I/SIGMA(I)> FOR SHELL : NULL 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 (%): 37.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS, 38% PEG 3350, PH 7.4, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 23.16500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.38500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.16500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.38500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 TRP A 1 REMARK 465 SER A 2 REMARK 465 SER A 3 REMARK 465 THR A 4 REMARK 465 ASP A 5 REMARK 465 LYS A 6 REMARK 465 ASN A 7 REMARK 465 PHE A 8 REMARK 465 ASP A 9 REMARK 465 ASN A 10 REMARK 465 ARG A 11 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4HCS RELATED DB: PDB DBREF 4HED A 1 81 UNP F1Q6N2 F1Q6N2_DANRE 35 115 SEQRES 1 A 81 TRP SER SER THR ASP LYS ASN PHE ASP ASN ARG PRO GLY SEQRES 2 A 81 VAL CYS PHE LYS VAL LEU THR THR LYS GLU PRO LYS ALA SEQRES 3 A 81 ASN ILE LYS ARG CYS TYR ASN LEU PRO LYS THR ASN ASN SEQRES 4 A 81 CYS LEU LYS CYS VAL LEU PHE VAL ASP ALA SER ASN ARG SEQRES 5 A 81 MET LYS CYS ILE ASP PRO ASN ALA SER TRP LEU ALA GLU SEQRES 6 A 81 ARG LEU TYR ARG LEU LYS GLU LYS GLY VAL THR CYS ARG SEQRES 7 A 81 GLY GLU ALA FORMUL 2 HOH *84(H2 O) HELIX 1 1 TRP A 62 LYS A 73 1 12 SHEET 1 A 3 ILE A 28 LEU A 34 0 SHEET 2 A 3 CYS A 43 ASP A 48 -1 O LEU A 45 N TYR A 32 SHEET 3 A 3 MET A 53 ILE A 56 -1 O ILE A 56 N VAL A 44 SSBOND 1 CYS A 15 CYS A 40 1555 1555 2.05 SSBOND 2 CYS A 31 CYS A 77 1555 1555 2.04 SSBOND 3 CYS A 43 CYS A 55 1555 1555 2.01 CRYST1 46.330 56.770 27.670 90.00 90.00 90.00 P 21 21 2 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 0.021584 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017615 0.000000 0.00000 SCALE3 0.000000 0.000000 0.036140 0.00000