PDB Short entry for 1NR2 HEADER CYTOKINE 23-JAN-03 1NR2 TITLE HIGH RESOLUTION CRYSTAL STRUCTURES OF THYMUS AND ACTIVATION-REGULATED TITLE 2 CHEMOKINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: THYMUS AND ACTIVATION-REGULATED CHEMOKINE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: SMALL INDUCIBLE CYTOKINE A17; CCL17; CC CHEMOKINE TARC; T COMPND 5 CELL-DIRECTED CC; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HUMANS KEYWDS TARC, CHEMOKINE, CYTOKINE, CC-CHEMOKINE, CHEMOTAXIS EXPDTA X-RAY DIFFRACTION AUTHOR O.A.ASOJO,C.BOULEGUE,D.M.HOOVER,W.LU,J.LUBKOWSKI REVDAT 4 03-APR-24 1NR2 1 REMARK REVDAT 3 24-JAN-18 1NR2 1 JRNL REVDAT 2 24-FEB-09 1NR2 1 VERSN REVDAT 1 05-AUG-03 1NR2 0 JRNL AUTH O.A.ASOJO,C.BOULEGUE,D.M.HOOVER,W.LU,J.LUBKOWSKI JRNL TITL STRUCTURES OF THYMUS AND ACTIVATION-REGULATED CHEMOKINE JRNL TITL 2 (TARC). JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 59 1165 2003 JRNL REFN ISSN 0907-4449 JRNL PMID 12832759 JRNL DOI 10.1107/S0907444903009454 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH O.A.ASOJO,D.HOOVER,C.BOULEGUE,S.CATER,W.LU,J.LUBKOWSKI REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY STUDIES OF THYMUS AND REMARK 1 TITL 2 ACTIVATION-REGULATED CHEMOKINE REMARK 1 REF ACTA CRYSTALLOGR.,SECT.D V. 59 163 2003 REMARK 1 REFN ISSN 0907-4449 REMARK 1 DOI 10.1107/S0907444902018863 REMARK 2 REMARK 2 RESOLUTION. 2.18 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.18 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.8 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.186 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.186 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.299 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 334 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 6225 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.182 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.182 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.294 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 328 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 6019 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1004 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 225 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1231.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 4927 REMARK 3 NUMBER OF RESTRAINTS : 4188 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 ANGLE DISTANCES (A) : 0.018 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.021 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.023 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.026 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.016 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.086 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1NR2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-FEB-03. REMARK 100 THE DEPOSITION ID IS D_1000018132. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUN-02 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9790 REMARK 200 MONOCHROMATOR : MIRRORS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6647 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.180 REMARK 200 RESOLUTION RANGE LOW (A) : 10.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.2 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : 0.06400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.18 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.26 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.19400 REMARK 200 R SYM FOR SHELL (I) : 0.27100 REMARK 200 <I/SIGMA(I)> 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: AMORE REMARK 200 STARTING MODEL: RANTES REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.17M AMMONIUM ACETATE, 0.085M REMARK 280 TRISODIUM CITRATE, 25.5% PEG 4000, 15% W/V GLYCEROL, PH 5.6, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 288K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 29.08300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 14.54150 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 43.62450 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 ALA A 1 REMARK 465 ARG A 2 REMARK 465 GLY A 3 REMARK 465 THR A 4 REMARK 465 ASN A 5 REMARK 465 VAL A 6 REMARK 465 GLY A 7 REMARK 465 ARG A 70 REMARK 465 SER A 71 REMARK 465 ALA B 1 REMARK 465 ARG B 2 REMARK 465 GLY B 3 REMARK 465 THR B 4 REMARK 465 ASN B 5 REMARK 465 VAL B 6 REMARK 465 GLY B 7 REMARK 465 ARG B 70 REMARK 465 SER B 71 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 69 C GLU A 69 O 0.410 REMARK 500 GLU B 69 C GLU B 69 O 0.127 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 GLU B 69 CA - C - O ANGL. DEV. = 49.3 DEGREES 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 9 99.84 30.43 REMARK 500 TYR A 64 -71.38 -49.46 REMARK 500 LEU A 65 -70.42 -31.83 REMARK 500 THR B 26 175.59 177.81 REMARK 500 THR B 30 151.73 -44.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NR4 RELATED DB: PDB REMARK 900 TARC STRUCTURE IN P 1 DBREF 1NR2 A 1 71 UNP Q92583 CCL17_HUMAN 24 94 DBREF 1NR2 B 1 71 UNP Q92583 CCL17_HUMAN 24 94 SEQRES 1 A 71 ALA ARG GLY THR ASN VAL GLY ARG GLU CYS CYS LEU GLU SEQRES 2 A 71 TYR PHE LYS GLY ALA ILE PRO LEU ARG LYS LEU LYS THR SEQRES 3 A 71 TRP TYR GLN THR SER GLU ASP CYS SER ARG ASP ALA ILE SEQRES 4 A 71 VAL PHE VAL THR VAL GLN GLY ARG ALA ILE CYS SER ASP SEQRES 5 A 71 PRO ASN ASN LYS ARG VAL LYS ASN ALA VAL LYS TYR LEU SEQRES 6 A 71 GLN SER LEU GLU ARG SER SEQRES 1 B 71 ALA ARG GLY THR ASN VAL GLY ARG GLU CYS CYS LEU GLU SEQRES 2 B 71 TYR PHE LYS GLY ALA ILE PRO LEU ARG LYS LEU LYS THR SEQRES 3 B 71 TRP TYR GLN THR SER GLU ASP CYS SER ARG ASP ALA ILE SEQRES 4 B 71 VAL PHE VAL THR VAL GLN GLY ARG ALA ILE CYS SER ASP SEQRES 5 B 71 PRO ASN ASN LYS ARG VAL LYS ASN ALA VAL LYS TYR LEU SEQRES 6 B 71 GLN SER LEU GLU ARG SER FORMUL 3 HOH *225(H2 O) HELIX 1 1 ASN A 55 SER A 67 1 13 HELIX 2 2 ASN B 55 LEU B 68 1 14 SHEET 1 A 3 LEU A 24 GLN A 29 0 SHEET 2 A 3 ILE A 39 THR A 43 -1 O VAL A 42 N THR A 26 SHEET 3 A 3 ALA A 48 SER A 51 -1 O SER A 51 N ILE A 39 SHEET 1 B 3 LEU B 24 GLN B 29 0 SHEET 2 B 3 ILE B 39 THR B 43 -1 O VAL B 42 N THR B 26 SHEET 3 B 3 ALA B 48 SER B 51 -1 O ILE B 49 N PHE B 41 SSBOND 1 CYS A 10 CYS A 34 1555 1555 2.03 SSBOND 2 CYS A 11 CYS A 50 1555 1555 2.02 SSBOND 3 CYS B 10 CYS B 34 1555 1555 2.03 SSBOND 4 CYS B 11 CYS B 50 1555 1555 2.03 CRYST1 47.772 47.772 58.166 90.00 90.00 90.00 P 41 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 0.020933 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020933 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017192 0.00000