PDB Short entry for 1SDF HEADER CYTOKINE 15-NOV-97 1SDF TITLE SOLUTION STRUCTURE OF STROMAL CELL-DERIVED FACTOR-1 (SDF-1), NMR, TITLE 2 MINIMIZED AVERAGE STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: STROMAL CELL-DERIVED FACTOR-1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SDF; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS CYTOKINE, CHEMOKINES, PROTEIN SYNTHESIS, STROMAL CELL-DERIVED FACTOR- KEYWDS 2 1/G-COUPLED RECEPTORS, SOLUTION STRUCTURE EXPDTA SOLUTION NMR AUTHOR M.P.CRUMP,K.RAJARATHNAM,I.CLARK-LEWIS,B.D.SYKES REVDAT 3 02-MAR-22 1SDF 1 REMARK REVDAT 2 24-FEB-09 1SDF 1 VERSN REVDAT 1 28-JAN-98 1SDF 0 JRNL AUTH M.P.CRUMP,J.H.GONG,P.LOETSCHER,K.RAJARATHNAM,A.AMARA, JRNL AUTH 2 F.ARENZANA-SEISDEDOS,J.L.VIRELIZIER,M.BAGGIOLINI,B.D.SYKES, JRNL AUTH 3 I.CLARK-LEWIS JRNL TITL SOLUTION STRUCTURE AND BASIS FOR FUNCTIONAL ACTIVITY OF JRNL TITL 2 STROMAL CELL-DERIVED FACTOR-1; DISSOCIATION OF CXCR4 JRNL TITL 3 ACTIVATION FROM BINDING AND INHIBITION OF HIV-1. JRNL REF EMBO J. V. 16 6996 1997 JRNL REFN ISSN 0261-4189 JRNL PMID 9384579 JRNL DOI 10.1093/EMBOJ/16.23.6996 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.1 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: STRUCTURES WERE REFINED WITH MULTIPLE REMARK 3 ROUNDS OF SIMULATED ANNEALING, WITH THE ADDITION OF NEW NOES AND REMARK 3 CORRECTION OF AMBIGUOUS NOES. DETAILS OF THE NUMBER OF REMARK 3 RESTRAINTS ETC. CAN BE FOUND IN THE JRNL CITATION ABOVE. REMARK 4 REMARK 4 1SDF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000176330. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 303 REMARK 210 PH : 4.9 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : NULL REMARK 210 SAMPLE CONTENTS : NULL REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : COSY; NOESY; TOCSY; 13C-HSQC; REMARK 210 13C EDITED HMQC-NOESY; 15N-HSQC; REMARK 210 3D 15N-EDITED NOESY-HSQC REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : VARIAN INOVA; UNITY REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : X-PLOR REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 30 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 1 REMARK 210 CONFORMERS, SELECTION CRITERIA : AVERAGE STRUCTURE REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : NULL REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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 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 2 -79.39 -78.83 REMARK 500 VAL A 3 -43.14 -178.81 REMARK 500 SER A 4 35.73 -174.39 REMARK 500 SER A 6 -72.90 -174.19 REMARK 500 ARG A 8 -172.66 -59.27 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 8 0.30 SIDE CHAIN REMARK 500 ARG A 12 0.28 SIDE CHAIN REMARK 500 ARG A 20 0.19 SIDE CHAIN REMARK 500 ARG A 41 0.20 SIDE CHAIN REMARK 500 ARG A 47 0.30 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 1SDF A 1 67 UNP P48061 SDF1_HUMAN 22 88 SEQRES 1 A 67 LYS PRO VAL SER LEU SER TYR ARG CYS PRO CYS ARG PHE SEQRES 2 A 67 PHE GLU SER HIS VAL ALA ARG ALA ASN VAL LYS HIS LEU SEQRES 3 A 67 LYS ILE LEU ASN THR PRO ASN CYS ALA LEU GLN ILE VAL SEQRES 4 A 67 ALA ARG LEU LYS ASN ASN ASN ARG GLN VAL CYS ILE ASP SEQRES 5 A 67 PRO LYS LEU LYS TRP ILE GLN GLU TYR LEU GLU LYS ALA SEQRES 6 A 67 LEU ASN HELIX 1 1 ILE A 58 ALA A 65 1 8 SHEET 1 A 3 ARG A 47 ILE A 51 0 SHEET 2 A 3 GLN A 37 LEU A 42 -1 N LEU A 42 O ARG A 47 SHEET 3 A 3 VAL A 23 LEU A 29 -1 N LEU A 29 O GLN A 37 SSBOND 1 CYS A 9 CYS A 34 1555 1555 2.02 SSBOND 2 CYS A 11 CYS A 50 1555 1555 2.02 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000