HEADER PROTEIN BINDING 09-DEC-05 2D9C TITLE SOLUTION STRUCTURE OF THE FIRST IG-LIKE DOMAIN OF SIGNAL-REGULATORY TITLE 2 PROTEIN BETA-1 (SIRP-BETA-1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SIGNAL-REGULATORY PROTEIN BETA-1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: IG-LIKE DOMAIN; COMPND 5 SYNONYM: SIRP-BETA-1, CD172B ANTIGEN; 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: SIRPB1; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P050302-61; SOURCE 8 OTHER_DETAILS: CELL FREE PROTEIN SYNTHESIS KEYWDS BETA-SANDWICH, SIRP-BETA-1, CD172B ANTIGEN, STRUCTURAL GENOMICS, KEYWDS 2 NPPSFA, NATIONAL PROJECT ON PROTEIN STRUCTURAL AND FUNCTIONAL KEYWDS 3 ANALYSES, RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE, RSGI, KEYWDS 4 PROTEIN BINDING EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.NAGASHIMA,F.HAYASHI,M.YOSHIDA,S.YOKOYAMA,RIKEN STRUCTURAL AUTHOR 2 GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 3 09-MAR-22 2D9C 1 REMARK SEQADV REVDAT 2 24-FEB-09 2D9C 1 VERSN REVDAT 1 09-DEC-06 2D9C 0 JRNL AUTH K.NAGASHIMA,F.HAYASHI,M.YOSHIDA,S.YOKOYAMA JRNL TITL SOLUTION STRUCTURE OF THE FIRST IG-LIKE DOMAIN OF JRNL TITL 2 SIGNAL-REGULATORY PROTEIN BETA-1 ( SIRP-BETA-1) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : VNMR 6.1C, CYANA 2.0.17 REMARK 3 AUTHORS : VARIAN (VNMR), GUNTERT, P. (CYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2D9C COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1000025147. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 120MM REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.38MM 13C,15N-LABELED PROTEIN; REMARK 210 20MM D-TRIS-HCL(PH 7.0); 100MM REMARK 210 NACL; 1MM D-DTT; 0.02% NAN3; 10% REMARK 210 D2O; 90% H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D_13C-SEPARATED_NOESY; 3D_15N REMARK 210 -SEPARATED_NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE 20031121, NMRVIEW 5.0.4, REMARK 210 KUJIRA 0.932, CYANA 2.0.17 REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION,STRUCTURES WITH REMARK 210 THE LEAST RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 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 1 ALA A 22 102.61 -41.69 REMARK 500 1 PRO A 40 -163.77 -69.70 REMARK 500 1 LYS A 73 173.41 -49.16 REMARK 500 1 ASP A 78 109.81 -52.65 REMARK 500 1 PRO A 88 2.36 -69.78 REMARK 500 1 ALA A 91 170.40 -53.55 REMARK 500 1 ALA A 121 150.43 -39.97 REMARK 500 1 LYS A 122 152.28 -47.74 REMARK 500 1 PRO A 123 -178.15 -69.75 REMARK 500 1 VAL A 127 103.99 -58.94 REMARK 500 2 ALA A 22 108.19 -44.89 REMARK 500 2 PRO A 40 -168.61 -69.80 REMARK 500 2 ALA A 47 138.97 -33.41 REMARK 500 2 ARG A 51 149.63 -33.78 REMARK 500 2 LEU A 53 120.12 -37.48 REMARK 500 2 THR A 72 -36.45 -37.39 REMARK 500 2 LYS A 73 151.40 -44.87 REMARK 500 2 PHE A 79 40.92 -95.19 REMARK 500 2 ALA A 91 176.34 -51.25 REMARK 500 2 ASP A 106 174.82 -58.00 REMARK 500 2 SER A 118 73.88 -105.28 REMARK 500 2 ALA A 121 151.58 -47.51 REMARK 500 2 LYS A 122 148.59 -37.28 REMARK 500 2 PRO A 123 -176.10 -69.71 REMARK 500 2 VAL A 128 129.24 -33.94 REMARK 500 2 SER A 134 -60.43 -104.00 REMARK 500 2 SER A 135 135.49 -172.99 REMARK 500 3 LEU A 9 156.21 -45.16 REMARK 500 3 GLU A 15 86.71 -64.68 REMARK 500 3 ALA A 22 101.49 -44.03 REMARK 500 3 CYS A 30 135.68 -175.41 REMARK 500 3 PRO A 40 -165.32 -69.84 REMARK 500 3 ALA A 47 145.86 -34.21 REMARK 500 3 ALA A 49 69.83 -108.80 REMARK 500 3 ARG A 51 142.52 -37.27 REMARK 500 3 THR A 67 109.45 -57.37 REMARK 500 3 LYS A 73 144.65 -37.35 REMARK 500 3 ASP A 78 94.00 -67.49 REMARK 500 3 ASP A 106 176.30 -58.12 REMARK 500 3 ALA A 121 155.23 -43.24 REMARK 500 3 LYS A 122 156.03 -47.67 REMARK 500 3 PRO A 123 85.77 -69.77 REMARK 500 4 ALA A 22 99.29 -41.33 REMARK 500 4 ALA A 31 144.39 -170.63 REMARK 500 4 PRO A 40 -163.88 -69.77 REMARK 500 4 ALA A 49 37.51 33.97 REMARK 500 4 LEU A 53 115.77 -35.46 REMARK 500 4 ASP A 78 102.57 -56.57 REMARK 500 4 ALA A 91 173.57 -47.80 REMARK 500 4 THR A 93 114.64 -160.23 REMARK 500 REMARK 500 THIS ENTRY HAS 290 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2D9C A 8 130 UNP O00241 SIRB1_HUMAN 32 154 SEQADV 2D9C GLY A 1 UNP O00241 CLONING ARTIFACT SEQADV 2D9C SER A 2 UNP O00241 CLONING ARTIFACT SEQADV 2D9C SER A 3 UNP O00241 CLONING ARTIFACT SEQADV 2D9C GLY A 4 UNP O00241 CLONING ARTIFACT SEQADV 2D9C SER A 5 UNP O00241 CLONING ARTIFACT SEQADV 2D9C SER A 6 UNP O00241 CLONING ARTIFACT SEQADV 2D9C GLY A 7 UNP O00241 CLONING ARTIFACT SEQADV 2D9C SER A 131 UNP O00241 CLONING ARTIFACT SEQADV 2D9C GLY A 132 UNP O00241 CLONING ARTIFACT SEQADV 2D9C PRO A 133 UNP O00241 CLONING ARTIFACT SEQADV 2D9C SER A 134 UNP O00241 CLONING ARTIFACT SEQADV 2D9C SER A 135 UNP O00241 CLONING ARTIFACT SEQADV 2D9C GLY A 136 UNP O00241 CLONING ARTIFACT SEQRES 1 A 136 GLY SER SER GLY SER SER GLY GLU LEU GLN VAL ILE GLN SEQRES 2 A 136 PRO GLU LYS SER VAL SER VAL ALA ALA GLY GLU SER ALA SEQRES 3 A 136 THR LEU ARG CYS ALA MET THR SER LEU ILE PRO VAL GLY SEQRES 4 A 136 PRO ILE MET TRP PHE ARG GLY ALA GLY ALA GLY ARG GLU SEQRES 5 A 136 LEU ILE TYR ASN GLN LYS GLU GLY HIS PHE PRO ARG VAL SEQRES 6 A 136 THR THR VAL SER GLU LEU THR LYS ARG ASN ASN LEU ASP SEQRES 7 A 136 PHE SER ILE SER ILE SER ASN ILE THR PRO ALA ASP ALA SEQRES 8 A 136 GLY THR TYR TYR CYS VAL LYS PHE ARG LYS GLY SER PRO SEQRES 9 A 136 ASP ASP VAL GLU PHE LYS SER GLY ALA GLY THR GLU LEU SEQRES 10 A 136 SER VAL ARG ALA LYS PRO SER ALA PRO VAL VAL SER GLY SEQRES 11 A 136 SER GLY PRO SER SER GLY SHEET 1 A 2 VAL A 11 ILE A 12 0 SHEET 2 A 2 ALA A 31 MET A 32 -1 O ALA A 31 N ILE A 12 SHEET 1 B 5 SER A 17 ALA A 21 0 SHEET 2 B 5 THR A 115 ARG A 120 1 O ARG A 120 N VAL A 20 SHEET 3 B 5 GLY A 92 ARG A 100 -1 N TYR A 94 O THR A 115 SHEET 4 B 5 MET A 42 ARG A 45 -1 N PHE A 44 O TYR A 95 SHEET 5 B 5 GLU A 52 ASN A 56 -1 O ILE A 54 N TRP A 43 SHEET 1 C 4 SER A 17 ALA A 21 0 SHEET 2 C 4 THR A 115 ARG A 120 1 O ARG A 120 N VAL A 20 SHEET 3 C 4 GLY A 92 ARG A 100 -1 N TYR A 94 O THR A 115 SHEET 4 C 4 VAL A 107 SER A 111 -1 O VAL A 107 N ARG A 100 SHEET 1 D 2 ALA A 26 LEU A 28 0 SHEET 2 D 2 ILE A 81 ILE A 83 -1 O ILE A 81 N LEU A 28 SSBOND 1 CYS A 30 CYS A 96 1555 1555 2.08 CISPEP 1 ILE A 36 PRO A 37 1 -0.12 CISPEP 2 SER A 103 PRO A 104 1 -0.06 CISPEP 3 ILE A 36 PRO A 37 2 -0.11 CISPEP 4 SER A 103 PRO A 104 2 0.01 CISPEP 5 ILE A 36 PRO A 37 3 -0.14 CISPEP 6 SER A 103 PRO A 104 3 0.07 CISPEP 7 ILE A 36 PRO A 37 4 -0.09 CISPEP 8 SER A 103 PRO A 104 4 -0.05 CISPEP 9 ILE A 36 PRO A 37 5 -0.12 CISPEP 10 SER A 103 PRO A 104 5 -0.02 CISPEP 11 ILE A 36 PRO A 37 6 -0.07 CISPEP 12 SER A 103 PRO A 104 6 -0.02 CISPEP 13 ILE A 36 PRO A 37 7 -0.18 CISPEP 14 SER A 103 PRO A 104 7 -0.04 CISPEP 15 ILE A 36 PRO A 37 8 -0.07 CISPEP 16 SER A 103 PRO A 104 8 -0.02 CISPEP 17 ILE A 36 PRO A 37 9 -0.12 CISPEP 18 SER A 103 PRO A 104 9 -0.05 CISPEP 19 ILE A 36 PRO A 37 10 -0.08 CISPEP 20 SER A 103 PRO A 104 10 -0.08 CISPEP 21 ILE A 36 PRO A 37 11 -0.16 CISPEP 22 SER A 103 PRO A 104 11 0.03 CISPEP 23 ILE A 36 PRO A 37 12 -0.18 CISPEP 24 SER A 103 PRO A 104 12 -0.02 CISPEP 25 ILE A 36 PRO A 37 13 -0.20 CISPEP 26 SER A 103 PRO A 104 13 0.02 CISPEP 27 ILE A 36 PRO A 37 14 -0.07 CISPEP 28 SER A 103 PRO A 104 14 0.02 CISPEP 29 ILE A 36 PRO A 37 15 -0.02 CISPEP 30 SER A 103 PRO A 104 15 0.00 CISPEP 31 ILE A 36 PRO A 37 16 -0.03 CISPEP 32 SER A 103 PRO A 104 16 -0.07 CISPEP 33 ILE A 36 PRO A 37 17 -0.08 CISPEP 34 SER A 103 PRO A 104 17 -0.07 CISPEP 35 ILE A 36 PRO A 37 18 -0.10 CISPEP 36 SER A 103 PRO A 104 18 -0.03 CISPEP 37 ILE A 36 PRO A 37 19 -0.15 CISPEP 38 SER A 103 PRO A 104 19 -0.04 CISPEP 39 ILE A 36 PRO A 37 20 -0.11 CISPEP 40 SER A 103 PRO A 104 20 0.00 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 MODEL 1