PDB Short entry for 2JP0 HEADER IMMUNE SYSTEM 16-APR-07 2JP0 TITLE SOLUTION STRUCTURE OF THE N-TERMINAL EXTRACEULLULAR DOMAIN OF THE TITLE 2 LYMPHOCYTE RECEPTOR CD5 CALCULATED USING INFERENTIAL STRUCTURE TITLE 3 DETERMINATION (ISD) COMPND MOL_ID: 1; COMPND 2 MOLECULE: T-CELL SURFACE GLYCOPROTEIN CD5; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 25-134; COMPND 5 SYNONYM: LYMPHOCYTE ANTIGEN T1/LEU- 1; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: CD5, LEU1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: VECTOR; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET15B KEYWDS CD5, DOMAIN 1, SCAVENGER RECEPTOR CYSTEINE RICH, SRCR, INFERENTIAL KEYWDS 2 STRUCTURE DETERMINATION, IMMUNE SYSTEM EXPDTA SOLUTION NMR NUMMDL 50 AUTHOR A.GARZA-GARCIA,R.HARRIS,D.ESPOSITO,P.C.DRISCOLL,W.RIEPING REVDAT 5 20-DEC-23 2JP0 1 REMARK REVDAT 4 20-OCT-21 2JP0 1 REMARK SEQADV REVDAT 3 24-FEB-09 2JP0 1 VERSN REVDAT 2 22-APR-08 2JP0 1 JRNL REVDAT 1 26-FEB-08 2JP0 0 JRNL AUTH A.GARZA-GARCIA,D.ESPOSITO,W.RIEPING,R.HARRIS,C.BRIGGS, JRNL AUTH 2 M.H.BROWN,P.C.DRISCOLL JRNL TITL THREE-DIMENSIONAL SOLUTION STRUCTURE AND CONFORMATIONAL JRNL TITL 2 PLASTICITY OF THE N-TERMINAL SCAVENGER RECEPTOR JRNL TITL 3 CYSTEINE-RICH DOMAIN OF HUMAN CD5 JRNL REF J.MOL.BIOL. V. 378 129 2008 JRNL REFN ISSN 0022-2836 JRNL PMID 18339402 JRNL DOI 10.1016/J.JMB.2008.02.006 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : NMRPIPE 3.3, INFERENTIAL_STRUCTURE_DETERMINATION REMARK 3 AUTHORS : DELAGLIO, GRZESIEK, VUISTER, ZHU, PFEIFER AND BAX REMARK 3 (NMRPIPE), RIEPING (INFERENTIAL_STRUCTURE_ REMARK 3 DETERMINATION) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: A BAYESIAN INFERENCE WAS USED TO DERIVE REMARK 3 A PROBABILTY DISTRIBUTION THAT REPRESENTS THE STRUCTURE AND ITS REMARK 3 PRECISION. REMARK 4 REMARK 4 2JP0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-APR-07. REMARK 100 THE DEPOSITION ID IS D_1000100108. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 318 REMARK 210 PH : 5.0 REMARK 210 IONIC STRENGTH : 0.2 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1 MM [U-15N] CD5D1, 50 MM SODIUM REMARK 210 PHOSPHATE, 200 MM SODIUM REMARK 210 CHLORIDE, 1 MM EDTA, 90% H2O/10% REMARK 210 D2O; 1 MM [U-13C; U-15N] CD5D1, REMARK 210 1 MM EDTA, 50 MM SODIUM REMARK 210 PHOSPHATE, 200 MM SODIUM REMARK 210 CHLORIDE, 90% H2O/10% D2O; 1 MM REMARK 210 [U-13C; U-15N] CD5D1, 1 MM EDTA, REMARK 210 50 MM SODIUM PHOSPHATE, 200 MM REMARK 210 SODIUM CHLORIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D 1H-15N NOESY; REMARK 210 3D 1H-15N TOCSY; 3D HNCA; 3D REMARK 210 HNCO; 3D HA(CACO)NH; 3D CBCA(CO) REMARK 210 NH; 3D HNCACB; 2D 1H-13C HSQC; REMARK 210 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 500 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : INOVA; UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ANSIG 3.3, CNS 1.1, X-PLOR NIH REMARK 210 METHOD USED : INFERENTIAL STRUCTURE REMARK 210 DETERMINATION REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 500 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 50 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LOWEST REMARK 210 ENERGY 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-50 REMARK 465 RES C SSSEQI REMARK 465 MET A 4 REMARK 465 GLY A 5 REMARK 465 GLY A 6 REMARK 465 SER A 7 REMARK 465 HIS A 8 REMARK 465 HIS A 9 REMARK 465 HIS A 10 REMARK 465 HIS A 11 REMARK 465 HIS A 12 REMARK 465 HIS A 13 REMARK 465 SER A 14 REMARK 465 SER A 15 REMARK 465 GLY A 16 REMARK 465 LEU A 17 REMARK 465 VAL A 18 REMARK 465 PRO A 19 REMARK 465 ARG A 20 REMARK 465 GLY A 21 REMARK 465 SER A 22 REMARK 465 HIS A 23 REMARK 465 MET A 24 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE 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 1 SER A 40 -93.49 48.85 REMARK 500 1 ASN A 41 -40.41 -138.47 REMARK 500 1 SER A 61 41.85 -79.95 REMARK 500 1 LEU A 96 -178.23 69.13 REMARK 500 1 TYR A 99 104.34 63.52 REMARK 500 1 THR A 100 82.13 -150.15 REMARK 500 1 PRO A 101 68.71 -65.34 REMARK 500 1 GLN A 102 -49.49 178.63 REMARK 500 1 ASN A 116 79.23 65.36 REMARK 500 1 MET A 124 68.48 -155.07 REMARK 500 2 TRP A 28 24.27 -74.08 REMARK 500 2 ASN A 41 -62.45 -122.76 REMARK 500 2 GLN A 45 114.53 -161.42 REMARK 500 2 GLU A 72 41.21 -101.31 REMARK 500 2 ASP A 73 80.23 -155.62 REMARK 500 2 TYR A 99 -25.91 70.67 REMARK 500 2 THR A 100 107.19 -50.72 REMARK 500 2 SER A 120 92.89 -69.94 REMARK 500 3 SER A 40 -66.92 -90.60 REMARK 500 3 ASN A 41 -59.37 -124.39 REMARK 500 3 LEU A 96 120.37 69.64 REMARK 500 3 TYR A 99 -12.63 70.14 REMARK 500 3 THR A 100 101.79 -51.75 REMARK 500 3 PHE A 114 43.19 -105.51 REMARK 500 4 ARG A 39 47.47 -77.59 REMARK 500 4 TRP A 64 -84.83 60.84 REMARK 500 4 LYS A 97 67.11 -118.58 REMARK 500 4 PRO A 101 58.53 -92.29 REMARK 500 4 GLN A 102 -53.72 -144.94 REMARK 500 4 LEU A 111 108.29 -56.39 REMARK 500 4 SER A 115 -64.31 -99.01 REMARK 500 5 ASN A 41 -59.24 -157.62 REMARK 500 5 GLN A 62 39.30 -93.73 REMARK 500 5 SER A 68 49.49 -77.78 REMARK 500 5 LEU A 96 90.98 57.91 REMARK 500 5 TYR A 99 73.65 59.30 REMARK 500 5 SER A 103 -22.52 -146.73 REMARK 500 5 LEU A 111 100.91 -51.26 REMARK 500 5 PHE A 114 41.62 -93.64 REMARK 500 5 ARG A 121 66.65 -103.10 REMARK 500 5 ASP A 123 22.24 -79.60 REMARK 500 6 ARG A 39 63.24 -69.63 REMARK 500 6 SER A 40 -78.88 -86.93 REMARK 500 6 LEU A 52 -158.80 -100.28 REMARK 500 6 GLN A 70 84.11 -153.62 REMARK 500 6 TRP A 71 69.71 -118.89 REMARK 500 6 GLU A 72 -77.55 -105.64 REMARK 500 6 GLN A 102 -35.31 -152.87 REMARK 500 7 SER A 40 -152.60 -96.10 REMARK 500 7 GLN A 62 44.14 -108.93 REMARK 500 REMARK 500 THIS ENTRY HAS 456 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 15189 RELATED DB: BMRB REMARK 900 CHEMICAL SHIFT ASSIGNMENTS REMARK 900 RELATED ID: 2JOP RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE CALCULATED USING XPLOR-NIH DBREF 2JP0 A 25 134 UNP P06127 CD5_HUMAN 25 134 SEQADV 2JP0 MET A 4 UNP P06127 CLONING ARTIFACT SEQADV 2JP0 GLY A 5 UNP P06127 CLONING ARTIFACT SEQADV 2JP0 GLY A 6 UNP P06127 CLONING ARTIFACT SEQADV 2JP0 SER A 7 UNP P06127 CLONING ARTIFACT SEQADV 2JP0 HIS A 8 UNP P06127 EXPRESSION TAG SEQADV 2JP0 HIS A 9 UNP P06127 EXPRESSION TAG SEQADV 2JP0 HIS A 10 UNP P06127 EXPRESSION TAG SEQADV 2JP0 HIS A 11 UNP P06127 EXPRESSION TAG SEQADV 2JP0 HIS A 12 UNP P06127 EXPRESSION TAG SEQADV 2JP0 HIS A 13 UNP P06127 EXPRESSION TAG SEQADV 2JP0 SER A 14 UNP P06127 CLONING ARTIFACT SEQADV 2JP0 SER A 15 UNP P06127 CLONING ARTIFACT SEQADV 2JP0 GLY A 16 UNP P06127 CLONING ARTIFACT SEQADV 2JP0 LEU A 17 UNP P06127 CLONING ARTIFACT SEQADV 2JP0 VAL A 18 UNP P06127 CLONING ARTIFACT SEQADV 2JP0 PRO A 19 UNP P06127 CLONING ARTIFACT SEQADV 2JP0 ARG A 20 UNP P06127 CLONING ARTIFACT SEQADV 2JP0 GLY A 21 UNP P06127 CLONING ARTIFACT SEQADV 2JP0 SER A 22 UNP P06127 CLONING ARTIFACT SEQADV 2JP0 HIS A 23 UNP P06127 CLONING ARTIFACT SEQADV 2JP0 MET A 24 UNP P06127 CLONING ARTIFACT SEQADV 2JP0 ASP A 88 UNP P06127 VAL 88 ENGINEERED MUTATION SEQADV 2JP0 LYS A 97 UNP P06127 VAL 97 ENGINEERED MUTATION SEQRES 1 A 131 MET GLY GLY SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 131 LEU VAL PRO ARG GLY SER HIS MET ARG LEU SER TRP TYR SEQRES 3 A 131 ASP PRO ASP PHE GLN ALA ARG LEU THR ARG SER ASN SER SEQRES 4 A 131 LYS CYS GLN GLY GLN LEU GLU VAL TYR LEU LYS ASP GLY SEQRES 5 A 131 TRP HIS MET VAL CYS SER GLN SER TRP GLY ARG SER SER SEQRES 6 A 131 LYS GLN TRP GLU ASP PRO SER GLN ALA SER LYS VAL CYS SEQRES 7 A 131 GLN ARG LEU ASN CYS GLY ASP PRO LEU SER LEU GLY PRO SEQRES 8 A 131 PHE LEU LYS THR TYR THR PRO GLN SER SER ILE ILE CYS SEQRES 9 A 131 TYR GLY GLN LEU GLY SER PHE SER ASN CYS SER HIS SER SEQRES 10 A 131 ARG ASN ASP MET CYS HIS SER LEU GLY LEU THR CYS LEU SEQRES 11 A 131 GLU HELIX 1 1 ALA A 77 LEU A 84 1 8 SHEET 1 A 3 ALA A 35 LEU A 37 0 SHEET 2 A 3 LEU A 48 TYR A 51 -1 O GLU A 49 N ARG A 36 SHEET 3 A 3 TRP A 56 MET A 58 -1 O HIS A 57 N VAL A 50 SHEET 1 B 3 GLN A 45 GLY A 46 0 SHEET 2 B 3 LEU A 128 CYS A 132 -1 O LEU A 130 N GLY A 46 SHEET 3 B 3 PRO A 89 PRO A 94 -1 N GLY A 93 O GLY A 129 SHEET 1 C 2 ILE A 105 ILE A 106 0 SHEET 2 C 2 SER A 118 HIS A 119 -1 O SER A 118 N ILE A 106 SSBOND 1 CYS A 44 CYS A 86 1555 1555 2.03 SSBOND 2 CYS A 60 CYS A 125 1555 1555 2.04 SSBOND 3 CYS A 81 CYS A 132 1555 1555 2.04 SSBOND 4 CYS A 107 CYS A 117 1555 1555 2.03 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