HEADER IMMUNE SYSTEM 16-JUN-03 1POQ TITLE SOLUTION STRUCTURE OF A SUPERANTIGEN FROM YERSINIA PSEUDOTUBERCULOSIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: YPM; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: YPM(RESIDUES 33-151); COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA PSEUDOTUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 633; SOURCE 4 GENE: YPMA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: NOVABLUE; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PMAL-P2X KEYWDS JELLY ROLL FOLD, IMMUNE SYSTEM EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR R.DONADINI,C.W.LIEW,A.H.KWAN,J.P.MACKAY,B.A.FIELDS REVDAT 3 02-MAR-22 1POQ 1 REMARK REVDAT 2 24-FEB-09 1POQ 1 VERSN REVDAT 1 27-JAN-04 1POQ 0 JRNL AUTH R.DONADINI,C.W.LIEW,A.H.KWAN,J.P.MACKAY,B.A.FIELDS JRNL TITL CRYSTAL AND SOLUTION STRUCTURES OF A SUPERANTIGEN FROM JRNL TITL 2 YERSINIA PSEUDOTUBERCULOSIS REVEAL A JELLY-ROLL FOLD. JRNL REF STRUCTURE V. 12 145 2004 JRNL REFN ISSN 0969-2126 JRNL PMID 14725774 JRNL DOI 10.1016/J.STR.2003.12.002 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : XWINNMR 2.6, DYANA 1.5 REMARK 3 AUTHORS : BRUKER (XWINNMR), GUNTERT ET AL (DYANA) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FINAL STRUCTURES WERE BASED ON 1934 REMARK 3 UNAMBIGUOUS NOE-DERIVED DISTANCE CONSTRAINTS, 139 AMBIGUOUS REMARK 3 CONSTRAINTS, 135 DIHEDRAL ANGLE RESTRAINTS AND 26 HYDROGEN BOND REMARK 3 DISTANCE RESTRAINTS. REMARK 4 REMARK 4 1POQ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-JUL-03. REMARK 100 THE DEPOSITION ID IS D_1000019466. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : NULL REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5MM YPM PROTEIN (33-151), 95% REMARK 210 H2O, 5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D NOESY; 2D TOCSY; DQF-COSY; REMARK 210 HNHA; HN(CO)CA; HNCA; CBCA(CO)NH; REMARK 210 HNCACB REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : DRX REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : XEASY 1.3.13, ARIA 1.1.2 REMARK 210 METHOD USED : SIMULATED ANNEALING, MOLECULAR REMARK 210 DYNAMICS, TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 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: THIS STRUCTURE WAS DETERMINED USING STANDARD 2D REMARK 210 HOMONUCLEAR AND TRIPLE-RESONANCE NMR SPECTROSCOPY. 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: 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 HA LEU A 64 HB2 GLU A 74 1.23 REMARK 500 HG2 ARG A 65 HG3 GLU A 74 1.26 REMARK 500 HG LEU A 64 H GLU A 74 1.29 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 PRO A 16 -94.45 -48.35 REMARK 500 1 ILE A 34 22.21 -144.67 REMARK 500 1 LYS A 37 34.88 -162.78 REMARK 500 1 GLU A 38 -159.21 -129.51 REMARK 500 1 GLU A 45 99.54 -57.78 REMARK 500 1 ASN A 54 -150.91 -167.30 REMARK 500 1 VAL A 55 -86.72 -72.10 REMARK 500 1 THR A 91 60.40 65.23 REMARK 500 1 SER A 92 34.85 -78.34 REMARK 500 1 ASP A 119 14.17 -158.21 REMARK 500 1 LEU A 126 -77.88 -152.03 REMARK 500 1 THR A 127 77.46 -157.03 REMARK 500 2 PRO A 16 42.12 -73.55 REMARK 500 2 ASN A 17 -65.04 -156.70 REMARK 500 2 LYS A 40 -162.13 -171.94 REMARK 500 2 THR A 41 -74.42 -57.56 REMARK 500 2 GLU A 45 121.15 -171.04 REMARK 500 2 LEU A 46 135.55 72.11 REMARK 500 2 VAL A 55 -74.26 -53.39 REMARK 500 2 ASP A 58 57.98 -107.36 REMARK 500 2 VAL A 67 10.68 -168.93 REMARK 500 2 TRP A 72 -166.68 -77.83 REMARK 500 2 ILE A 75 -62.05 -129.60 REMARK 500 2 GLU A 87 -74.07 -78.90 REMARK 500 2 TYR A 90 -91.87 -163.06 REMARK 500 2 THR A 91 -54.14 -151.84 REMARK 500 2 LYS A 120 68.28 -178.06 REMARK 500 2 LEU A 126 -44.91 -176.42 REMARK 500 2 LYS A 128 -53.51 -130.07 REMARK 500 3 ALA A 19 79.71 -160.39 REMARK 500 3 ILE A 34 101.30 47.44 REMARK 500 3 LYS A 40 33.10 -147.91 REMARK 500 3 THR A 41 -60.04 -109.24 REMARK 500 3 ASN A 54 -151.81 -176.21 REMARK 500 3 ASP A 58 48.08 -109.46 REMARK 500 3 ILE A 75 -86.37 -124.59 REMARK 500 3 GLU A 87 -82.50 -73.96 REMARK 500 3 TYR A 90 -64.70 68.13 REMARK 500 3 LEU A 94 -74.46 -79.68 REMARK 500 3 THR A 107 106.95 -57.61 REMARK 500 3 ASP A 118 -122.84 -122.18 REMARK 500 3 ASP A 119 126.48 -172.73 REMARK 500 3 LYS A 120 -176.21 134.73 REMARK 500 3 ASP A 124 -80.47 -91.26 REMARK 500 3 LEU A 126 -144.45 -134.16 REMARK 500 4 LYS A 40 96.69 59.75 REMARK 500 4 GLU A 45 -164.51 57.77 REMARK 500 4 VAL A 55 -74.40 -47.52 REMARK 500 4 ASP A 58 56.39 -119.53 REMARK 500 4 ASN A 70 20.65 -141.15 REMARK 500 REMARK 500 THIS ENTRY HAS 305 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 30 VAL A 31 16 -145.76 REMARK 500 GLU A 106 THR A 107 20 148.33 REMARK 500 REMARK 500 REMARK: NULL DBREF 1POQ A 14 131 UNP Q57221 Q57221_YERPS 34 151 SEQRES 1 A 118 ARG ILE PRO ASN ILE ALA THR TYR THR GLY THR ILE GLN SEQRES 2 A 118 GLY LYS GLY GLU VAL CYS ILE ILE GLY ASN LYS GLU GLY SEQRES 3 A 118 LYS THR ARG GLY GLY GLU LEU TYR ALA VAL LEU HIS SER SEQRES 4 A 118 THR ASN VAL ASN ALA ASP MET THR LEU ILE LEU LEU ARG SEQRES 5 A 118 ASN VAL GLY GLY ASN GLY TRP GLY GLU ILE LYS ARG ASN SEQRES 6 A 118 ASP ILE ASP LYS PRO LEU LYS TYR GLU ASP TYR TYR THR SEQRES 7 A 118 SER GLY LEU SER TRP ILE TRP LYS ILE LYS ASN ASN SER SEQRES 8 A 118 SER GLU THR SER ASN TYR SER LEU ASP ALA THR VAL HIS SEQRES 9 A 118 ASP ASP LYS GLU ASP SER ASP VAL LEU THR LYS CYS PRO SEQRES 10 A 118 VAL SHEET 1 A 4 ALA A 19 ILE A 25 0 SHEET 2 A 4 SER A 108 ALA A 114 -1 O LEU A 112 N TYR A 21 SHEET 3 A 4 TYR A 47 HIS A 51 -1 N HIS A 51 O SER A 111 SHEET 4 A 4 LYS A 82 LYS A 85 -1 O LEU A 84 N ALA A 48 SHEET 1 B 4 GLU A 30 ILE A 33 0 SHEET 2 B 4 TRP A 96 ASN A 102 -1 O TRP A 98 N ILE A 33 SHEET 3 B 4 MET A 59 ARG A 65 -1 N LEU A 64 O ILE A 97 SHEET 4 B 4 LYS A 76 ASN A 78 -1 O LYS A 76 N LEU A 63 SSBOND 1 CYS A 32 CYS A 129 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 MODEL 1