HEADER PEPTIDE BINDING PROTEIN 11-FEB-11 2L9I TITLE NMR STRUCTURE OF THYMOSIN ALPHA-1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: THYMOSIN ALPHA-1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 4 ORGANISM_COMMON: HUMAN; SOURCE 5 ORGANISM_TAXID: 9606; SOURCE 6 OTHER_DETAILS: THE PROTEIN WAS MADE ON A PROTEIN SYNTHESIZER. KEYWDS LYMPHOCYTE MEMBRANE BINDING PEPTIDE, T-CELL DIFFERENTIATION, KEYWDS 2 IMMUNOPOTENTIATION, TRANSCRIPTION, PEPTIDE BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 21 AUTHOR M.A.ELIZONDO-RIOJAS,D.G.GORENSTEIN,D.E.VOLK REVDAT 1 28-DEC-11 2L9I 0 JRNL AUTH M.A.ELIZONDO-RIOJAS,S.M.CHAMOW,C.W.TUTHILL,D.G.GORENSTEIN, JRNL AUTH 2 D.E.VOLK JRNL TITL NMR STRUCTURE OF HUMAN THYMOSIN ALPHA-1. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 416 356 2011 JRNL REFN ISSN 0006-291X JRNL PMID 22115779 JRNL DOI 10.1016/J.BBRC.2011.11.041 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM,FERGUSON, REMARK 3 SEIBEL,SINGH,WEINER,KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: 25 NS AT 300K ON A EXPLICIT SOLVENT REMARK 3 RATIO 40% TFE/H2O (V/V), WITH A LINEAR-HELIX INITIAL STRUCTURE, REMARK 3 AFTER THE 25 NS ON EXPLICIT SOLVENT, 1 NS GB SIMULATION FOLLOWS REMARK 3 WITH ALL (549)RESTRAINS AT 300K., AFTER THE 1NS GB RESTRAINED REMARK 3 SIMULATION, A 10NS RESTRAINED MD SIMULATION FOLLOWS ON A EXPLICIT REMARK 3 SOLVENT RATIO 40% TFE/WATER (V/V). 1000 STRUCTURES WERE COLLECTED REMARK 3 (1 EVERY 10PS), MINIMIZED AND SORTED BY TOTAL ENERGY. THE BEST 20 REMARK 3 STRUCTURES WITH THE LOWEST ENERGY WERE SELECTED., THE AVERAGE REMARK 3 STRUCTURE WAS OBTAINED FROM THE AVERAGE OF THE 20 BEST STRUCTURES REMARK 3 WITH THE LOWEST ENERGY AND MINIMIZED WITH THE 549 RESTRAINTS AND REMARK 3 THE GB METHOD IN ORDER TO TAKING IN ACCOUNT THE SALVATION REMARK 3 IMPLICITLY. REMARK 4 REMARK 4 2L9I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-FEB-11. REMARK 100 THE RCSB ID CODE IS RCSB102125. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 4.9 REMARK 210 IONIC STRENGTH : 0 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 28.8 MG THYMOSIN-ALPHA1, 40 % REMARK 210 TFE, 10% D2O, 50% H2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-1H NOESY; 2D 1H-1H TOCSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ REMARK 210 SPECTROMETER MODEL : UNITYPLUS REMARK 210 SPECTROMETER MANUFACTURER : VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : AMBER 9.0 REMARK 210 METHOD USED : MOLECULAR DYNAMICS, RESTRAINED REMARK 210 MOLECULAR DYNAMICS, RESTRAINED REMARK 210 MOLECULAR DYNAMICS AND SELECTION, REMARK 210 AVERAGE STRUCTURE REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 1000 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 21 REMARK 210 CONFORMERS, SELECTION CRITERIA : 1 AVERAGE STRUCTURE + 20 REMARK 210 STRUCTURES WITH THE LOWEST 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 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 OD1 ASP A 3 HG SER A 9 1.56 REMARK 500 OD2 ASP A 3 HG SER A 10 1.58 REMARK 500 REMARK 500 REMARK: NULL 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 12 GLU A 26 CG GLU A 26 CD 0.091 REMARK 500 13 GLU A 11 CD GLU A 11 OE2 0.071 REMARK 500 19 GLU A 11 CG GLU A 11 CD 0.107 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 2 VAL A 23 CA - CB - CG1 ANGL. DEV. = 9.2 DEGREES REMARK 500 2 GLU A 28 OE1 - CD - OE2 ANGL. DEV. = -9.3 DEGREES REMARK 500 3 VAL A 6 CG1 - CB - CG2 ANGL. DEV. = -10.7 DEGREES REMARK 500 4 ASP A 3 CB - CG - OD1 ANGL. DEV. = -6.5 DEGREES REMARK 500 5 ASP A 16 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 5 GLU A 22 OE1 - CD - OE2 ANGL. DEV. = -7.7 DEGREES REMARK 500 8 GLU A 11 OE1 - CD - OE2 ANGL. DEV. = -9.0 DEGREES REMARK 500 9 ALA A 4 N - CA - CB ANGL. DEV. = -9.1 DEGREES REMARK 500 9 ASP A 16 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 9 VAL A 24 CG1 - CB - CG2 ANGL. DEV. = -11.5 DEGREES REMARK 500 11 ASP A 3 CB - CG - OD2 ANGL. DEV. = 6.9 DEGREES REMARK 500 11 VAL A 6 CG1 - CB - CG2 ANGL. DEV. = -10.2 DEGREES REMARK 500 11 ILE A 12 CG1 - CB - CG2 ANGL. DEV. = 13.7 DEGREES REMARK 500 11 VAL A 23 CA - CB - CG1 ANGL. DEV. = 9.9 DEGREES REMARK 500 12 ASP A 7 CB - CG - OD1 ANGL. DEV. = 7.2 DEGREES REMARK 500 13 ASP A 16 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 14 ASP A 7 CB - CG - OD1 ANGL. DEV. = -7.5 DEGREES REMARK 500 14 ASP A 7 CB - CG - OD2 ANGL. DEV. = 8.3 DEGREES REMARK 500 14 ASP A 16 CB - CG - OD1 ANGL. DEV. = 7.0 DEGREES REMARK 500 14 VAL A 23 CA - CB - CG1 ANGL. DEV. = 10.7 DEGREES REMARK 500 14 GLU A 25 OE1 - CD - OE2 ANGL. DEV. = -8.5 DEGREES REMARK 500 15 VAL A 6 CA - CB - CG1 ANGL. DEV. = 9.7 DEGREES REMARK 500 15 ASP A 16 CB - CG - OD1 ANGL. DEV. = -8.0 DEGREES REMARK 500 15 ASP A 16 CB - CG - OD2 ANGL. DEV. = 8.0 DEGREES REMARK 500 16 ASP A 7 CB - CG - OD2 ANGL. DEV. = 5.6 DEGREES REMARK 500 16 GLU A 22 OE1 - CD - OE2 ANGL. DEV. = -8.4 DEGREES REMARK 500 16 GLU A 28 OE1 - CD - OE2 ANGL. DEV. = -8.0 DEGREES REMARK 500 17 ASP A 7 CB - CG - OD1 ANGL. DEV. = 5.7 DEGREES REMARK 500 18 ALA A 4 N - CA - CB ANGL. DEV. = -8.9 DEGREES REMARK 500 19 ASP A 7 CB - CG - OD1 ANGL. DEV. = 7.4 DEGREES REMARK 500 19 THR A 14 CA - CB - CG2 ANGL. DEV. = -12.4 DEGREES REMARK 500 20 VAL A 23 CA - CB - CG1 ANGL. DEV. = 9.5 DEGREES REMARK 500 20 VAL A 24 CA - CB - CG1 ANGL. DEV. = 10.1 DEGREES REMARK 500 21 VAL A 23 CA - CB - CG1 ANGL. DEV. = 9.9 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 3 ASP A 3 -8.12 -51.92 REMARK 500 6 THR A 8 71.19 55.85 REMARK 500 7 SER A 10 -2.54 -54.37 REMARK 500 7 THR A 13 -34.44 -37.81 REMARK 500 8 THR A 8 61.22 65.67 REMARK 500 8 THR A 13 -17.09 -45.34 REMARK 500 10 THR A 8 81.00 34.81 REMARK 500 10 THR A 13 -31.37 -34.95 REMARK 500 12 ASP A 7 34.18 70.67 REMARK 500 13 THR A 8 90.04 49.23 REMARK 500 13 THR A 13 -29.97 -35.62 REMARK 500 14 THR A 8 83.34 54.76 REMARK 500 16 ALA A 5 -7.38 -56.92 REMARK 500 16 THR A 8 72.67 61.51 REMARK 500 18 SER A 10 -5.21 -57.52 REMARK 500 18 THR A 13 -35.05 -38.29 REMARK 500 18 GLU A 22 -71.47 -91.85 REMARK 500 19 THR A 8 77.43 68.06 REMARK 500 19 THR A 13 -34.45 -32.93 REMARK 500 21 THR A 8 70.03 52.87 REMARK 500 21 THR A 13 -35.98 -39.21 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CHIRAL CENTERS REMARK 500 REMARK 500 UNEXPECTED CONFIGURATION OF THE FOLLOWING CHIRAL REMARK 500 CENTER(S) USING IMPROPER CA--C--CB--N CHIRALITY REMARK 500 FOR AMINO ACIDS AND C1'--O4'--N1(N9)--C2' FOR REMARK 500 NUCLEIC ACIDS OR EQUIVALENT ANGLE REMARK 500 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,A1,6X,F5.1,6X,A1,10X,A1,3X,A16) REMARK 500 REMARK 500 M RES CSSEQI IMPROPER EXPECTED FOUND DETAILS REMARK 500 4 SER A 10 24.0 L L OUTSIDE RANGE REMARK 500 5 ASP A 7 24.2 L L OUTSIDE RANGE REMARK 500 6 ILE A 12 23.6 L L OUTSIDE RANGE REMARK 500 7 ASP A 7 25.0 L L OUTSIDE RANGE REMARK 500 8 ASP A 7 21.9 L L OUTSIDE RANGE REMARK 500 9 VAL A 24 24.4 L L OUTSIDE RANGE REMARK 500 14 LEU A 17 23.3 L L OUTSIDE RANGE REMARK 500 15 ILE A 12 24.7 L L OUTSIDE RANGE REMARK 500 16 GLU A 11 24.1 L L OUTSIDE RANGE REMARK 500 16 GLU A 28 22.7 L L OUTSIDE RANGE REMARK 500 18 ASP A 7 23.9 L L OUTSIDE RANGE REMARK 500 19 ASP A 7 24.7 L L OUTSIDE RANGE REMARK 500 19 VAL A 24 23.4 L L OUTSIDE RANGE REMARK 500 21 ILE A 12 24.7 L L OUTSIDE RANGE REMARK 500 21 THR A 13 22.7 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 17458 RELATED DB: BMRB DBREF 2L9I A 2 29 UNP P06454 PTMA_HUMAN 2 29 SEQADV 2L9I ACE A 1 UNP P06454 ACETYLATION SEQRES 1 A 29 ACE SER ASP ALA ALA VAL ASP THR SER SER GLU ILE THR SEQRES 2 A 29 THR LYS ASP LEU LYS GLU LYS LYS GLU VAL VAL GLU GLU SEQRES 3 A 29 ALA GLU ASN HET ACE A 1 6 HETNAM ACE ACETYL GROUP FORMUL 1 ACE C2 H4 O HELIX 1 1 SER A 2 ASP A 7 5 6 HELIX 2 2 THR A 8 ASN A 29 1 22 LINK C ACE A 1 N SER A 2 1555 1555 1.33 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 MODEL 2 MODEL 3 MODEL 4 MODEL 5 MODEL 6 MODEL 7 MODEL 8 MODEL 9 MODEL 10 MODEL 11 MODEL 12 MODEL 13 MODEL 14 MODEL 15 MODEL 16 MODEL 17 MODEL 18 MODEL 19 MODEL 20 MODEL 21