PDB Short entry for 2MY9 HEADER HYDROLASE 21-JAN-15 2MY9 TITLE SOLUTION STRUCTURE OF N-TERMINAL DOMAIN OF HUMAN TIG3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: RETINOIC ACID RECEPTOR RESPONDER PROTEIN 3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN (UNP RESIDUES 1-125); COMPND 5 SYNONYM: HRAS-LIKE SUPPRESSOR 4, HRSL4, RAR-RESPONSIVE PROTEIN TIG3, COMPND 6 RETINOID-INDUCIBLE GENE 1 PROTEIN, TAZAROTENE-INDUCED GENE 3 PROTEIN; COMPND 7 EC: 3.1.1.-; COMPND 8 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: RARRES3, RIG1, TIG3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: ROSETTA; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET21A KEYWDS TIG3, H-REV107 FAMILY, NLPC/P60, PHOSPHOLIPASE, HYDROLASE EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR H.WEI,L.WANG,B.XIA REVDAT 2 26-AUG-15 2MY9 1 JRNL REVDAT 1 15-APR-15 2MY9 0 JRNL AUTH H.WEI,L.WANG,X.REN,W.YU,J.LIN,C.JIN,B.XIA JRNL TITL STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF TUMOR JRNL TITL 2 SUPPRESSORS TIG3 AND H-REV107. JRNL REF FEBS LETT. V. 589 1179 2015 JRNL REFN ISSN 0014-5793 JRNL PMID 25871522 JRNL DOI 10.1016/J.FEBSLET.2015.04.002 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER 9.0 REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM, III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2MY9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-JAN-15. REMARK 100 THE RCSB ID CODE IS RCSB104194. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 308 REMARK 210 PH : 7.0 REMARK 210 IONIC STRENGTH : 100 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-13C; U-15N] TIG3N, REMARK 210 0.03% DSS, 20 MM DTT, 50 MM REMARK 210 SODIUM CHLORIDE, 50 MM POTASSIUM REMARK 210 CHLORIDE, 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D CBCA(CO)NH; 3D HNCA; 3D REMARK 210 HNCACB; 3D HBHA(CO)NH; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY; 3D HCCH- REMARK 210 COSY REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 500 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CYANA 3.0, DYANA 3.0, NMRDRAW, REMARK 210 NMRPIPE, NMRVIEW 5, PROCHECKNMR, REMARK 210 TALOS, SANE, TOPSPIN 3.0 REMARK 210 METHOD USED : DGSA-DISTANCE GEOMETRY SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : 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: 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 1 ARG A 111 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 2 ARG A 75 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 3 ARG A 121 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 ARG A 75 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 4 ARG A 111 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 5 ARG A 111 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 ARG A 111 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 6 ARG A 111 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 7 ARG A 111 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 7 ARG A 111 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 7 ARG A 121 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG A 87 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 10 ARG A 111 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 10 ARG A 111 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 10 ARG A 121 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 12 ARG A 75 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 13 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 13 ARG A 75 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 14 ARG A 111 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 14 ARG A 111 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 16 ARG A 64 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 18 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 19 ARG A 64 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 19 ARG A 111 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 20 ARG A 75 NE - CZ - NH2 ANGL. DEV. = -3.0 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 1 SER A 47 -2.07 76.78 REMARK 500 1 LYS A 105 -174.46 -67.29 REMARK 500 1 TYR A 106 -172.37 -68.06 REMARK 500 1 SER A 110 -144.41 57.32 REMARK 500 1 ASN A 112 -17.50 -142.57 REMARK 500 2 PHE A 17 59.83 -90.55 REMARK 500 2 VAL A 50 -46.58 73.09 REMARK 500 2 ASN A 77 80.55 -150.88 REMARK 500 2 ILE A 108 -31.45 58.10 REMARK 500 3 TYR A 42 -9.82 86.71 REMARK 500 3 ASN A 56 157.00 78.77 REMARK 500 3 SER A 107 -31.12 71.01 REMARK 500 4 LEU A 54 -166.13 66.44 REMARK 500 4 ASN A 77 93.52 -163.06 REMARK 500 4 ILE A 108 -31.81 57.63 REMARK 500 5 ASN A 56 -77.42 -128.36 REMARK 500 6 GLU A 41 92.37 -160.57 REMARK 500 6 SER A 47 -111.88 -158.44 REMARK 500 6 SER A 55 -35.81 -131.99 REMARK 500 6 ARG A 111 133.52 82.07 REMARK 500 6 ASN A 112 -58.80 -177.57 REMARK 500 7 TYR A 21 142.89 -170.51 REMARK 500 7 SER A 40 -22.20 70.80 REMARK 500 7 VAL A 50 18.21 59.13 REMARK 500 7 SER A 52 -26.55 70.07 REMARK 500 7 SER A 55 -49.45 -135.48 REMARK 500 7 ASN A 77 85.41 -154.94 REMARK 500 7 ASN A 78 46.99 -79.11 REMARK 500 7 ILE A 108 21.42 -68.37 REMARK 500 8 GLU A 41 -58.95 74.26 REMARK 500 8 SER A 47 -156.44 -80.00 REMARK 500 8 LEU A 54 -25.45 65.14 REMARK 500 8 ARG A 111 86.14 66.64 REMARK 500 9 HIS A 5 160.69 80.13 REMARK 500 9 SER A 40 -18.99 72.07 REMARK 500 9 SER A 52 42.70 -75.12 REMARK 500 9 LYS A 124 -144.85 43.60 REMARK 500 10 SER A 48 -98.15 -90.79 REMARK 500 10 SER A 49 -51.33 65.90 REMARK 500 10 ASN A 56 41.05 -75.11 REMARK 500 10 ASN A 77 84.77 -152.65 REMARK 500 10 ILE A 108 97.42 -167.06 REMARK 500 10 VAL A 109 -61.85 69.73 REMARK 500 11 CYS A 72 -160.86 -126.31 REMARK 500 11 SER A 107 36.28 -76.79 REMARK 500 11 ILE A 108 -14.21 55.54 REMARK 500 11 ARG A 111 -20.59 117.05 REMARK 500 11 ASN A 112 -6.96 -59.14 REMARK 500 12 SER A 49 -147.20 -98.29 REMARK 500 12 ASN A 77 85.24 -152.71 REMARK 500 REMARK 500 THIS ENTRY HAS 86 RAMACHANDRAN OUTLIERS. 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 13 ARG A 87 0.08 SIDE CHAIN 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 1 TYR A 42 24.0 L L OUTSIDE RANGE REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2LKT RELATED DB: PDB REMARK 900 SOLUTION STRUCTURE OF N-TERMINAL DOMAIN OF HUMAN TIG3 IN 2 REMARK 900 M UREA REMARK 900 RELATED ID: 25448 RELATED DB: BMRB DBREF 2MY9 A 1 125 UNP Q9UL19 HRSL4_HUMAN 1 125 SEQRES 1 A 125 MET ALA SER PRO HIS GLN GLU PRO LYS PRO GLY ASP LEU SEQRES 2 A 125 ILE GLU ILE PHE ARG LEU GLY TYR GLU HIS TRP ALA LEU SEQRES 3 A 125 TYR ILE GLY ASP GLY TYR VAL ILE HIS LEU ALA PRO PRO SEQRES 4 A 125 SER GLU TYR PRO GLY ALA GLY SER SER SER VAL PHE SER SEQRES 5 A 125 VAL LEU SER ASN SER ALA GLU VAL LYS ARG GLU ARG LEU SEQRES 6 A 125 GLU ASP VAL VAL GLY GLY CYS CYS TYR ARG VAL ASN ASN SEQRES 7 A 125 SER LEU ASP HIS GLU TYR GLN PRO ARG PRO VAL GLU VAL SEQRES 8 A 125 ILE ILE SER SER ALA LYS GLU MET VAL GLY GLN LYS MET SEQRES 9 A 125 LYS TYR SER ILE VAL SER ARG ASN CYS GLU HIS PHE VAL SEQRES 10 A 125 THR GLN LEU ARG TYR GLY LYS SER HELIX 1 1 GLU A 41 ALA A 45 5 5 HELIX 2 2 LEU A 65 GLY A 70 1 6 HELIX 3 3 ASN A 78 GLU A 83 5 6 HELIX 4 4 PRO A 88 VAL A 100 1 13 HELIX 5 5 TYR A 106 SER A 110 5 5 HELIX 6 6 ASN A 112 GLY A 123 1 12 SHEET 1 A 6 CYS A 73 VAL A 76 0 SHEET 2 A 6 LEU A 13 PHE A 17 -1 N GLU A 15 O ARG A 75 SHEET 3 A 6 GLU A 22 GLY A 29 -1 O HIS A 23 N ILE A 16 SHEET 4 A 6 TYR A 32 ALA A 37 -1 O ILE A 34 N LEU A 26 SHEET 5 A 6 ALA A 58 ARG A 64 -1 O GLU A 63 N VAL A 33 SHEET 6 A 6 LYS A 103 MET A 104 -1 O MET A 104 N ALA A 58 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