HEADER METAL BINDING PROTEIN 02-APR-10 2KWB TITLE MINIMAL CONSTRAINT SOLUTION NMR STRUCTURE OF TRANSLATIONALLY- TITLE 2 CONTROLLED TUMOR PROTEIN (TCTP) FROM C.ELEGANS, NORTHEAST STRUCTURAL TITLE 3 GENOMICS CONSORTIUM TARGET WR73 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSLATIONALLY-CONTROLLED TUMOR PROTEIN HOMOLOG; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TCTP; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CAENORHABDITIS ELEGANS; SOURCE 3 ORGANISM_COMMON: NEMATODE; SOURCE 4 ORGANISM_TAXID: 6239; SOURCE 5 GENE: F25H2.11, TCT-1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PMGK; SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET21 KEYWDS STRUCTURAL GENOMICS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), KEYWDS 2 PSI-2, PROTEIN STRUCTURE INITIATIVE, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR J.M.ARAMINI,P.ROSSI,J.R.CORT,B.COOPER,M.MAGLAQUI,H.JANJUA,R.XIAO, AUTHOR 2 T.B.ACTON,J.K.EVERETT,G.T.MONTELIONE,NORTHEAST STRUCTURAL GENOMICS AUTHOR 3 CONSORTIUM (NESG) REVDAT 3 15-MAY-24 2KWB 1 REMARK REVDAT 2 16-MAR-22 2KWB 1 REMARK SEQADV REVDAT 1 28-APR-10 2KWB 0 JRNL AUTH J.M.ARAMINI,P.ROSSI,J.R.CORT,B.COOPER,M.MAGLAQUI,H.JANJUA, JRNL AUTH 2 R.XIAO,T.B.ACTON,J.K.EVERETT,G.T.MONTELIONE JRNL TITL MINIMAL CONSTRAINT SOLUTION NMR STRUCTURE OF JRNL TITL 2 TRANSLATIONALLY-CONTROLLED TUMOR PROTEIN (TCTP) FROM JRNL TITL 3 C.ELEGANS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET JRNL TITL 4 WR73 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER, ADAMS, CLORE, GROS, NILGES AND READ REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: THE FINAL MINIMAL CONSTRAINT STRUCTURES REMARK 3 ARE BASED ON A TOTAL OF 976 CONFORMATIONALLY-RESTRICTING REMARK 3 DISTANCE CONSTRAINTS, 272 DIHEDRAL ANGLE CONSTRAINTS, AND 126 REMARK 3 HYDROGEN BOND CONSTRAINTS (7.6 CONSTRAINTS PER RESIDUE, 2.3 LONG REMARK 3 RANGE CONSTRAINTS PER RESIDUE, COMPUTED FOR RESIDUES 1 TO 183 BY REMARK 3 PSVS 1.4). STRUCTURE DETERMINATION WAS PERFORMED ITERATIVELY REMARK 3 USING CYANA 3.0. THE 20 STRUCTURES OUT OF 100 WITH THE LOWEST REMARK 3 TARGET FUNCTION WERE FURTHER REFINED BY RESTRAINED MOLECULAR REMARK 3 DYNAMICS/ENERGY MINIMIZATION IN EXPLICIT WATER (CNS) WITH REMARK 3 PARAM19. REMARK 4 REMARK 4 2KWB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-APR-10. REMARK 100 THE DEPOSITION ID IS D_1000101653. 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 : 0.82 MM [U-13C; U-15N; U-2H; REMARK 210 ILVFY-1H] WR73, 20 MM MES, 100 REMARK 210 MM SODIUM CHLORIDE, 5 MM CALCIUM REMARK 210 CHLORIDE, 10 MM DTT, 50 UM DSS, REMARK 210 0.02 % SODIUM AZIDE, 90% H2O/10% REMARK 210 D2O; 0.85 MM [U-5% 13C; U-100% REMARK 210 15N] WR73, 20 MM MES, 100 MM REMARK 210 SODIUM CHLORIDE, 5 MM CALCIUM REMARK 210 CHLORIDE, 10 MM DTT, 50 UM DSS, REMARK 210 0.02 % SODIUM AZIDE, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-15N TROSY REMARK 210 -HSQC; 2D 1H-13C HSQC ALIPHATIC; REMARK 210 3D HNCO; 3D HN(CA)CO; 3D TROSY- REMARK 210 HNCACB; 3D TROSY-HN(CO)CACB; 3D REMARK 210 1H-15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 15N-15N-1H NOESY; REMARK 210 3D 13C-13C-1H NOESY; 3D 15N-13C- REMARK 210 1H NOESY; 3D 13C-15N-1H NOESY; REMARK 210 3D C(CO)NH TOCSY; 2D 1H-13C HSQC REMARK 210 HIGH RESOLUTION REMARK 210 SPECTROMETER FIELD STRENGTH : 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CNS 1.2, CYANA 3.0, PINE 1.0, REMARK 210 NMRPIPE 2.3, SPARKY 3, TOPSPIN REMARK 210 2.1, VNMRJ, PSVS 1.4, TALOS PLUS, REMARK 210 PDBSTAT 5.1 REMARK 210 METHOD USED : SIMULATED ANNEALING 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: THE PROTEIN IS MONOMERIC AT 298 K BY 15N T1/T2 RELAXATION REMARK 210 AND STATIC LIGHT SCATTERING. THE STRUCTURE IS A MINIMAL REMARK 210 CONSTRAINT STRUCTURE DETERMINED USING TRIPLE RESONANCE NMR REMARK 210 SPECTROSCOPY. ALL NOESY DATA WERE ACQUIRED AT 800 MHZ USING A 5- REMARK 210 MM CRYOPROBE. BACKBONE ASSIGNMENTS WERE MADE USING PINE, AND THE REMARK 210 SIDE CHAIN METHYL ASSIGNMENTS WERE COMPLETED MANUALLY. AUTOMATIC REMARK 210 NOESY ASSIGNMENTS WERE DETERMINED USING CYANA 3.0. BACKBONE (PHI/ REMARK 210 PSI) DIHEDRAL ANGLE CONSTRAINTS WERE OBTAINED FROM TALOSPLUS. REMARK 210 FINAL STRUCTURE QUALITY FACTORS (FOR RESIDUE NUMBERS 1 TO 183, REMARK 210 PSVS 1.4), WHERE ORDERED RESIDUES [S(PHI) + S(PSI) > 1.8] REMARK 210 COMPRISE: 2-12,14-16,18-38,66-106,111-146,152-181: (A) RMSD REMARK 210 (ORDERED RESIDUES): BB, 1.0, HEAVY ATOM, 1.5. (B) RAMACHANDRAN REMARK 210 STATISTICS FOR ORDERED RESIDUES: MOST FAVORED, 89.0%, REMARK 210 ADDITIONALLY ALLOWED, 10.9%, GENEROUSLY ALLOWED, 0.1%, REMARK 210 DISALLOWED, 0.0%. (C) PROCHECK SCORES FOR ORDERED RESIDUES (RAW/ REMARK 210 Z-): PHI-PSI, -0.34/-1.02, ALL, -0.31/-1.83. (D) MOLPROBITY REMARK 210 CLASH SCORE (RAW/Z-): 20.78/-2.04 (E) NUMBER OF CLOSE CONTACTS REMARK 210 PER 20 MODELS: 55. THE C-TERMINAL HIS TAG RESIDUES OF THE REMARK 210 PROTEIN (HHHHHH) WERE NOT INCLUDED IN THE STRUCTURE CALCULATIONS REMARK 210 AND HAVE BEEN OMITTED FROM THIS DEPOSITION. COORDINATES FOR THE REMARK 210 FOLLOWING RESIDUES ARE NOT WELL DETERMINED [S(PHI) + S(PSI) < REMARK 210 1.8]: 1,13,17,39-65,107-110,147-151,182-183. 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 1-20 REMARK 465 RES C SSSEQI REMARK 465 HIS A 184 REMARK 465 HIS A 185 REMARK 465 HIS A 186 REMARK 465 HIS A 187 REMARK 465 HIS A 188 REMARK 465 HIS A 189 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 ASP A 24 14.24 59.22 REMARK 500 1 ASN A 48 -53.64 -172.38 REMARK 500 1 ALA A 51 -62.32 -133.65 REMARK 500 1 GLU A 52 -58.30 69.00 REMARK 500 1 ASP A 58 45.32 -77.23 REMARK 500 1 SER A 60 152.39 73.24 REMARK 500 1 GLU A 65 -40.90 -27.95 REMARK 500 1 LYS A 75 71.12 58.06 REMARK 500 1 ARG A 108 -35.70 71.59 REMARK 500 1 ALA A 129 89.06 -62.62 REMARK 500 1 LYS A 134 -32.32 -35.79 REMARK 500 1 ASN A 135 35.11 -96.85 REMARK 500 1 LEU A 182 -63.80 -122.69 REMARK 500 2 LEU A 13 112.20 57.20 REMARK 500 2 ASP A 16 -147.87 -171.61 REMARK 500 2 SER A 17 30.01 -150.06 REMARK 500 2 LEU A 26 -44.01 -134.17 REMARK 500 2 GLU A 39 -68.29 63.13 REMARK 500 2 LEU A 44 99.33 58.42 REMARK 500 2 PRO A 49 68.37 -64.00 REMARK 500 2 LYS A 75 70.86 59.56 REMARK 500 2 ARG A 108 -23.81 -38.41 REMARK 500 2 LYS A 110 4.64 -68.95 REMARK 500 2 ALA A 129 87.07 -66.89 REMARK 500 2 ASP A 162 17.92 58.41 REMARK 500 2 LEU A 182 -176.22 175.19 REMARK 500 3 LEU A 13 120.32 -31.28 REMARK 500 3 ASP A 24 13.38 57.70 REMARK 500 3 GLU A 39 12.41 59.45 REMARK 500 3 ASN A 48 89.93 61.72 REMARK 500 3 ALA A 51 16.16 -141.75 REMARK 500 3 ALA A 55 -57.82 -158.24 REMARK 500 3 GLU A 56 90.14 59.29 REMARK 500 3 ASP A 58 -63.96 70.27 REMARK 500 3 SER A 60 67.81 -156.14 REMARK 500 3 HIS A 63 19.80 56.59 REMARK 500 3 VAL A 64 -76.27 -63.32 REMARK 500 3 GLU A 65 -32.05 70.41 REMARK 500 3 LYS A 75 71.20 54.76 REMARK 500 3 ASN A 80 -162.28 -115.93 REMARK 500 3 ASN A 107 -80.34 -123.64 REMARK 500 3 ARG A 108 -15.74 72.25 REMARK 500 3 ALA A 129 86.41 -66.46 REMARK 500 3 ALA A 148 -71.72 -63.12 REMARK 500 3 GLU A 149 -77.39 -123.80 REMARK 500 3 ASN A 150 -59.98 -134.79 REMARK 500 4 LEU A 13 90.80 40.30 REMARK 500 4 ALA A 45 34.08 -80.88 REMARK 500 4 SER A 50 101.25 -165.35 REMARK 500 4 GLU A 53 19.60 59.64 REMARK 500 REMARK 500 THIS ENTRY HAS 270 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 16833 RELATED DB: BMRB REMARK 900 RELATED ID: WR73 RELATED DB: TARGETDB DBREF 2KWB A 1 181 UNP Q93573 TCTP_CAEEL 1 181 SEQADV 2KWB LEU A 182 UNP Q93573 EXPRESSION TAG SEQADV 2KWB GLU A 183 UNP Q93573 EXPRESSION TAG SEQADV 2KWB HIS A 184 UNP Q93573 EXPRESSION TAG SEQADV 2KWB HIS A 185 UNP Q93573 EXPRESSION TAG SEQADV 2KWB HIS A 186 UNP Q93573 EXPRESSION TAG SEQADV 2KWB HIS A 187 UNP Q93573 EXPRESSION TAG SEQADV 2KWB HIS A 188 UNP Q93573 EXPRESSION TAG SEQADV 2KWB HIS A 189 UNP Q93573 EXPRESSION TAG SEQRES 1 A 189 MET LEU ILE TYR LYS ASP ILE PHE THR ASP ASP GLU LEU SEQRES 2 A 189 SER SER ASP SER PHE PRO MET LYS LEU VAL ASP ASP LEU SEQRES 3 A 189 VAL TYR GLU PHE LYS GLY LYS HIS VAL VAL ARG LYS GLU SEQRES 4 A 189 GLY GLU ILE VAL LEU ALA GLY SER ASN PRO SER ALA GLU SEQRES 5 A 189 GLU GLY ALA GLU ASP ASP GLY SER ASP GLU HIS VAL GLU SEQRES 6 A 189 ARG GLY ILE ASP ILE VAL LEU ASN HIS LYS LEU VAL GLU SEQRES 7 A 189 MET ASN CYS TYR GLU ASP ALA SER MET PHE LYS ALA TYR SEQRES 8 A 189 ILE LYS LYS PHE MET LYS ASN VAL ILE ASP HIS MET GLU SEQRES 9 A 189 LYS ASN ASN ARG ASP LYS ALA ASP VAL ASP ALA PHE LYS SEQRES 10 A 189 LYS LYS ILE GLN GLY TRP VAL VAL SER LEU LEU ALA LYS SEQRES 11 A 189 ASP ARG PHE LYS ASN LEU ALA PHE PHE ILE GLY GLU ARG SEQRES 12 A 189 ALA ALA GLU GLY ALA GLU ASN GLY GLN VAL ALA ILE ILE SEQRES 13 A 189 GLU TYR ARG ASP VAL ASP GLY THR GLU VAL PRO THR LEU SEQRES 14 A 189 MET LEU VAL LYS GLU ALA ILE ILE GLU GLU LYS CYS LEU SEQRES 15 A 189 GLU HIS HIS HIS HIS HIS HIS HELIX 1 1 SER A 60 VAL A 64 5 5 HELIX 2 2 ASP A 69 ASN A 73 1 5 HELIX 3 3 ASN A 80 ASN A 107 1 28 HELIX 4 4 ASP A 109 LEU A 128 1 20 HELIX 5 5 ALA A 129 LYS A 134 1 6 HELIX 6 6 GLU A 142 ALA A 148 1 7 SHEET 1 A 3 SER A 14 ASP A 16 0 SHEET 2 A 3 LEU A 2 ASP A 6 -1 N TYR A 4 O SER A 14 SHEET 3 A 3 ILE A 176 GLU A 179 -1 O ILE A 177 N LYS A 5 SHEET 1 B 6 LYS A 21 VAL A 23 0 SHEET 2 B 6 VAL A 27 LYS A 31 -1 O VAL A 27 N VAL A 23 SHEET 3 B 6 THR A 164 VAL A 172 -1 O LEU A 171 N TYR A 28 SHEET 4 B 6 VAL A 153 VAL A 161 -1 N GLU A 157 O THR A 168 SHEET 5 B 6 ALA A 137 GLY A 141 -1 N PHE A 139 O ALA A 154 SHEET 6 B 6 LEU A 76 MET A 79 -1 N MET A 79 O PHE A 138 SHEET 1 C 2 HIS A 34 VAL A 35 0 SHEET 2 C 2 GLY A 67 ILE A 68 -1 O GLY A 67 N VAL A 35 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