HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 05-JUL-04 1TXJ TITLE CRYSTAL STRUCTURE OF TRANSLATIONALLY CONTROLLED TUMOUR-ASSOCIATED TITLE 2 PROTEIN (TCTP) FROM PLASMODIUM KNOWLESI COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSLATIONALLY CONTROLLED TUMOUR-ASSOCIATED PROTEIN (TCTP) COMPND 3 FROM PLASMODIUM KNOWLESI, PKN_PFE0545C; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PLASMODIUM KNOWLESI; SOURCE 3 ORGANISM_TAXID: 5850; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: P11 KEYWDS STRUCTURAL GENOMICS CONSORTIUM, SGC, GUANINE NUCLEOTIDE-FREE KEYWDS 2 CHAPERONES, GUANINE NUCLEOTIDE EXCHANGE FACTOR, BETA-SANDWICH, KEYWDS 3 HELIX-TURN-HELIX, STRUCTURAL GENOMICS, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR J.R.WALKER,M.VEDADI,S.SHARMA,S.HOUSTON,J.LEW,M.AMANI,G.WASNEY, AUTHOR 2 T.SKARINA,J.BRAY,M.SUNDSTROM,C.ARROWSMITH,A.EDWARDS,R.HUI,STRUCTURAL AUTHOR 3 GENOMICS CONSORTIUM (SGC) REVDAT 6 14-FEB-24 1TXJ 1 REMARK REVDAT 5 24-FEB-09 1TXJ 1 VERSN REVDAT 4 26-DEC-06 1TXJ 1 JRNL REVDAT 3 10-OCT-06 1TXJ 1 AUTHOR REVDAT 2 24-JAN-06 1TXJ 1 JRNL REVDAT 1 20-JUL-04 1TXJ 0 JRNL AUTH M.VEDADI,J.LEW,J.ARTZ,M.AMANI,Y.ZHAO,A.DONG,G.A.WASNEY, JRNL AUTH 2 M.GAO,T.HILLS,S.BROKX,W.QIU,S.SHARMA,A.DIASSITI,Z.ALAM, JRNL AUTH 3 M.MELONE,A.MULICHAK,A.WERNIMONT,J.BRAY,P.LOPPNAU, JRNL AUTH 4 O.PLOTNIKOVA,K.NEWBERRY,E.SUNDARARAJAN,S.HOUSTON,J.WALKER, JRNL AUTH 5 W.TEMPEL,A.BOCHKAREV,I.KOZIERADZKI,A.EDWARDS,C.ARROWSMITH, JRNL AUTH 6 D.ROOS,K.KAIN,R.HUI JRNL TITL GENOME-SCALE PROTEIN EXPRESSION AND STRUCTURAL BIOLOGY OF JRNL TITL 2 PLASMODIUM FALCIPARUM AND RELATED APICOMPLEXAN ORGANISMS. JRNL REF MOL.BIOCHEM.PARASITOL. V. 151 100 2007 JRNL REFN ISSN 0166-6851 JRNL PMID 17125854 JRNL DOI 10.1016/J.MOLBIOPARA.2006.10.011 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1173452.910 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 16129 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 817 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.13 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2522 REMARK 3 BIN R VALUE (WORKING SET) : 0.2270 REMARK 3 BIN FREE R VALUE : 0.2740 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 141 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.023 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1294 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 118 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 40.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.72000 REMARK 3 B22 (A**2) : 6.72000 REMARK 3 B33 (A**2) : -13.44000 REMARK 3 B12 (A**2) : 3.66000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.15 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.020 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.640 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.540 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.330 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.530 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.54 REMARK 3 BSOL : 83.40 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1TXJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-JUL-04. REMARK 100 THE DEPOSITION ID IS D_1000023004. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-APR-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : CONFOCAL MULTILAYER OPTICS REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16150 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.04300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 54.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.31400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CITRATE, HEPES, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.09067 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 18.54533 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 27.81800 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 9.27267 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 46.36333 REMARK 290 REMARK 290 REMARK: NULL 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 ASP A 46 REMARK 465 ASP A 47 REMARK 465 TYR A 48 REMARK 465 GLY A 49 REMARK 465 ILE A 50 REMARK 465 ALA A 51 REMARK 465 ASP A 52 REMARK 465 ASN A 53 REMARK 465 SER A 54 REMARK 465 GLU A 55 REMARK 465 GLU A 56 REMARK 465 ALA A 57 REMARK 465 VAL A 58 REMARK 465 ASP A 59 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 PHE A 24 19.32 58.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE OF THE PROTEIN CAN BE FOUND IN THE REMARK 999 PLASMODB PK_353F04Q1C. DBREF 1TXJ A 1 171 UNP P84152 TCTP_PLAKN 1 171 SEQRES 1 A 171 MET LYS VAL TYR LYS ASP VAL PHE THR ASN ASP GLU VAL SEQRES 2 A 171 CYS SER ASP SER TYR ASN GLN GLU ASP PRO PHE GLY ILE SEQRES 3 A 171 ALA ASP PHE ARG GLU ILE ALA PHE GLU VAL LYS SER ASN SEQRES 4 A 171 LYS ARG ILE LYS GLY ASN ASP ASP TYR GLY ILE ALA ASP SEQRES 5 A 171 ASN SER GLU GLU ALA VAL ASP GLY MET GLY ALA ASP VAL SEQRES 6 A 171 GLU GLN VAL ILE ASP ILE VAL ASP SER PHE GLN LEU THR SEQRES 7 A 171 SER THR SER LEU SER LYS LYS GLU TYR SER VAL TYR ILE SEQRES 8 A 171 LYS ASN TYR MET GLN LYS ILE LEU LYS TYR LEU GLU GLU SEQRES 9 A 171 LYS LYS PRO ASP ARG VAL ASP VAL PHE LYS THR LYS ALA SEQRES 10 A 171 GLN PRO LEU ILE LYS HIS ILE LEU THR ASN PHE ASP ASP SEQRES 11 A 171 PHE GLU PHE TYR MET GLY GLU SER LEU ASP MET ASP ALA SEQRES 12 A 171 GLY LEU THR TYR SER TYR TYR LYS GLY GLU GLU VAL THR SEQRES 13 A 171 PRO ARG PHE VAL TYR ILE SER ASP GLY LEU TYR GLU GLU SEQRES 14 A 171 LYS PHE FORMUL 2 HOH *118(H2 O) HELIX 1 1 ASP A 22 ARG A 30 5 9 HELIX 2 2 ASP A 70 GLN A 76 1 7 HELIX 3 3 SER A 83 LYS A 106 1 24 HELIX 4 4 ARG A 109 ASN A 127 1 19 HELIX 5 5 PHE A 128 PHE A 131 5 4 SHEET 1 A 3 GLU A 12 SER A 15 0 SHEET 2 A 3 LYS A 2 ASP A 6 -1 N TYR A 4 O CYS A 14 SHEET 3 A 3 LEU A 166 LYS A 170 -1 O TYR A 167 N LYS A 5 SHEET 1 B 5 ALA A 33 LYS A 37 0 SHEET 2 B 5 ARG A 158 ILE A 162 -1 O PHE A 159 N VAL A 36 SHEET 3 B 5 THR A 146 TYR A 149 -1 N TYR A 147 O VAL A 160 SHEET 4 B 5 GLU A 132 MET A 135 -1 N GLU A 132 O SER A 148 SHEET 5 B 5 THR A 78 THR A 80 -1 N THR A 80 O PHE A 133 SHEET 1 C 2 LYS A 40 ILE A 42 0 SHEET 2 C 2 GLN A 67 ILE A 69 -1 O VAL A 68 N ARG A 41 CRYST1 86.633 86.633 55.636 90.00 90.00 120.00 P 65 6 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 0.011543 0.006664 0.000000 0.00000 SCALE2 0.000000 0.013329 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017974 0.00000