HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 27-JUN-05 2CX1 TITLE CRYSTAL STRUCTURE OF A PUA DOMAIN (APE0525) FROM THE AEROPYRUM PERNIX TITLE 2 K1 (TARTRATE COMPLEX) COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN APE0525; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AEROPYRUM PERNIX; SOURCE 3 ORGANISM_TAXID: 272557; SOURCE 4 STRAIN: K1; SOURCE 5 GENE: APE0525; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: B834(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS PUA DOMAIN, STRUCTURAL GENOMICS, NPPSFA, NATIONAL PROJECT ON PROTEIN KEYWDS 2 STRUCTURAL AND FUNCTIONAL ANALYSES, RIKEN STRUCTURAL KEYWDS 3 GENOMICS/PROTEOMICS INITIATIVE, RSGI, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR E.MIZOHATA,S.MORITA,K.NAGANO,H.UDA,T.TERADA,M.SHIROUZU,S.YOKOYAMA, AUTHOR 2 RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE (RSGI) REVDAT 4 30-OCT-24 2CX1 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 2CX1 1 VERSN REVDAT 2 24-FEB-09 2CX1 1 VERSN REVDAT 1 27-DEC-05 2CX1 0 JRNL AUTH E.MIZOHATA,S.MORITA,K.NAGANO,H.UDA,T.TERADA,M.SHIROUZU, JRNL AUTH 2 S.YOKOYAMA JRNL TITL CRYSTAL STRUCTURE OF A PUA DOMAIN (APE0525) FROM THE JRNL TITL 2 AEROPYRUM PERNIX K1 (TARTRATE COMPLEX) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 344334.520 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 17676 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) : 0.163 REMARK 3 FREE R VALUE : 0.192 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 847 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.007 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2299 REMARK 3 BIN R VALUE (WORKING SET) : 0.1840 REMARK 3 BIN FREE R VALUE : 0.2300 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 103 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 : 1445 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 178 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.35000 REMARK 3 B22 (A**2) : -3.12000 REMARK 3 B33 (A**2) : 2.77000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -1.58000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.16 REMARK 3 ESD FROM SIGMAA (A) : 0.11 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) : 0.21 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.18 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.019 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.80 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.170 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 52.01 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 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2CX1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-JUL-05. REMARK 100 THE DEPOSITION ID IS D_1000024722. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-MAY-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44B2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17683 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.42 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350, SODIUM TARTRATE, SODIUM REMARK 280 CHLORIDE, TRIS, PH 8, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-Z 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 24.56950 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 300 REMARK: UNKNOWN. PROBABLY MONOMER FROM THE CRYSTAL STRUCTURE. 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 ARG A 184 REMARK 465 LEU A 185 REMARK 465 SER A 186 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 2158 O HOH A 2176 2757 2.19 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 LEU A 6 -51.96 69.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TLA A 2001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CX0 RELATED DB: PDB REMARK 900 THE SAME PROTEIN REMARK 900 RELATED ID: APE001000525.2 RELATED DB: TARGETDB DBREF 2CX1 A 1 186 UNP Q9YEQ6 Q9YEQ6_AERPE 1 186 SEQADV 2CX1 HIS A 0 UNP Q9YEQ6 EXPRESSION TAG SEQADV 2CX1 MSE A 1 UNP Q9YEQ6 MET 1 MODIFIED RESIDUE SEQADV 2CX1 MSE A 111 UNP Q9YEQ6 MET 111 MODIFIED RESIDUE SEQADV 2CX1 MSE A 140 UNP Q9YEQ6 MET 140 MODIFIED RESIDUE SEQRES 1 A 187 HIS MSE LEU TRP ALA ARG LEU VAL GLY LEU ALA ARG LEU SEQRES 2 A 187 GLU ALA ARG ALA LEU SER LYS LYS GLU ARG ARG SER LEU SEQRES 3 A 187 LEU GLU ARG LEU LYS PRO TYR TYR THR ARG ILE PRO PHE SEQRES 4 A 187 SER GLU LYS ALA ASP LEU ARG LEU VAL LYS ALA ARG THR SEQRES 5 A 187 ASP SER GLY GLU TYR GLU ILE ILE THR VAL ASP GLY VAL SEQRES 6 A 187 PRO CYS LEU PHE GLU TRP SER ASP GLY ARG ILE TYR PRO SEQRES 7 A 187 THR LEU GLN CYS LEU LYS ALA PHE GLY VAL ASP TRP LEU SEQRES 8 A 187 LYS GLY VAL VAL LEU VAL ASP LYS GLY ALA ALA ILE ALA SEQRES 9 A 187 LEU ALA LYS GLY ALA HIS LEU MSE ILE PRO GLY VAL VAL SEQRES 10 A 187 GLY VAL GLU GLY SER PHE THR ARG GLY ASP VAL VAL ALA SEQRES 11 A 187 ALA LEU TYR HIS GLU THR ARG THR PRO VAL MSE VAL GLY SEQRES 12 A 187 VAL ALA GLU VAL ASP SER SER ALA LEU GLU LYS LEU TYR SEQRES 13 A 187 ARG GLU LYS ALA ARG GLY ARG ALA VAL ARG ARG VAL HIS SEQRES 14 A 187 ARG LEU GLY ASP ALA LEU TRP GLU LEU ALA GLN GLU VAL SEQRES 15 A 187 GLY LYS ARG LEU SER MODRES 2CX1 MSE A 1 MET SELENOMETHIONINE MODRES 2CX1 MSE A 111 MET SELENOMETHIONINE MODRES 2CX1 MSE A 140 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 111 8 HET MSE A 140 8 HET TLA A2001 10 HETNAM MSE SELENOMETHIONINE HETNAM TLA L(+)-TARTARIC ACID FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 TLA C4 H6 O6 FORMUL 3 HOH *178(H2 O) HELIX 1 1 SER A 18 LYS A 30 1 13 HELIX 2 2 PRO A 31 TYR A 33 5 3 HELIX 3 3 THR A 78 GLY A 86 1 9 HELIX 4 4 ASP A 97 LYS A 106 1 10 HELIX 5 5 ASP A 147 LYS A 158 1 12 HELIX 6 6 ASP A 172 LYS A 183 1 12 SHEET 1 A 6 MSE A 1 ALA A 4 0 SHEET 2 A 6 GLY A 8 ALA A 16 -1 O ALA A 10 N LEU A 2 SHEET 3 A 6 LEU A 44 ARG A 50 -1 O LYS A 48 N GLU A 13 SHEET 4 A 6 GLU A 55 VAL A 61 -1 O THR A 60 N ARG A 45 SHEET 5 A 6 VAL A 64 GLU A 69 -1 O LEU A 67 N ILE A 59 SHEET 6 A 6 ILE A 75 PRO A 77 -1 O TYR A 76 N PHE A 68 SHEET 1 B 6 LEU A 110 MSE A 111 0 SHEET 2 B 6 ARG A 162 ARG A 169 -1 O ALA A 163 N LEU A 110 SHEET 3 B 6 THR A 137 ALA A 144 -1 N VAL A 141 O HIS A 168 SHEET 4 B 6 VAL A 127 TYR A 132 -1 N ALA A 130 O VAL A 139 SHEET 5 B 6 GLY A 92 VAL A 96 1 N VAL A 96 O LEU A 131 SHEET 6 B 6 VAL A 115 GLY A 120 -1 O VAL A 116 N LEU A 95 LINK C HIS A 0 N MSE A 1 1555 1555 1.33 LINK C MSE A 1 N LEU A 2 1555 1555 1.33 LINK C LEU A 110 N MSE A 111 1555 1555 1.34 LINK C MSE A 111 N ILE A 112 1555 1555 1.34 LINK C VAL A 139 N MSE A 140 1555 1555 1.32 LINK C MSE A 140 N VAL A 141 1555 1555 1.35 SITE 1 AC1 9 ASP A 97 PRO A 113 VAL A 116 LYS A 158 SITE 2 AC1 9 HOH A2030 HOH A2039 HOH A2065 HOH A2157 SITE 3 AC1 9 HOH A2176 CRYST1 39.271 49.139 53.491 90.00 103.21 90.00 P 1 21 1 2 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 0.025464 0.000000 0.005978 0.00000 SCALE2 0.000000 0.020350 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019203 0.00000