HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 27-JUN-05 2CX0 TITLE CRYSTAL STRUCTURE OF A PUA DOMAIN (APE0525) FROM THE AEROPYRUM PERNIX TITLE 2 K1 (SULFATE 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 23-OCT-24 2CX0 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 2CX0 1 VERSN REVDAT 2 24-FEB-09 2CX0 1 VERSN REVDAT 1 27-DEC-05 2CX0 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 (SULFATE 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.02 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 291511.030 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.6 REMARK 3 NUMBER OF REFLECTIONS : 33102 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) : 0.173 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1613 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.005 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) : 4414 REMARK 3 BIN R VALUE (WORKING SET) : 0.2510 REMARK 3 BIN FREE R VALUE : 0.2490 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 224 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.017 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 : 5 REMARK 3 SOLVENT ATOMS : 158 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 12.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.45000 REMARK 3 B22 (A**2) : -1.63000 REMARK 3 B33 (A**2) : 1.18000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.73000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.17 REMARK 3 ESD FROM SIGMAA (A) : 0.21 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) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.021 REMARK 3 BOND ANGLES (DEGREES) : 1.800 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.140 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 : 0.42 REMARK 3 BSOL : 73.99 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: THE FILE CONTAINS FRIEDEL PAIRS REMARK 4 REMARK 4 2CX0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 30-JUN-05. REMARK 100 THE DEPOSITION ID IS D_1000024721. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-APR-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.96300, 0.97916, 0.97948 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU JUPITER 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 33103 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: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE, RESOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: THE FILE CONTAINS FRIEDEL PAIRS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.40 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, TRIS, PEG3350, REMARK 280 SODIUM CHLORIDE, PH 7.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 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 24.06750 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: UNKOWN. PROBABLY MONOMER FROM 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 IN SAME ASYMMETRIC UNIT 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 O HOH A 1124 O HOH A 1125 1.89 REMARK 500 O HOH A 1057 O HOH A 1108 2.00 REMARK 500 O HOH A 1087 O HOH A 1112 2.02 REMARK 500 O HOH A 1054 O HOH A 1105 2.03 REMARK 500 NE1 TRP A 70 O HOH A 1139 2.03 REMARK 500 O HOH A 1088 O HOH A 1111 2.07 REMARK 500 O HOH A 1100 O HOH A 1152 2.18 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 -65.80 78.61 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 SO4 A 1001 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CX1 RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH TARTARIC ACID REMARK 900 RELATED ID: APE001000525.1 RELATED DB: TARGETDB DBREF 2CX0 A 1 186 UNP Q9YEQ6 Q9YEQ6_AERPE 1 186 SEQADV 2CX0 HIS A 0 UNP Q9YEQ6 EXPRESSION TAG SEQADV 2CX0 MSE A 1 UNP Q9YEQ6 MET 1 MODIFIED RESIDUE SEQADV 2CX0 MSE A 111 UNP Q9YEQ6 MET 111 MODIFIED RESIDUE SEQADV 2CX0 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 2CX0 MSE A 1 MET SELENOMETHIONINE MODRES 2CX0 MSE A 111 MET SELENOMETHIONINE MODRES 2CX0 MSE A 140 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 111 8 HET MSE A 140 8 HET SO4 A1001 5 HETNAM MSE SELENOMETHIONINE HETNAM SO4 SULFATE ION FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 SO4 O4 S 2- FORMUL 3 HOH *158(H2 O) HELIX 1 1 SER A 18 LYS A 30 1 13 HELIX 2 2 THR A 78 GLY A 86 1 9 HELIX 3 3 ASP A 97 LYS A 106 1 10 HELIX 4 4 ASP A 147 LYS A 158 1 12 HELIX 5 5 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 ILE A 58 N VAL A 47 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 94 O LEU A 131 SHEET 6 B 6 VAL A 115 GLY A 120 -1 O GLU A 119 N VAL A 93 LINK C HIS A 0 N MSE A 1 1555 1555 1.33 LINK C MSE A 1 N LEU A 2 1555 1555 1.32 LINK C LEU A 110 N MSE A 111 1555 1555 1.33 LINK C MSE A 111 N ILE A 112 1555 1555 1.33 LINK C VAL A 139 N MSE A 140 1555 1555 1.33 LINK C MSE A 140 N VAL A 141 1555 1555 1.33 SITE 1 AC1 6 ASP A 97 LYS A 98 HIS A 133 HOH A1081 SITE 2 AC1 6 HOH A1095 HOH A1096 CRYST1 39.331 48.135 53.847 90.00 102.50 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 0.025425 0.000000 0.005638 0.00000 SCALE2 0.000000 0.020775 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019022 0.00000