10 20 30 40 50 60 70 80 1VAJ - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 17-FEB-04 1VAJ
TITLE CRYSTAL STRUCTURE OF UNCHARACTERIZED PROTEIN PH0010 FROM TITLE 2 PYROCOCCUS HORIKOSHII
COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN PH0010; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 53953; SOURCE 4 GENE: PH0010; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-RIL SOURCE 8 (STRATAGENE); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET-26B(+)
KEYWDS ALPHA + BETA FOLD, STRUCTURAL GENOMICS, UNKNOWN FUNCTION
EXPDTA X-RAY DIFFRACTION
AUTHOR Y.TAJIKA,N.SAKAI,T.TAMURA,M.YAO,N.WATANABE,I.TANAKA
REVDAT 2 24-FEB-09 1VAJ 1 VERSN REVDAT 1 25-JAN-05 1VAJ 0
JRNL AUTH Y.TAJIKA,N.SAKAI,T.TAMURA,M.YAO,N.WATANABE,I.TANAKA JRNL TITL CRYSTAL STRUCTURE OF PH0010 FROM PYROCOCCUS JRNL TITL 2 HORIKOSHII, WHICH IS HIGHLY HOMOLOGOUS TO HUMAN JRNL TITL 3 AMMECR 1C-TERMINAL REGION JRNL REF PROTEINS V. 58 501 2005 JRNL REFN ISSN 0887-3585 JRNL PMID 15558565 JRNL DOI 10.1002/PROT.20315
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.82 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 19319 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) : 0.202 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.600 REMARK 3 FREE R VALUE TEST SET COUNT : 1960 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 10 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.82 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.88 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 66.73 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1236 REMARK 3 BIN R VALUE (WORKING SET) : 0.3020 REMARK 3 BIN FREE R VALUE : 0.3140 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.60 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 132 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1646 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 165 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.24 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.33000 REMARK 3 B22 (A**2) : -4.21000 REMARK 3 B33 (A**2) : 5.54000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.56000 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) : NULL 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) : 0.26 REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.41 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.54 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.88 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.109 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.541 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 2.167 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.963 ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL 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 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4 REMARK 4 1VAJ COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 19-FEB-04. REMARK 100 THE RCSB ID CODE IS RCSB006408.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-DEC-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9742, 0.9785, 0.9600 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19449 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.820 REMARK 200 RESOLUTION RANGE LOW (A) : 38.630 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.07100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.82 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.33600 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 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, MAGNESIUM CHLORIDE, PH REMARK 280 7.9, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 30.33600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.61150 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 30.33600 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.61150 REMARK 290 SMTRY3 4 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 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 MSE A 1 REMARK 465 VAL A 2 REMARK 465 VAL A 206 REMARK 465 LEU A 207 REMARK 465 GLU A 208 REMARK 465 HIS A 209 REMARK 465 HIS A 210 REMARK 465 HIS A 211 REMARK 465 HIS A 212 REMARK 465 HIS A 213 REMARK 465 HIS A 214
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 GLY A 134 N - CA - C ANGL. DEV. = -15.7 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 CYS A 65 111.64 -160.19 REMARK 500 ARG A 132 -52.00 -136.59 REMARK 500 REMARK 500 REMARK: NULL
DBREF 1VAJ A 1 206 UNP O57770 Y010_PYRHO 1 206
SEQADV 1VAJ MSE A 1 UNP O57770 MET 1 MODIFIED RESIDUE SEQADV 1VAJ MSE A 45 UNP O57770 MET 45 MODIFIED RESIDUE SEQADV 1VAJ MSE A 101 UNP O57770 MET 101 MODIFIED RESIDUE SEQADV 1VAJ LEU A 207 UNP O57770 EXPRESSION TAG SEQADV 1VAJ GLU A 208 UNP O57770 EXPRESSION TAG SEQADV 1VAJ HIS A 209 UNP O57770 EXPRESSION TAG SEQADV 1VAJ HIS A 210 UNP O57770 EXPRESSION TAG SEQADV 1VAJ HIS A 211 UNP O57770 EXPRESSION TAG SEQADV 1VAJ HIS A 212 UNP O57770 EXPRESSION TAG SEQADV 1VAJ HIS A 213 UNP O57770 EXPRESSION TAG SEQADV 1VAJ HIS A 214 UNP O57770 EXPRESSION TAG
SEQRES 1 A 214 MSE VAL PHE LYS ILE LYS ASP GLU TRP GLY GLU PHE LEU SEQRES 2 A 214 VAL ARG LEU ALA ARG ARG ALA ILE GLU GLU TYR LEU LYS SEQRES 3 A 214 THR GLY LYS GLU ILE GLU PRO PRO LYS ASP THR PRO PRO SEQRES 4 A 214 GLU LEU TRP GLU LYS MSE GLY VAL PHE VAL THR LEU ASN SEQRES 5 A 214 ARG TYR ASN VAL PRO PRO GLN THR ALA LEU ARG GLY CYS SEQRES 6 A 214 ILE GLY PHE PRO THR PRO ILE TYR PRO LEU VAL GLU ALA SEQRES 7 A 214 THR ILE LYS ALA ALA ILE TYR SER ALA VAL ASP ASP PRO SEQRES 8 A 214 ARG PHE PRO PRO VAL LYS LEU GLU GLU MSE ASP ASN LEU SEQRES 9 A 214 VAL VAL GLU VAL SER VAL LEU THR PRO PRO GLU LEU ILE SEQRES 10 A 214 GLU GLY PRO PRO GLU GLU ARG PRO ARG LYS ILE LYS VAL SEQRES 11 A 214 GLY ARG ASP GLY LEU ILE VAL GLU LYS GLY ILE TYR SER SEQRES 12 A 214 GLY LEU LEU LEU PRO GLN VAL PRO VAL GLU TRP GLY TRP SEQRES 13 A 214 ASP GLU GLU GLU PHE LEU ALA GLU THR CYS TRP LYS ALA SEQRES 14 A 214 GLY LEU PRO PRO ASP CYS TRP LEU ASP GLU ASP THR LYS SEQRES 15 A 214 VAL TYR LYS PHE THR ALA GLU ILE PHE GLU GLU GLU TYR SEQRES 16 A 214 PRO ARG GLY PRO ILE LYS ARG LYS PRO LEU VAL LEU GLU SEQRES 17 A 214 HIS HIS HIS HIS HIS HIS
MODRES 1VAJ MSE A 45 MET SELENOMETHIONINE MODRES 1VAJ MSE A 101 MET SELENOMETHIONINE
HET MSE A 45 8 HET MSE A 101 8
HETNAM MSE SELENOMETHIONINE
FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 HOH *165(H2 O)
HELIX 1 1 LYS A 6 GLY A 28 1 23 HELIX 2 2 PRO A 38 GLU A 43 5 6 HELIX 3 3 PRO A 57 THR A 60 5 4 HELIX 4 4 PRO A 74 ASP A 89 1 16 HELIX 5 5 LYS A 97 ASP A 102 5 6 HELIX 6 6 PRO A 120 ILE A 128 5 9 HELIX 7 7 PRO A 148 GLY A 155 1 8 HELIX 8 8 ASP A 157 ALA A 169 1 13 HELIX 9 9 ASP A 174 ASP A 178 5 5
SHEET 1 A 5 LEU A 62 PHE A 68 0 SHEET 2 A 5 GLY A 46 ARG A 53 -1 N LEU A 51 O ARG A 63 SHEET 3 A 5 LEU A 104 LEU A 111 -1 O GLU A 107 N THR A 50 SHEET 4 A 5 ALA A 188 GLU A 193 -1 O PHE A 191 N VAL A 108 SHEET 5 A 5 ILE A 200 ARG A 202 -1 O LYS A 201 N GLU A 192 SHEET 1 B 4 GLU A 115 LEU A 116 0 SHEET 2 B 4 LYS A 182 PHE A 186 -1 O LYS A 185 N GLU A 115 SHEET 3 B 4 GLY A 134 LYS A 139 -1 N GLU A 138 O LYS A 182 SHEET 4 B 4 TYR A 142 LEU A 146 -1 O GLY A 144 N VAL A 137
LINK C LYS A 44 N MSE A 45 1555 1555 1.33 LINK C MSE A 45 N GLY A 46 1555 1555 1.33 LINK C GLU A 100 N MSE A 101 1555 1555 1.33 LINK C MSE A 101 N ASP A 102 1555 1555 1.33
CRYST1 60.672 67.223 58.728 90.00 104.27 90.00 C 1 2 1 4
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 0.016482 0.000000 0.004192 0.00000
SCALE2 0.000000 0.014876 0.000000 0.00000
SCALE3 0.000000 0.000000 0.017570 0.00000