HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 23-JUN-04 1TTZ TITLE X-RAY STRUCTURE OF NORTHEAST STRUCTURAL GENOMICS TARGET PROTEIN XCR50 TITLE 2 FROM X. CAMPESTRIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CONSERVED HYPOTHETICAL PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: XANTHOMONAS CAMPESTRIS; SOURCE 3 ORGANISM_TAXID: 339; SOURCE 4 STRAIN: ATCC33913; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS STRUCTURAL GENOMICS, UNKNOWN FUNCTION, PSI, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG EXPDTA X-RAY DIFFRACTION AUTHOR A.P.KUZIN,S.M.VOROBIEV,I.LEE,T.B.ACTON,C.K.HO,B.COOPER,L.-C.MA, AUTHOR 2 R.XIAO,G.MONTELIONE,L.TONG,J.F.HUNT,NORTHEAST STRUCTURAL GENOMICS AUTHOR 3 CONSORTIUM (NESG) REVDAT 5 04-APR-18 1TTZ 1 REMARK REVDAT 4 24-FEB-09 1TTZ 1 VERSN REVDAT 3 24-OCT-06 1TTZ 1 KEYWDS AUTHOR REMARK MASTER REVDAT 2 27-JUL-04 1TTZ 1 AUTHOR REVDAT 1 13-JUL-04 1TTZ 0 JRNL AUTH A.P.KUZIN,S.M.VOROBIEV,I.LEE,W.EDSTROM,T.B.ACTON,C.K.HO, JRNL AUTH 2 B.COOPER,L.-C.MA,R.XIAO,G.MONTELIONE,L.TONG,J.F.HUNT JRNL TITL X-RAY STRUCTURE OF NORTHEAST STRUCTURAL GENOMICS TARGET JRNL TITL 2 PROTEIN XCR50 FROM X. CAMPESTRIS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.11 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) : 2.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 202406.730 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.9 REMARK 3 NUMBER OF REFLECTIONS : 8998 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) : 0.189 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 482 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.23 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 78.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1155 REMARK 3 BIN R VALUE (WORKING SET) : 0.2060 REMARK 3 BIN FREE R VALUE : 0.2210 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 7.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 93 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 : 589 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 109 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.47300 REMARK 3 B22 (A**2) : 0.47300 REMARK 3 B33 (A**2) : -0.94700 REMARK 3 B12 (A**2) : -1.14600 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) : 0.17 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) : 0.28 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.12 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.820 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) : 1.541 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.482 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.307 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.167 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.35 REMARK 3 BSOL : 48.34 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 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1TTZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUN-04. REMARK 100 THE DEPOSITION ID IS D_1000022899. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUN-04; 17-MAY-04 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; N REMARK 200 RADIATION SOURCE : NSLS; ROTATING ANODE REMARK 200 BEAMLINE : X4A; NULL REMARK 200 X-RAY GENERATOR MODEL : NULL; OTHER REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.97896; 1.5418 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4; RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12147 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 79.8 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.04500 REMARK 200 FOR THE DATA SET : 23.9800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86 REMARK 200 COMPLETENESS FOR SHELL (%) : 31.6 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.21100 REMARK 200 FOR SHELL : 3.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS 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 (%): 43.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES, 0.1M NACL, 1.6M (NH4)2SO4, REMARK 280 PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 26.02867 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 13.01433 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 19.52150 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 6.50717 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 32.53583 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 HIS A 77 REMARK 465 ALA A 78 REMARK 465 LEU A 79 REMARK 465 GLU A 80 REMARK 465 HIS A 81 REMARK 465 HIS A 82 REMARK 465 HIS A 83 REMARK 465 HIS A 84 REMARK 465 HIS A 85 REMARK 465 HIS A 86 REMARK 465 HIS A 87 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: XCR50 RELATED DB: TARGETDB DBREF 1TTZ A 1 78 UNP Q8P6W3 Q8P6W3_XANCP 1 78 SEQADV 1TTZ MSE A 1 UNP Q8P6W3 MET 1 MODIFIED RESIDUE SEQADV 1TTZ MSE A 55 UNP Q8P6W3 MET 55 MODIFIED RESIDUE SEQADV 1TTZ LEU A 79 UNP Q8P6W3 CLONING ARTIFACT SEQADV 1TTZ GLU A 80 UNP Q8P6W3 CLONING ARTIFACT SEQADV 1TTZ HIS A 81 UNP Q8P6W3 EXPRESSION TAG SEQADV 1TTZ HIS A 82 UNP Q8P6W3 EXPRESSION TAG SEQADV 1TTZ HIS A 83 UNP Q8P6W3 EXPRESSION TAG SEQADV 1TTZ HIS A 84 UNP Q8P6W3 EXPRESSION TAG SEQADV 1TTZ HIS A 85 UNP Q8P6W3 EXPRESSION TAG SEQADV 1TTZ HIS A 86 UNP Q8P6W3 EXPRESSION TAG SEQADV 1TTZ HIS A 87 UNP Q8P6W3 EXPRESSION TAG SEQRES 1 A 87 MSE ALA LEU THR LEU TYR GLN ARG ASP ASP CYS HIS LEU SEQRES 2 A 87 CYS ASP GLN ALA VAL GLU ALA LEU ALA GLN ALA ARG ALA SEQRES 3 A 87 GLY ALA PHE PHE SER VAL PHE ILE ASP ASP ASP ALA ALA SEQRES 4 A 87 LEU GLU SER ALA TYR GLY LEU ARG VAL PRO VAL LEU ARG SEQRES 5 A 87 ASP PRO MSE GLY ARG GLU LEU ASP TRP PRO PHE ASP ALA SEQRES 6 A 87 PRO ARG LEU ARG ALA TRP LEU ASP ALA ALA PRO HIS ALA SEQRES 7 A 87 LEU GLU HIS HIS HIS HIS HIS HIS HIS MODRES 1TTZ MSE A 55 MET SELENOMETHIONINE HET MSE A 55 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE C5 H11 N O2 SE FORMUL 2 HOH *109(H2 O) HELIX 1 1 CYS A 11 ALA A 24 1 14 HELIX 2 2 ASP A 37 GLY A 45 1 9 HELIX 3 3 ASP A 64 ALA A 74 1 11 SHEET 1 A 4 PHE A 29 PHE A 33 0 SHEET 2 A 4 LEU A 3 GLN A 7 1 N LEU A 3 O PHE A 30 SHEET 3 A 4 VAL A 50 ARG A 52 -1 O VAL A 50 N TYR A 6 SHEET 4 A 4 GLU A 58 ASP A 60 -1 O LEU A 59 N LEU A 51 LINK C PRO A 54 N MSE A 55 1555 1555 1.33 LINK C MSE A 55 N GLY A 56 1555 1555 1.33 CISPEP 1 VAL A 48 PRO A 49 0 0.01 CISPEP 2 TRP A 61 PRO A 62 0 0.03 CISPEP 3 ALA A 75 PRO A 76 0 -0.18 CRYST1 61.690 61.690 39.043 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 0.016210 0.009359 0.000000 0.00000 SCALE2 0.000000 0.018718 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025613 0.00000