HEADER STRUCTURAL GENOMICS, UNKNOWN FUNCTION 11-FEB-04 1SC0 TITLE X-RAY STRUCTURE OF YB61_HAEIN NORTHEAST STRUCTURAL GENOMICS TITLE 2 CONSORTIUM TARGET IR63 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL PROTEIN HI1161; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HAEMOPHILUS INFLUENZAE; SOURCE 3 ORGANISM_TAXID: 727; SOURCE 4 GENE: HI1161; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PET21D; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PIR63-21-1 KEYWDS STRUCTURAL GENOMICS, UNKNOWN FUNCTION, PSI-2, PROTEIN KEYWDS 2 STRUCTURE INITIATIVE, NORTHEAST STRUCTURAL GENOMICS KEYWDS 3 CONSORTIUM, NESG EXPDTA X-RAY DIFFRACTION AUTHOR A.P.KUZIN,I.LEE,Y.CHIANG,T.B.ACTON,G.T.MONTELIONE,J.F.HUNT, AUTHOR 2 L.TONG,NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 4 31-MAR-10 1SC0 1 AUTHOR KEYWDS REVDAT 3 03-NOV-09 1SC0 1 SPRSDE REVDAT 2 24-FEB-09 1SC0 1 VERSN REVDAT 1 30-MAR-04 1SC0 0 SPRSDE 03-NOV-09 1SC0 1O0I JRNL AUTH A.P.KUZIN,I.LEE,Y.CHIANG,T.B.ACTON,G.T.MONTELIONE, JRNL AUTH 2 J.F.HUNT,L.TONG JRNL TITL X-RAY STRUCTURE OF YB61_HAEIN NORTHEAST STRUCTURAL JRNL TITL 2 GENOMICS CONSORTIUM TARGET IR63. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.70 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 191248.370 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 82.2 REMARK 3 NUMBER OF REFLECTIONS : 53748 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) : 0.203 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 2640 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 52.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 5452 REMARK 3 BIN R VALUE (WORKING SET) : 0.2530 REMARK 3 BIN FREE R VALUE : 0.2680 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 279 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.016 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2092 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 243 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 13.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.95000 REMARK 3 B22 (A**2) : -1.32000 REMARK 3 B33 (A**2) : -2.62000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.95000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.20 REMARK 3 ESD FROM SIGMAA (A) : 0.16 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) : 0.22 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.14 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.20 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.67 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 : 0.36 REMARK 3 BSOL : 41.19 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 1SC0 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-MAR-04. REMARK 100 THE RCSB ID CODE IS RCSB021588. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-FEB-03 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 : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65061 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 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 (%) : NULL REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.10200 REMARK 200 R SYM (I) : 0.10200 REMARK 200 FOR THE DATA SET : 15.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.26100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD 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 (%): 51.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 200 MM POTASSIUM SODIUM TARTRATE REMARK 280 TETRAHYDRATE, 18% PEG 3350, PH 7.5, VAPOR DIFFUSION, HANGING REMARK 280 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 49.75000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.45000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 49.75000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 30.45000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B 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 MSE B 1 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 GLU B 75 -162.84 -77.46 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1O0I RELATED DB: PDB REMARK 900 THE SAME PROTEIN MODEL WITH POOR GEOMETRY. REMARK 900 RELATED ID: IR63 RELATED DB: TARGETDB DBREF 1SC0 A 1 138 UNP P45083 Y1161_HAEIN 1 138 DBREF 1SC0 B 1 138 UNP P45083 Y1161_HAEIN 1 138 SEQADV 1SC0 MSE A 1 UNP P45083 MET 1 MODIFIED RESIDUE SEQADV 1SC0 MSE A 40 UNP P45083 MET 40 MODIFIED RESIDUE SEQADV 1SC0 MSE A 47 UNP P45083 MET 47 MODIFIED RESIDUE SEQADV 1SC0 MSE B 1 UNP P45083 MET 1 MODIFIED RESIDUE SEQADV 1SC0 MSE B 40 UNP P45083 MET 40 MODIFIED RESIDUE SEQADV 1SC0 MSE B 47 UNP P45083 MET 47 MODIFIED RESIDUE SEQRES 1 A 138 MSE LEU TRP LYS LYS THR PHE THR LEU GLU ASN LEU ASN SEQRES 2 A 138 GLN LEU CYS SER ASN SER ALA VAL SER HIS LEU GLY ILE SEQRES 3 A 138 GLU ILE SER ALA PHE GLY GLU ASP TRP ILE GLU ALA THR SEQRES 4 A 138 MSE PRO VAL ASP HIS ARG THR MSE GLN PRO PHE GLY VAL SEQRES 5 A 138 LEU HIS GLY GLY VAL SER VAL ALA LEU ALA GLU THR ILE SEQRES 6 A 138 GLY SER LEU ALA GLY SER LEU CYS LEU GLU GLU GLY LYS SEQRES 7 A 138 THR VAL VAL GLY LEU ASP ILE ASN ALA ASN HIS LEU ARG SEQRES 8 A 138 PRO VAL ARG SER GLY LYS VAL THR ALA ARG ALA THR PRO SEQRES 9 A 138 ILE ASN LEU GLY ARG ASN ILE GLN VAL TRP GLN ILE ASP SEQRES 10 A 138 ILE ARG THR GLU GLU ASN LYS LEU CYS CYS VAL SER ARG SEQRES 11 A 138 LEU THR LEU SER VAL ILE ASN LEU SEQRES 1 B 138 MSE LEU TRP LYS LYS THR PHE THR LEU GLU ASN LEU ASN SEQRES 2 B 138 GLN LEU CYS SER ASN SER ALA VAL SER HIS LEU GLY ILE SEQRES 3 B 138 GLU ILE SER ALA PHE GLY GLU ASP TRP ILE GLU ALA THR SEQRES 4 B 138 MSE PRO VAL ASP HIS ARG THR MSE GLN PRO PHE GLY VAL SEQRES 5 B 138 LEU HIS GLY GLY VAL SER VAL ALA LEU ALA GLU THR ILE SEQRES 6 B 138 GLY SER LEU ALA GLY SER LEU CYS LEU GLU GLU GLY LYS SEQRES 7 B 138 THR VAL VAL GLY LEU ASP ILE ASN ALA ASN HIS LEU ARG SEQRES 8 B 138 PRO VAL ARG SER GLY LYS VAL THR ALA ARG ALA THR PRO SEQRES 9 B 138 ILE ASN LEU GLY ARG ASN ILE GLN VAL TRP GLN ILE ASP SEQRES 10 B 138 ILE ARG THR GLU GLU ASN LYS LEU CYS CYS VAL SER ARG SEQRES 11 B 138 LEU THR LEU SER VAL ILE ASN LEU MODRES 1SC0 MSE A 40 MET SELENOMETHIONINE MODRES 1SC0 MSE A 47 MET SELENOMETHIONINE MODRES 1SC0 MSE B 40 MET SELENOMETHIONINE MODRES 1SC0 MSE B 47 MET SELENOMETHIONINE HET MSE A 40 8 HET MSE A 47 8 HET MSE B 40 8 HET MSE B 47 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 4(C5 H11 N O2 SE) FORMUL 3 HOH *243(H2 O) HELIX 1 1 THR A 8 CYS A 16 1 9 HELIX 2 2 SER A 19 LEU A 24 1 6 HELIX 3 3 HIS A 54 CYS A 73 1 20 HELIX 4 4 THR B 8 CYS B 16 1 9 HELIX 5 5 SER B 19 LEU B 24 1 6 HELIX 6 6 HIS B 54 LEU B 72 1 19 SHEET 1 A 6 GLU A 27 PHE A 31 0 SHEET 2 A 6 ILE A 36 PRO A 41 -1 O GLU A 37 N ALA A 30 SHEET 3 A 6 LYS A 97 LEU A 107 -1 O ALA A 100 N ALA A 38 SHEET 4 A 6 ILE A 111 ARG A 119 -1 O ASP A 117 N ARG A 101 SHEET 5 A 6 LEU A 125 ILE A 136 -1 O LEU A 133 N GLN A 112 SHEET 6 A 6 THR A 79 HIS A 89 -1 N LEU A 83 O THR A 132 SHEET 1 B 6 GLU B 27 PHE B 31 0 SHEET 2 B 6 ILE B 36 PRO B 41 -1 O GLU B 37 N ALA B 30 SHEET 3 B 6 LYS B 97 LEU B 107 -1 O ALA B 100 N ALA B 38 SHEET 4 B 6 ILE B 111 ARG B 119 -1 O GLN B 115 N THR B 103 SHEET 5 B 6 LEU B 125 ILE B 136 -1 O LEU B 133 N GLN B 112 SHEET 6 B 6 THR B 79 HIS B 89 -1 N LEU B 83 O THR B 132 LINK C THR A 39 N MSE A 40 1555 1555 1.32 LINK C MSE A 40 N PRO A 41 1555 1555 1.34 LINK C THR A 46 N MSE A 47 1555 1555 1.33 LINK C MSE A 47 N GLN A 48 1555 1555 1.33 LINK C THR B 39 N MSE B 40 1555 1555 1.32 LINK C MSE B 40 N PRO B 41 1555 1555 1.34 LINK C THR B 46 N MSE B 47 1555 1555 1.33 LINK C MSE B 47 N GLN B 48 1555 1555 1.33 CRYST1 99.500 60.900 70.960 90.00 134.50 90.00 C 1 2 1 8 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 0.010050 0.000000 0.009876 0.00000 SCALE2 0.000000 0.016420 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019758 0.00000