HEADER TRANSCRIPTION 24-DEC-04 1YDL TITLE CRYSTAL STRUCTURE OF THE HUMAN TFIIH, NORTHEAST STRUCTURAL GENOMICS TITLE 2 TARGET HR2045. COMPND MOL_ID: 1; COMPND 2 MOLECULE: GENERAL TRANSCRIPTION FACTOR IIH, POLYPEPTIDE 5; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TFIIH; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: C6ORF175; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)+MAGIC; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PET21; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: BL21 KEYWDS ALPHA-BETA PROTEIN, STRUCTURAL GENOMICS, PSI, PROTEIN STRUCTURE KEYWDS 2 INITIATIVE, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, KEYWDS 3 TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR F.FOROUHAR,W.EDSTROM,R.XIAO,T.B.ACTON,G.T.MONTELIONE,L.TONG,J.F.HUNT, AUTHOR 2 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 4 20-OCT-21 1YDL 1 SEQADV LINK REVDAT 3 11-OCT-17 1YDL 1 REMARK REVDAT 2 24-FEB-09 1YDL 1 VERSN REVDAT 1 08-FEB-05 1YDL 0 JRNL AUTH F.FOROUHAR,W.EDSTROM,R.XIAO,T.B.ACTON,G.T.MONTELIONE,L.TONG, JRNL AUTH 2 J.F.HUNT JRNL TITL CRYSTAL STRUCTURE OF THE HUMAN TFIIH, NORTHEAST STRUCTURAL JRNL TITL 2 GENOMICS TARGET HR2045. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.30 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.25 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 444155.030 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 88.4 REMARK 3 NUMBER OF REFLECTIONS : 5916 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) : 0.236 REMARK 3 FREE R VALUE : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.700 REMARK 3 FREE R VALUE TEST SET COUNT : 634 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.012 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.44 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 70.50 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 715 REMARK 3 BIN R VALUE (WORKING SET) : 0.2110 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 8.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 70 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.034 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 565 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 35 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -12.97000 REMARK 3 B22 (A**2) : -7.05000 REMARK 3 B33 (A**2) : 20.02000 REMARK 3 B12 (A**2) : 0.00000 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) : 0.28 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) : 0.39 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.600 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : OVERALL 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 : 51.80 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 1YDL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1000031407. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-NOV-04 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 : SI 111 CHANNEL REMARK 200 OPTICS : MIRRORS 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 : 6602 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 29.250 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.09000 REMARK 200 R SYM (I) : 0.08300 REMARK 200 FOR THE DATA SET : 22.2300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.5 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : 0.30200 REMARK 200 R SYM FOR SHELL (I) : 0.31600 REMARK 200 FOR SHELL : 5.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SNB, SOLVE, RESOLVE 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): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22% PEG 3350, 100 MM MGCL2, AND 10 MM REMARK 280 DTT, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 20.70600 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.96100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.70600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.96100 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 300 REMARK: POSSIBLY DIMER 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 MET A -7 REMARK 465 GLY A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 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 HIS A 2 -60.50 -106.35 REMARK 500 ILE A 38 -78.66 -128.77 REMARK 500 GLU A 48 39.63 -93.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: HR2045 RELATED DB: TARGETDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE FIRST FIVE N-TERMINAL RESIDUES OF THE NATIVE PROTEIN, REMARK 999 1-MVNVL-5, WERE SUBSTITUTED BY GTR AND AN N-TAG REMARK 999 (MGHHHHHHSH). DBREF 1YDL A -7 71 UNP Q6ZYL4 TF2H5_HUMAN 1 71 SEQADV 1YDL GLY A -6 UNP Q6ZYL4 CLONING ARTIFACT SEQADV 1YDL HIS A -5 UNP Q6ZYL4 CLONING ARTIFACT SEQADV 1YDL HIS A -4 UNP Q6ZYL4 EXPRESSION TAG SEQADV 1YDL HIS A -3 UNP Q6ZYL4 EXPRESSION TAG SEQADV 1YDL HIS A -2 UNP Q6ZYL4 EXPRESSION TAG SEQADV 1YDL HIS A -1 UNP Q6ZYL4 EXPRESSION TAG SEQADV 1YDL HIS A 0 UNP Q6ZYL4 EXPRESSION TAG SEQADV 1YDL SER A 1 UNP Q6ZYL4 MET SEE REMARK 999 SEQADV 1YDL HIS A 2 UNP Q6ZYL4 VAL 2 SEE REMARK 999 SEQADV 1YDL GLY A 3 UNP Q6ZYL4 ASN 3 SEE REMARK 999 SEQADV 1YDL THR A 4 UNP Q6ZYL4 VAL 4 SEE REMARK 999 SEQADV 1YDL ARG A 5 UNP Q6ZYL4 LEU 5 SEE REMARK 999 SEQADV 1YDL MSE A 8 UNP Q6ZYL4 VAL 8 ENGINEERED MUTATION SEQADV 1YDL MSE A 16 UNP Q6ZYL4 MET 16 MODIFIED RESIDUE SEQADV 1YDL MSE A 61 UNP Q6ZYL4 MET 61 MODIFIED RESIDUE SEQRES 1 A 79 MET GLY HIS HIS HIS HIS HIS HIS SER HIS GLY THR ARG SEQRES 2 A 79 LYS GLY MSE LEU ILE GLU CYS ASP PRO ALA MSE LYS GLN SEQRES 3 A 79 PHE LEU LEU TYR LEU ASP GLU SER ASN ALA LEU GLY LYS SEQRES 4 A 79 LYS PHE ILE ILE GLN ASP ILE ASP ASP THR HIS VAL PHE SEQRES 5 A 79 VAL ILE ALA GLU LEU VAL ASN VAL LEU GLN GLU ARG VAL SEQRES 6 A 79 GLY GLU LEU MSE ASP GLN ASN ALA PHE SER LEU THR GLN SEQRES 7 A 79 LYS MODRES 1YDL MSE A 8 MET SELENOMETHIONINE MODRES 1YDL MSE A 16 MET SELENOMETHIONINE MODRES 1YDL MSE A 61 MET SELENOMETHIONINE HET MSE A 8 8 HET MSE A 16 8 HET MSE A 61 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 HOH *35(H2 O) HELIX 1 1 ASP A 13 SER A 26 1 14 HELIX 2 2 GLU A 48 LEU A 60 1 13 SHEET 1 A 3 MSE A 8 GLU A 11 0 SHEET 2 A 3 HIS A 42 VAL A 45 -1 O VAL A 45 N MSE A 8 SHEET 3 A 3 ILE A 34 ASP A 37 -1 N GLN A 36 O PHE A 44 LINK C GLY A 7 N MSE A 8 1555 1555 1.32 LINK C MSE A 8 N LEU A 9 1555 1555 1.33 LINK C ALA A 15 N MSE A 16 1555 1555 1.33 LINK C MSE A 16 N LYS A 17 1555 1555 1.33 LINK C LEU A 60 N MSE A 61 1555 1555 1.33 LINK C MSE A 61 N ASP A 62 1555 1555 1.33 CRYST1 41.412 53.922 34.818 90.00 90.00 90.00 P 21 21 2 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 0.024148 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018545 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028721 0.00000