PDB Short entry for 1I27 HEADER TRANSCRIPTION 07-FEB-01 1I27 TITLE CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF THE RAP74 SUBUNIT OF TITLE 2 HUMAN TRANSCRIPTION FACTOR IIF (TFIIF) COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION FACTOR IIF; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RAP74 SUBUNIT, C-TERMINAL DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: RAP74; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1 KEYWDS GENERAL TRANSCRIPTION FACTOR, RAP74, RAP30, TFIIF, RNA POLYMERASE II, KEYWDS 2 WINGED-HELIX DOMAIN, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR K.KAMADA,J.DE ANGELIS,R.G.ROEDER,S.K.BURLEY REVDAT 4 07-FEB-24 1I27 1 REMARK REVDAT 3 03-FEB-21 1I27 1 AUTHOR JRNL REMARK SEQADV REVDAT 3 2 1 LINK REVDAT 2 24-FEB-09 1I27 1 VERSN REVDAT 1 07-MAR-01 1I27 0 JRNL AUTH K.KAMADA,J.DE ANGELIS,R.G.ROEDER,S.K.BURLEY JRNL TITL CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF THE RAP74 JRNL TITL 2 SUBUNIT OF HUMAN TRANSCRIPTION FACTOR IIF. JRNL REF PROC.NATL.ACAD.SCI.USA V. 98 3115 2001 JRNL REFN ISSN 0027-8424 JRNL PMID 11248041 JRNL DOI 10.1073/PNAS.051631098 REMARK 2 REMARK 2 RESOLUTION. 1.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.127 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.126 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.146 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 2927 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 58608 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.115 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.115 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.134 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 2437 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 48549 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 585 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 151 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : NULL REMARK 3 NUMBER OF RESTRAINTS : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 ANGLE DISTANCES (A) : 0.025 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.317 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.068 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.071 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.010 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH & HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1I27 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-FEB-01. REMARK 100 THE DEPOSITION ID IS D_1000012810. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-00 REMARK 200 TEMPERATURE (KELVIN) : 200.0 REMARK 200 PH : 6.4 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97000 REMARK 200 MONOCHROMATOR : ROSENBAUM-ROCK MONOCHROMATOR REMARK 200 OPTICS : VERTICAL FOCUSING MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : SBC-2 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 58701 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.020 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 (%) : 99.0 REMARK 200 DATA REDUNDANCY : 12.30 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : 0.05900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.54 REMARK 200 R MERGE FOR SHELL (I) : 0.33500 REMARK 200 R SYM FOR SHELL (I) : 0.33500 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: ZINC SULFATE, LITHIUM CHLORIDE, PEG REMARK 280 2000 MME, POLYVINYLPYRROLIDONE 15K, GLUCOSAMINE HYDROCHLORIDE, REMARK 280 PH 6.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 282K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 14.52600 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 24.08050 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.51200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 24.08050 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.52600 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.51200 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 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 GLN A 495 CA - CB - CG ANGL. DEV. = 15.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 999 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 503 OE1 REMARK 620 2 GLU A 503 OE2 54.9 REMARK 620 3 HIS A 512 NE2 86.1 123.9 REMARK 620 4 GLU A 517 O 166.7 119.1 105.9 REMARK 620 5 GLU A 517 OXT 130.3 86.6 93.0 56.0 REMARK 620 6 HOH A1001 O 77.5 102.9 105.9 93.7 148.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 999 DBREF 1I27 A 449 517 UNP P35269 T2FA_HUMAN 449 517 SEQADV 1I27 GLY A 445 UNP P35269 CLONING ARTIFACT SEQADV 1I27 PRO A 446 UNP P35269 CLONING ARTIFACT SEQADV 1I27 LEU A 447 UNP P35269 CLONING ARTIFACT SEQADV 1I27 GLY A 448 UNP P35269 CLONING ARTIFACT SEQRES 1 A 73 GLY PRO LEU GLY SER GLY ASP VAL GLN VAL THR GLU ASP SEQRES 2 A 73 ALA VAL ARG ARG TYR LEU THR ARG LYS PRO MET THR THR SEQRES 3 A 73 LYS ASP LEU LEU LYS LYS PHE GLN THR LYS LYS THR GLY SEQRES 4 A 73 LEU SER SER GLU GLN THR VAL ASN VAL LEU ALA GLN ILE SEQRES 5 A 73 LEU LYS ARG LEU ASN PRO GLU ARG LYS MET ILE ASN ASP SEQRES 6 A 73 LYS MET HIS PHE SER LEU LYS GLU HET ZN A 999 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *151(H2 O) HELIX 1 1 GLY A 445 SER A 449 5 5 HELIX 2 2 THR A 455 LYS A 466 1 12 HELIX 3 3 THR A 469 LYS A 476 1 8 HELIX 4 4 GLN A 478 GLY A 483 1 6 HELIX 5 5 SER A 485 ASN A 501 1 17 SHEET 1 A 2 GLU A 503 ILE A 507 0 SHEET 2 A 2 LYS A 510 SER A 514 -1 O LYS A 510 N ILE A 507 LINK OE1 GLU A 503 ZN ZN A 999 4466 1555 2.61 LINK OE2 GLU A 503 ZN ZN A 999 4466 1555 1.97 LINK NE2 HIS A 512 ZN ZN A 999 1555 1555 2.01 LINK O GLU A 517 ZN ZN A 999 4466 1555 2.09 LINK OXT GLU A 517 ZN ZN A 999 4466 1555 2.43 LINK ZN ZN A 999 O HOH A1001 1555 1555 2.02 SITE 1 AC1 4 GLU A 503 HIS A 512 GLU A 517 HOH A1001 CRYST1 29.052 43.024 48.161 90.00 90.00 90.00 P 21 21 21 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 0.034421 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023243 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020764 0.00000