PDB Short entry for 1J2X HEADER TRANSCRIPTION 15-JAN-03 1J2X TITLE CRYSTAL STRUCTURE OF RAP74 C-TERMINAL DOMAIN COMPLEXED WITH FCP1 C- TITLE 2 TERMINAL PEPTIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION INITIATION FACTOR IIF, ALPHA SUBUNIT; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: C-TERMINAL DOMAIN; COMPND 5 SYNONYM: RAP74 SUBUNIT OF TRANSCRIPTION FACTOR IIF, TFIIF; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: RNA POLYMERASE II CTD PHOSPHATASE; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: C-TERMINAL PEPTIDE; COMPND 11 SYNONYM: TFIIF-ASSOCIATING CTD PHOSPHATASE, FCP1; COMPND 12 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: RAP74; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: UT5600; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: CHEMICAL SYNTHESIS KEYWDS GENERAL TRANSCRIPTION FACTOR, RAP74, RAP30, TFIIF, RNA POLYMERASE II, KEYWDS 2 WINGED-HELIX DOMAIN, FCP1, CTD, PHOSPHATASE, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR K.KAMADA,R.G.ROEDER,S.K.BURLEY REVDAT 5 25-OCT-23 1J2X 1 REMARK REVDAT 4 03-FEB-21 1J2X 1 AUTHOR JRNL REMARK SEQADV REVDAT 4 2 1 LINK REVDAT 3 24-FEB-09 1J2X 1 VERSN REVDAT 2 01-APR-03 1J2X 1 JRNL REVDAT 1 30-JAN-03 1J2X 0 JRNL AUTH K.KAMADA,R.G.ROEDER,S.K.BURLEY JRNL TITL MOLECULAR MECHANISM OF RECRUITMENT OF TFIIF- ASSOCIATING RNA JRNL TITL 2 POLYMERASE C-TERMINAL DOMAIN PHOSPHATASE (FCP1) BY JRNL TITL 3 TRANSCRIPTION FACTOR IIF JRNL REF PROC.NATL.ACAD.SCI.USA V. 100 2296 2003 JRNL REFN ISSN 0027-8424 JRNL PMID 12591941 JRNL DOI 10.1073/PNAS.262798199 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.KAMADA,J.DE ANGELIS,R.G.ROEDER,S.K.BURLEY REMARK 1 TITL CRYSTAL STRUCTURE OF THE C-TERMINAL DOMAIN OF THE RAP74 REMARK 1 TITL 2 SUBUNIT OF HUMAN TRANSCRIPTION FACTOR IIF REMARK 1 REF PROC.NATL.ACAD.SCI.USA V. 98 3115 2001 REMARK 1 REFN ISSN 0027-8424 REMARK 1 DOI 10.1073/PNAS.051631098 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 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) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 5603 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 : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.200 REMARK 3 FREE R VALUE TEST SET COUNT : 403 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.013 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.09 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 644 REMARK 3 BIN R VALUE (WORKING SET) : 0.2050 REMARK 3 BIN FREE R VALUE : 0.2030 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 6.40 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 46 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.030 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 707 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 11 REMARK 3 SOLVENT ATOMS : 56 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.63000 REMARK 3 B22 (A**2) : -0.11000 REMARK 3 B33 (A**2) : -2.52000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.14000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.09 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) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.22 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.000 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : ISOTROPIC REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 2.034 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 3.061 ; 2.500 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.289 ; 2.500 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.886 ; 3.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : CNS BULK SOLVENT MODEL USED REMARK 3 KSOL : 0.38 REMARK 3 BSOL : 36.50 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 1J2X COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JAN-03. REMARK 100 THE DEPOSITION ID IS D_1000005563. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-OCT-01 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97899 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : FLAT CYLINDRICALLY BENT MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5657 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 22.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : 0.04500 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 3.80 REMARK 200 R MERGE FOR SHELL (I) : 0.16400 REMARK 200 R SYM FOR SHELL (I) : 0.16400 REMARK 200 <I/SIGMA(I)> FOR SHELL : 5.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1I27 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEGMME 550, ZINC SULFATE, MES, PH 6.5, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277.0K 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 29.80250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 15.22300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 29.80250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 15.22300 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5950 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -54.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 GLY A 448 REMARK 465 SER A 449 REMARK 465 GLY A 450 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 PRO A 446 178.87 -50.69 REMARK 500 ASN A 501 62.58 38.35 REMARK 500 ASP B 959 59.09 71.28 REMARK 500 LEU B 960 -118.60 -94.46 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 A1000 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 503 OE1 REMARK 620 2 GLU A 503 OE2 61.8 REMARK 620 3 HIS A 512 NE2 89.2 146.7 REMARK 620 4 GLU A 517 O 130.6 88.0 100.9 REMARK 620 5 HOH A1051 O 91.7 88.6 109.6 128.0 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 998 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 999 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1000 DBREF 1J2X A 449 517 UNP P35269 T2FA_HUMAN 449 517 DBREF 1J2X B 944 961 UNP Q9Y5B0 CTDP1_HUMAN 944 961 SEQADV 1J2X GLY A 445 UNP P35269 CLONING ARTIFACT SEQADV 1J2X PRO A 446 UNP P35269 CLONING ARTIFACT SEQADV 1J2X LEU A 447 UNP P35269 CLONING ARTIFACT SEQADV 1J2X 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 SEQRES 1 B 18 SER GLU ALA ASP GLU MET ALA LYS ALA LEU GLU ALA GLU SEQRES 2 B 18 LEU ASN ASP LEU MET HET SO4 A 998 5 HET SO4 A 999 5 HET ZN A1000 1 HETNAM SO4 SULFATE ION HETNAM ZN ZINC ION FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 ZN ZN 2+ FORMUL 6 HOH *56(H2 O) HELIX 1 1 THR A 455 LYS A 466 1 12 HELIX 2 2 THR A 469 LYS A 475 1 7 HELIX 3 3 GLN A 478 GLY A 483 1 6 HELIX 4 4 SER A 485 ASN A 501 1 17 HELIX 5 5 SER B 944 LEU B 957 1 14 SHEET 1 A 2 GLU A 503 ILE A 507 0 SHEET 2 A 2 LYS A 510 SER A 514 -1 O HIS A 512 N LYS A 505 LINK OE1 GLU A 503 ZN ZN A1000 1555 1555 1.99 LINK OE2 GLU A 503 ZN ZN A1000 1555 1555 2.25 LINK NE2 HIS A 512 ZN ZN A1000 4555 1555 2.01 LINK O GLU A 517 ZN ZN A1000 1555 1555 2.06 LINK ZN ZN A1000 O HOH A1051 1555 4555 2.02 SITE 1 AC1 5 LYS A 471 LYS A 475 ASN A 501 SER B 944 SITE 2 AC1 5 ALA B 946 SITE 1 AC2 4 LYS A 466 LYS A 476 LYS A 505 MET A 506 SITE 1 AC3 4 GLU A 503 HIS A 512 GLU A 517 HOH A1051 CRYST1 59.605 30.446 47.379 90.00 106.38 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 0.016777 0.000000 0.004930 0.00000 SCALE2 0.000000 0.032845 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021999 0.00000