HEADER TRANSCRIPTION 07-JUN-10 3NDQ TITLE STRUCTURE OF HUMAN TFIIS DOMAIN II COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION ELONGATION FACTOR A PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: TFIIS DOMAIN II, RESIDUES 131-232; COMPND 5 SYNONYM: TRANSCRIPTION ELONGATION FACTOR S-II PROTEIN 1, COMPND 6 TRANSCRIPTION ELONGATION FACTOR TFIIS.O; COMPND 7 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: GTF2S, TCEA1, TFIIS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 DE3 PLYS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET151 KEYWDS HELIX BUNDLE, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR X.P.HU,G.AVERELL,X.Y.YE,J.HOU,H.LUO REVDAT 2 06-SEP-23 3NDQ 1 REMARK SEQADV LINK REVDAT 1 18-MAY-11 3NDQ 0 JRNL AUTH X.YE,A.GNATT,X.P.HU JRNL TITL STRUCTURE OF HUMAN TFIIS DOMAIN II JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.6.1_357 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.69 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.100 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 8562 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.168 REMARK 3 R VALUE (WORKING SET) : 0.166 REMARK 3 FREE R VALUE : 0.208 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.770 REMARK 3 FREE R VALUE TEST SET COUNT : 408 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 21.6940 - 2.7870 0.97 2743 135 0.1710 0.2080 REMARK 3 2 2.7870 - 2.2130 1.00 2729 138 0.1620 0.2030 REMARK 3 3 2.2130 - 1.9330 1.00 2682 135 0.1590 0.2170 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : 0.39 REMARK 3 B_SOL : 39.80 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -7.31500 REMARK 3 B22 (A**2) : -0.70300 REMARK 3 B33 (A**2) : 6.28400 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 792 REMARK 3 ANGLE : 0.894 1066 REMARK 3 CHIRALITY : 0.065 118 REMARK 3 PLANARITY : 0.003 144 REMARK 3 DIHEDRAL : 10.656 323 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3NDQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JUN-10. REMARK 100 THE DEPOSITION ID IS D_1000059700. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-APR-10 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 : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97947 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-225 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8564 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.933 REMARK 200 RESOLUTION RANGE LOW (A) : 43.385 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 14.20 REMARK 200 R MERGE (I) : 0.07900 REMARK 200 R SYM (I) : 0.07900 REMARK 200 FOR THE DATA SET : 27.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 14.40 REMARK 200 R MERGE FOR SHELL (I) : 0.11000 REMARK 200 R SYM FOR SHELL (I) : 0.11000 REMARK 200 FOR SHELL : 5.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: PDB ENTRY 2DME REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 M AMMONIUM SULPHATE, 0.1 M 2-(N REMARK 280 -MORPHOLINO)ETHANESULFONIC ACID , PH 6.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 289K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 29.63500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 30.37500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 30.99000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 29.63500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 30.37500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 30.99000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 29.63500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 30.37500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 30.99000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 29.63500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 30.37500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 30.99000 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 NA NA A1229 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1339 LIES ON A SPECIAL POSITION. 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 125 REMARK 465 ILE A 126 REMARK 465 ASP A 127 REMARK 465 PRO A 128 REMARK 465 PHE A 129 REMARK 465 THR A 130 REMARK 465 PRO A 131 REMARK 465 ALA A 229 REMARK 465 SER A 230 REMARK 465 ASP A 231 REMARK 465 GLU A 232 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 1349 O HOH A 1355 1.98 REMARK 500 O HOH A 1325 O HOH A 1357 2.02 REMARK 500 O HOH A 1296 O HOH A 1311 2.02 REMARK 500 O HOH A 1360 O HOH A 1373 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 ASP A 184 -151.27 -87.23 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 NA A1229 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 201 O REMARK 620 2 HOH A1261 O 103.5 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1229 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1230 DBREF 3NDQ A 131 232 UNP P23193 TCEA1_HUMAN 131 232 SEQADV 3NDQ GLY A 125 UNP P23193 EXPRESSION TAG SEQADV 3NDQ ILE A 126 UNP P23193 EXPRESSION TAG SEQADV 3NDQ ASP A 127 UNP P23193 EXPRESSION TAG SEQADV 3NDQ PRO A 128 UNP P23193 EXPRESSION TAG SEQADV 3NDQ PHE A 129 UNP P23193 EXPRESSION TAG SEQADV 3NDQ THR A 130 UNP P23193 EXPRESSION TAG SEQRES 1 A 108 GLY ILE ASP PRO PHE THR PRO ARG ALA PRO SER THR SER SEQRES 2 A 108 ASP SER VAL ARG LEU LYS CYS ARG GLU MET LEU ALA ALA SEQRES 3 A 108 ALA LEU ARG THR GLY ASP ASP TYR ILE ALA ILE GLY ALA SEQRES 4 A 108 ASP GLU GLU GLU LEU GLY SER GLN ILE GLU GLU ALA ILE SEQRES 5 A 108 TYR GLN GLU ILE ARG ASN THR ASP MET LYS TYR LYS ASN SEQRES 6 A 108 ARG VAL ARG SER ARG ILE SER ASN LEU LYS ASP ALA LYS SEQRES 7 A 108 ASN PRO ASN LEU ARG LYS ASN VAL LEU CYS GLY ASN ILE SEQRES 8 A 108 PRO PRO ASP LEU PHE ALA ARG MET THR ALA GLU GLU MET SEQRES 9 A 108 ALA SER ASP GLU HET NA A1229 1 HET NA A1230 1 HETNAM NA SODIUM ION FORMUL 2 NA 2(NA 1+) FORMUL 4 HOH *149(H2 O) HELIX 1 1 ASP A 138 LEU A 152 1 15 HELIX 2 2 ARG A 153 GLY A 155 5 3 HELIX 3 3 ASP A 156 GLY A 162 1 7 HELIX 4 4 ASP A 164 ARG A 181 1 18 HELIX 5 5 ASP A 184 LYS A 199 1 16 HELIX 6 6 ASN A 203 CYS A 212 1 10 HELIX 7 7 PRO A 216 MET A 223 1 8 LINK O ALA A 201 NA NA A1229 1555 1555 2.97 LINK NA NA A1229 O HOH A1261 1555 1555 2.85 SITE 1 AC1 2 ALA A 201 HOH A1261 SITE 1 AC2 2 SER A 196 ASN A 197 CRYST1 59.270 60.750 61.980 90.00 90.00 90.00 I 2 2 2 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 0.016872 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016461 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016134 0.00000