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 <I/SIGMA(I)> 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 <I/SIGMA(I)> 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
(ATOM LINES ARE NOT SHOWN.)
END
