HEADER DNA BINDING PROTEIN 04-MAR-16 5ILV
TITLE UNINHIBITED ETV5
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: ETS TRANSLOCATION VARIANT 5;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: ETS-RELATED PROTEIN ERM;
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: ETV5, ERM;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562
KEYWDS ETV5, ETS, TRANSCRIPTION FACTOR, AUTOINHIBITION TRANSCRIPTION, DNA
KEYWDS 2 BINDING, DNA BINDING PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR F.G.WHITBY,S.L.CURRIE
REVDAT 4 25-DEC-19 5ILV 1 REMARK
REVDAT 3 20-SEP-17 5ILV 1 REMARK
REVDAT 2 03-MAY-17 5ILV 1 JRNL
REVDAT 1 22-FEB-17 5ILV 0
JRNL AUTH S.L.CURRIE,D.K.W.LAU,J.J.DOANE,F.G.WHITBY,M.OKON,
JRNL AUTH 2 L.P.MCINTOSH,B.J.GRAVES
JRNL TITL STRUCTURED AND DISORDERED REGIONS COOPERATIVELY MEDIATE
JRNL TITL 2 DNA-BINDING AUTOINHIBITION OF ETS FACTORS ETV1, ETV4 AND
JRNL TITL 3 ETV5.
JRNL REF NUCLEIC ACIDS RES. V. 45 2223 2017
JRNL REFN ESSN 1362-4962
JRNL PMID 28161714
JRNL DOI 10.1093/NAR/GKX068
REMARK 2
REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX
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 : NULL
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 22.49
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340
REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8
REMARK 3 NUMBER OF REFLECTIONS : 9542
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.189
REMARK 3 R VALUE (WORKING SET) : 0.186
REMARK 3 FREE R VALUE : 0.235
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020
REMARK 3 FREE R VALUE TEST SET COUNT : 479
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 22.4886 - 2.5825 0.99 3122 164 0.1633 0.2049
REMARK 3 2 2.5825 - 2.0502 1.00 3017 160 0.2128 0.2719
REMARK 3 3 2.0502 - 1.7912 0.97 2924 155 0.2438 0.2977
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : NULL
REMARK 3 SOLVENT RADIUS : 0.90
REMARK 3 SHRINKAGE RADIUS : 0.60
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.160
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.000
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 23.03
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.01
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
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 : 0.006 795
REMARK 3 ANGLE : 0.841 1074
REMARK 3 CHIRALITY : 0.049 107
REMARK 3 PLANARITY : 0.006 138
REMARK 3 DIHEDRAL : 12.833 472
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : 1
REMARK 3 TLS GROUP : 1
REMARK 3 SELECTION: ALL
REMARK 3 ORIGIN FOR THE GROUP (A): 13.4139 12.2850 -13.5747
REMARK 3 T TENSOR
REMARK 3 T11: 0.1403 T22: 0.0973
REMARK 3 T33: 0.1391 T12: 0.0159
REMARK 3 T13: -0.0055 T23: -0.0092
REMARK 3 L TENSOR
REMARK 3 L11: 2.8838 L22: 1.1096
REMARK 3 L33: 2.6346 L12: 0.1950
REMARK 3 L13: -0.0434 L23: -0.1944
REMARK 3 S TENSOR
REMARK 3 S11: 0.0726 S12: 0.0154 S13: -0.0855
REMARK 3 S21: 0.0019 S22: -0.0329 S23: -0.0116
REMARK 3 S31: -0.0133 S32: 0.0278 S33: -0.0072
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 5ILV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-MAR-16.
REMARK 100 THE DEPOSITION ID IS D_1000219020.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 12-JAN-13
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 5.0
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : SSRL
REMARK 200 BEAMLINE : BL7-1
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.1271
REMARK 200 MONOCHROMATOR : NULL
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9566
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800
REMARK 200 RESOLUTION RANGE LOW (A) : 30.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.2
REMARK 200 DATA REDUNDANCY : 5.200
REMARK 200 R MERGE (I) : 0.08200
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.2000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.86
REMARK 200 COMPLETENESS FOR SHELL (%) : 97.3
REMARK 200 DATA REDUNDANCY IN SHELL : 4.20
REMARK 200 R MERGE FOR SHELL (I) : 0.70500
REMARK 200 R SYM FOR SHELL (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER 2.3.0
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 45.99
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 200 MM (NH4)2SO4, PH
REMARK 280 5.0, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -X,Y,-Z+1/2
REMARK 290 4555 X,-Y,-Z
REMARK 290 5555 X+1/2,Y+1/2,Z
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
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 26.33850
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 26.33850
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 28.68550
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 32.80550
REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000
REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 28.68550
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 32.80550
REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 26.33850
REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 28.68550
REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 32.80550
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 26.33850
REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 28.68550
REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 32.80550
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000
REMARK 290
REMARK 290 REMARK: NULL
REMARK 300
REMARK 300 BIOMOLECULE: 1, 2
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 350
REMARK 350 BIOMOLECULE: 2
REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC
REMARK 350 SOFTWARE USED: PISA
REMARK 350 TOTAL BURIED SURFACE AREA: 1820 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 10090 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -14.0 KCAL/MOL
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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000
REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -26.33850
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 HOH A 519 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 524 LIES ON A SPECIAL POSITION.
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 567 O HOH A 592 2.15
REMARK 500
REMARK 500 REMARK: NULL
REMARK 500
REMARK 500 GEOMETRY AND STEREOCHEMISTRY
REMARK 500 SUBTOPIC: CLOSE CONTACTS
REMARK 500
REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC
REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15
REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A
REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375
REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE
REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS.
REMARK 500
REMARK 500 DISTANCE CUTOFF:
REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS
REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS
REMARK 500
REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE
REMARK 500 O HOH A 547 O HOH A 581 4554 2.17
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 ARG A 414 70.51 -159.27
REMARK 500
REMARK 500 REMARK: NULL
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 5ILS RELATED DB: PDB
REMARK 900 RELATED ID: 5ILU RELATED DB: PDB
DBREF 5ILV A 366 457 UNP P41161 ETV5_HUMAN 408 499
SEQRES 1 A 92 GLY SER LEU GLN LEU TRP GLN PHE LEU VAL THR LEU LEU
SEQRES 2 A 92 ASP ASP PRO ALA ASN ALA HIS PHE ILE ALA TRP THR GLY
SEQRES 3 A 92 ARG GLY MET GLU PHE LYS LEU ILE GLU PRO GLU GLU VAL
SEQRES 4 A 92 ALA ARG ARG TRP GLY ILE GLN LYS ASN ARG PRO ALA MET
SEQRES 5 A 92 ASN TYR ASP LYS LEU SER ARG SER LEU ARG TYR TYR TYR
SEQRES 6 A 92 GLU LYS GLY ILE MET GLN LYS VAL ALA GLY GLU ARG TYR
SEQRES 7 A 92 VAL TYR LYS PHE VAL CYS ASP PRO ASP ALA LEU PHE SER
SEQRES 8 A 92 MET
FORMUL 2 HOH *110(H2 O)
HELIX 1 AA1 GLN A 369 ASP A 379 1 11
HELIX 2 AA2 ASP A 380 ALA A 384 5 5
HELIX 3 AA3 GLU A 400 ASN A 413 1 14
HELIX 4 AA4 ASN A 418 LYS A 432 1 15
HELIX 5 AA5 ASP A 452 SER A 456 5 5
SHEET 1 AA1 4 ILE A 387 TRP A 389 0
SHEET 2 AA1 4 GLU A 395 LEU A 398 -1 O LYS A 397 N ALA A 388
SHEET 3 AA1 4 VAL A 444 PHE A 447 -1 O TYR A 445 N PHE A 396
SHEET 4 AA1 4 MET A 435 LYS A 437 -1 N GLN A 436 O LYS A 446
SSBOND 1 CYS A 449 CYS A 449 1555 3554 2.11
CISPEP 1 PRO A 415 ALA A 416 0 -1.60
CRYST1 57.371 65.611 52.677 90.00 90.00 90.00 C 2 2 21 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 0.017430 0.000000 0.000000 0.00000
SCALE2 0.000000 0.015241 0.000000 0.00000
SCALE3 0.000000 0.000000 0.018984 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
