HEADER TRANSCRIPTION REGULATOR 15-JUL-12 4G3W TITLE CRYSTAL STRUCTURE OF A. AEOLICUS NLH1 GAF DOMAIN IN AN INACTIVE STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR NLH1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: GAF DOMAIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS; SOURCE 3 ORGANISM_TAXID: 224324; SOURCE 4 STRAIN: VF5; SOURCE 5 GENE: NLH1, AQ_218; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GAF DOMAIN, TRANSCRIPTION REGULATOR EXPDTA X-RAY DIFFRACTION AUTHOR J.D.BATCHELOR,A.WANG,P.LEE,M.DOUCLEFF,D.E.WEMMER REVDAT 2 28-FEB-24 4G3W 1 REMARK REVDAT 1 29-MAY-13 4G3W 0 JRNL AUTH J.D.BATCHELOR,P.S.LEE,A.C.WANG,M.DOUCLEFF,D.E.WEMMER JRNL TITL STRUCTURAL MECHANISM OF GAF-REGULATED DELTA(54) ACTIVATORS JRNL TITL 2 FROM AQUIFEX AEOLICUS JRNL REF J.MOL.BIOL. V. 425 156 2013 JRNL REFN ISSN 0022-2836 JRNL PMID 23123379 JRNL DOI 10.1016/J.JMB.2012.10.017 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.3_928) 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.85 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.990 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 5539 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.590 REMARK 3 FREE R VALUE TEST SET COUNT : 254 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 19.8546 - 3.3994 0.96 2672 123 0.1871 0.2046 REMARK 3 2 3.3994 - 2.7004 0.99 2613 131 0.2446 0.3153 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.31 REMARK 3 B_SOL : 35.53 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.090 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 10.34830 REMARK 3 B22 (A**2) : 10.34830 REMARK 3 B33 (A**2) : -20.69660 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 : 0.016 1107 REMARK 3 ANGLE : 1.653 1488 REMARK 3 CHIRALITY : 0.079 171 REMARK 3 PLANARITY : 0.008 182 REMARK 3 DIHEDRAL : 15.325 422 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 4G3W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-SEP-12. REMARK 100 THE DEPOSITION ID IS D_1000073705. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 8.3.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.115872 REMARK 200 MONOCHROMATOR : SI 111 CHANNEL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5719 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.680 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M NA/K PHOSPHATE, 0.1M BIS TRIS REMARK 280 PROPANE PH 7.5, AND 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 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 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 53.12000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 29.89000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 29.89000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 79.68000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 29.89000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 29.89000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 26.56000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 29.89000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 29.89000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 79.68000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 29.89000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 29.89000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 26.56000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 53.12000 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A DIMER GENERATED FROM THE REMARK 300 ASYMMETRIC UNIT BY THE OPERATION Y, X, -Z. 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: 1540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14190 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 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 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 MET A 1 REMARK 465 ASP A 2 REMARK 465 LEU A 3 REMARK 465 LYS A 4 REMARK 465 VAL A 5 REMARK 465 GLU A 6 REMARK 465 ILE A 7 REMARK 465 GLU A 8 REMARK 465 THR A 9 REMARK 465 LEU A 10 REMARK 465 TYR A 11 REMARK 465 GLU A 12 REMARK 465 VAL A 13 REMARK 465 SER A 14 REMARK 465 LYS A 15 REMARK 465 ILE A 16 REMARK 465 LEU A 17 REMARK 465 SER A 18 REMARK 465 SER A 19 REMARK 465 SER A 20 REMARK 465 LEU A 21 REMARK 465 SER A 108 REMARK 465 LYS A 109 REMARK 465 LEU A 161 REMARK 465 GLU A 162 REMARK 465 ARG A 163 REMARK 465 LYS A 164 REMARK 465 VAL A 165 REMARK 465 GLN A 166 REMARK 465 ALA A 167 REMARK 465 GLU A 168 REMARK 465 ARG A 169 REMARK 465 LYS A 170 REMARK 465 SER A 171 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 LYS A 104 75.87 29.46 REMARK 500 PHE A 159 46.06 -76.86 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4G3K RELATED DB: PDB REMARK 900 RELATED ID: 4G3V RELATED DB: PDB DBREF 4G3W A 1 171 UNP O66591 O66591_AQUAE 1 171 SEQRES 1 A 171 MET ASP LEU LYS VAL GLU ILE GLU THR LEU TYR GLU VAL SEQRES 2 A 171 SER LYS ILE LEU SER SER SER LEU ASN LEU GLU THR THR SEQRES 3 A 171 VAL PRO TYR ILE PHE ARG LEU LEU LYS LYS LEU MET GLY SEQRES 4 A 171 PHE GLU ARG LEU THR LEU THR ILE TYR ASP PRO SER THR SEQRES 5 A 171 ASP GLN ILE VAL VAL ARG ALA THR SER SER GLY LYS PHE SEQRES 6 A 171 PRO LYS GLU GLY PHE LYS LYS GLY GLU GLY ILE THR GLY SEQRES 7 A 171 LYS VAL TRP LYS HIS GLY VAL PRO ILE VAL ILE PRO ASP SEQRES 8 A 171 ILE SER GLN GLU PRO GLU PHE LEU ASN LYS VAL TRP LYS SEQRES 9 A 171 ARG LYS LYS SER LYS LYS LYS ILE ALA PHE ILE ALA VAL SEQRES 10 A 171 PRO ILE LYS SER GLY GLY LYS VAL ILE GLY VAL LEU SER SEQRES 11 A 171 ALA ASP LYS GLU ILE ASN GLU LYS ASP SER LEU ASP GLU SEQRES 12 A 171 TYR THR ARG PHE LEU SER MET ILE ALA THR LEU ILE ALA SEQRES 13 A 171 ASN SER PHE SER LEU GLU ARG LYS VAL GLN ALA GLU ARG SEQRES 14 A 171 LYS SER FORMUL 2 HOH *18(H2 O) HELIX 1 1 ASN A 22 GLY A 39 1 18 HELIX 2 2 GLU A 74 GLY A 84 1 11 HELIX 3 3 ASP A 91 GLU A 95 5 5 HELIX 4 4 SER A 140 PHE A 159 1 20 SHEET 1 A 6 GLY A 69 PHE A 70 0 SHEET 2 A 6 GLN A 54 THR A 60 -1 N ILE A 55 O PHE A 70 SHEET 3 A 6 PHE A 40 ASP A 49 -1 N ILE A 47 O VAL A 56 SHEET 4 A 6 LYS A 124 GLU A 134 -1 O ASP A 132 N GLU A 41 SHEET 5 A 6 ILE A 112 SER A 121 -1 N VAL A 117 O LEU A 129 SHEET 6 A 6 ILE A 87 ILE A 89 -1 N ILE A 89 O PHE A 114 CRYST1 59.780 59.780 106.240 90.00 90.00 90.00 P 43 21 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 0.016728 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016728 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009413 0.00000