HEADER TRANSCRIPTION REGULATOR 14-JUL-12 4G3K 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, B; 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 D.E.WEMMER,J.D.BATCHELOR,A.WANG,P.LEE,M.DOUCLEFF REVDAT 2 28-FEB-24 4G3K 1 REMARK REVDAT 1 29-MAY-13 4G3K 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. 3.05 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) : 3.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.91 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.010 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 8681 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.212 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.243 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 868 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 19.9145 - 5.5099 0.99 1387 154 0.1956 0.1986 REMARK 3 2 5.5099 - 4.3888 1.00 1312 146 0.1715 0.2067 REMARK 3 3 4.3888 - 3.8385 1.00 1288 143 0.1955 0.2532 REMARK 3 4 3.8385 - 3.4896 1.00 1291 145 0.2287 0.3041 REMARK 3 5 3.4896 - 3.2406 1.00 1270 139 0.2756 0.3093 REMARK 3 6 3.2406 - 3.0503 1.00 1265 141 0.3046 0.3651 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 REMARK 3 SHRINKAGE RADIUS : 0.86 REMARK 3 K_SOL : 0.30 REMARK 3 B_SOL : 54.81 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.370 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.120 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) : -4.35050 REMARK 3 B22 (A**2) : -4.35050 REMARK 3 B33 (A**2) : 9.73260 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 : 0.002 2338 REMARK 3 ANGLE : 0.582 3145 REMARK 3 CHIRALITY : 0.037 384 REMARK 3 PLANARITY : 0.002 380 REMARK 3 DIHEDRAL : 10.305 887 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 4G3K 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_1000073693. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 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 : NULL 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 : 8699 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.050 REMARK 200 RESOLUTION RANGE LOW (A) : 19.914 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.13 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 8.70 REMARK 200 R MERGE FOR SHELL (I) : 1.39200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 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 (%): 54.53 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 32.5% PEG 3350, 250 MM NACL, AND 50 MM REMARK 280 MES PH 6.2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 4 21 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 -Y+1/2,X+1/2,Z REMARK 290 4555 Y+1/2,-X+1/2,Z REMARK 290 5555 -X+1/2,Y+1/2,-Z REMARK 290 6555 X+1/2,-Y+1/2,-Z REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.000000 -1.000000 0.000000 59.67500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 59.67500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 59.67500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 59.67500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 59.67500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 59.67500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 59.67500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 59.67500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 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 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 300 REMARK: THE ASYMMETRIC UNIT CONTAINS THE BIOLOGICALLY RELEVANT REMARK 300 DIMER. 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: 2140 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15760 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 MET A 1 REMARK 465 GLU A 95 REMARK 465 PRO A 96 REMARK 465 GLU A 97 REMARK 465 PHE A 98 REMARK 465 LEU A 99 REMARK 465 ASN A 100 REMARK 465 LYS A 101 REMARK 465 VAL A 102 REMARK 465 TRP A 103 REMARK 465 LYS A 104 REMARK 465 ARG A 105 REMARK 465 LYS A 106 REMARK 465 LYS A 107 REMARK 465 SER A 108 REMARK 465 LYS A 109 REMARK 465 LEU A 172 REMARK 465 GLU A 173 REMARK 465 GLU A 174 REMARK 465 GLU A 175 REMARK 465 MET B 1 REMARK 465 ASP B 53 REMARK 465 GLN B 54 REMARK 465 LYS B 64 REMARK 465 PHE B 65 REMARK 465 PRO B 66 REMARK 465 LYS B 67 REMARK 465 GLU B 68 REMARK 465 GLY B 69 REMARK 465 PHE B 70 REMARK 465 LYS B 71 REMARK 465 LYS B 72 REMARK 465 GLY B 73 REMARK 465 GLU B 74 REMARK 465 GLN B 94 REMARK 465 GLU B 95 REMARK 465 PRO B 96 REMARK 465 GLU B 97 REMARK 465 PHE B 98 REMARK 465 LEU B 99 REMARK 465 ASN B 100 REMARK 465 LYS B 101 REMARK 465 VAL B 102 REMARK 465 TRP B 103 REMARK 465 LYS B 104 REMARK 465 ARG B 105 REMARK 465 LYS B 106 REMARK 465 LYS B 107 REMARK 465 SER B 108 REMARK 465 LYS B 109 REMARK 465 GLU B 137 REMARK 465 LYS B 138 REMARK 465 GLU B 173 REMARK 465 GLU B 174 REMARK 465 GLU B 175 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 66 152.51 -48.01 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4G3V RELATED DB: PDB REMARK 900 RELATED ID: 4G3W RELATED DB: PDB DBREF 4G3K A 1 175 UNP O66591 O66591_AQUAE 1 175 DBREF 4G3K B 1 175 UNP O66591 O66591_AQUAE 1 175 SEQRES 1 A 175 MET ASP LEU LYS VAL GLU ILE GLU THR LEU TYR GLU VAL SEQRES 2 A 175 SER LYS ILE LEU SER SER SER LEU ASN LEU GLU THR THR SEQRES 3 A 175 VAL PRO TYR ILE PHE ARG LEU LEU LYS LYS LEU MET GLY SEQRES 4 A 175 PHE GLU ARG LEU THR LEU THR ILE TYR ASP PRO SER THR SEQRES 5 A 175 ASP GLN ILE VAL VAL ARG ALA THR SER SER GLY LYS PHE SEQRES 6 A 175 PRO LYS GLU GLY PHE LYS LYS GLY GLU GLY ILE THR GLY SEQRES 7 A 175 LYS VAL TRP LYS HIS GLY VAL PRO ILE VAL ILE PRO ASP SEQRES 8 A 175 ILE SER GLN GLU PRO GLU PHE LEU ASN LYS VAL TRP LYS SEQRES 9 A 175 ARG LYS LYS SER LYS LYS LYS ILE ALA PHE ILE ALA VAL SEQRES 10 A 175 PRO ILE LYS SER GLY GLY LYS VAL ILE GLY VAL LEU SER SEQRES 11 A 175 ALA ASP LYS GLU ILE ASN GLU LYS ASP SER LEU ASP GLU SEQRES 12 A 175 TYR THR ARG PHE LEU SER MET ILE ALA THR LEU ILE ALA SEQRES 13 A 175 ASN SER PHE SER LEU GLU ARG LYS VAL GLN ALA GLU ARG SEQRES 14 A 175 LYS SER LEU GLU GLU GLU SEQRES 1 B 175 MET ASP LEU LYS VAL GLU ILE GLU THR LEU TYR GLU VAL SEQRES 2 B 175 SER LYS ILE LEU SER SER SER LEU ASN LEU GLU THR THR SEQRES 3 B 175 VAL PRO TYR ILE PHE ARG LEU LEU LYS LYS LEU MET GLY SEQRES 4 B 175 PHE GLU ARG LEU THR LEU THR ILE TYR ASP PRO SER THR SEQRES 5 B 175 ASP GLN ILE VAL VAL ARG ALA THR SER SER GLY LYS PHE SEQRES 6 B 175 PRO LYS GLU GLY PHE LYS LYS GLY GLU GLY ILE THR GLY SEQRES 7 B 175 LYS VAL TRP LYS HIS GLY VAL PRO ILE VAL ILE PRO ASP SEQRES 8 B 175 ILE SER GLN GLU PRO GLU PHE LEU ASN LYS VAL TRP LYS SEQRES 9 B 175 ARG LYS LYS SER LYS LYS LYS ILE ALA PHE ILE ALA VAL SEQRES 10 B 175 PRO ILE LYS SER GLY GLY LYS VAL ILE GLY VAL LEU SER SEQRES 11 B 175 ALA ASP LYS GLU ILE ASN GLU LYS ASP SER LEU ASP GLU SEQRES 12 B 175 TYR THR ARG PHE LEU SER MET ILE ALA THR LEU ILE ALA SEQRES 13 B 175 ASN SER PHE SER LEU GLU ARG LYS VAL GLN ALA GLU ARG SEQRES 14 B 175 LYS SER LEU GLU GLU GLU FORMUL 3 HOH *3(H2 O) HELIX 1 1 ASP A 2 SER A 18 1 17 HELIX 2 2 THR A 26 LEU A 37 1 12 HELIX 3 3 LYS A 71 THR A 77 1 7 HELIX 4 4 VAL A 80 GLY A 84 5 5 HELIX 5 5 SER A 140 SER A 171 1 32 HELIX 6 6 LEU B 3 SER B 19 1 17 HELIX 7 7 ASN B 22 LEU B 37 1 16 HELIX 8 8 ILE B 76 GLY B 84 1 9 HELIX 9 9 SER B 140 LEU B 172 1 33 SHEET 1 A 5 ILE A 55 THR A 60 0 SHEET 2 A 5 GLU A 41 TYR A 48 -1 N ILE A 47 O VAL A 56 SHEET 3 A 5 VAL A 125 ILE A 135 -1 O ILE A 126 N TYR A 48 SHEET 4 A 5 LYS A 111 LYS A 120 -1 N ILE A 119 O ILE A 126 SHEET 5 A 5 ILE A 87 ILE A 89 -1 N ILE A 87 O ALA A 116 SHEET 1 B 5 VAL B 57 THR B 60 0 SHEET 2 B 5 GLU B 41 ILE B 47 -1 N ILE B 47 O VAL B 57 SHEET 3 B 5 LYS B 124 ILE B 135 -1 O ASP B 132 N GLU B 41 SHEET 4 B 5 LYS B 111 SER B 121 -1 N ILE B 119 O GLY B 127 SHEET 5 B 5 ILE B 87 ILE B 89 -1 N ILE B 87 O ALA B 116 CRYST1 119.350 119.350 60.290 90.00 90.00 90.00 P 4 21 2 16 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 0.008379 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008379 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016586 0.00000