HEADER DNA BINDING PROTEIN 12-JAN-09 3FT7 TITLE CRYSTAL STRUCTURE OF AN EXTREMELY STABLE DIMERIC PROTEIN FROM TITLE 2 SULFOLOBUS ISLANDICUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN ORF56; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS ISLANDICUS; SOURCE 3 ORGANISM_TAXID: 43080; SOURCE 4 GENE: PLASMID PRN1; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28C? KEYWDS PLASMID COPY CONTROL PROTEIN, RIBBON HELIX HELIX PROTEIN, DNA BINDING KEYWDS 2 PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.NEUMANN,C.LOEW,U.WEININGER,M.T.STUBBS REVDAT 6 01-NOV-23 3FT7 1 REMARK REVDAT 5 01-NOV-17 3FT7 1 REMARK REVDAT 4 14-DEC-16 3FT7 1 COMPND REVDAT 3 13-JUL-11 3FT7 1 VERSN REVDAT 2 27-OCT-09 3FT7 1 JRNL REVDAT 1 20-OCT-09 3FT7 0 JRNL AUTH U.WEININGER,M.ZEEB,P.NEUMANN,C.LOW,M.T.STUBBS,G.LIPPS, JRNL AUTH 2 J.BALBACH JRNL TITL STRUCTURE-BASED STABILITY ANALYSIS OF AN EXTREMELY STABLE JRNL TITL 2 DIMERIC DNA BINDING PROTEIN FROM SULFOLOBUS ISLANDICUS JRNL REF BIOCHEMISTRY V. 48 10030 2009 JRNL REFN ISSN 0006-2960 JRNL PMID 19788170 JRNL DOI 10.1021/BI900760N REMARK 2 REMARK 2 RESOLUTION. 2.00 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 : TWIN_LSQ_F REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.470 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 3 NUMBER OF REFLECTIONS : 5849 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.177 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1077 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 33.0350 - 3.6330 0.98 1804 177 0.1230 0.1720 REMARK 3 2 3.6330 - 2.8840 0.98 1795 201 0.1470 0.2450 REMARK 3 3 2.8840 - 2.5200 0.98 1766 174 0.1970 0.2920 REMARK 3 4 2.5200 - 2.2890 0.98 1836 144 0.2410 0.3330 REMARK 3 5 2.2890 - 2.1250 0.98 1757 172 0.2460 0.2960 REMARK 3 6 2.1250 - 2.0000 0.98 1803 163 0.2820 0.3440 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 : 0.36 REMARK 3 B_SOL : 89.47 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.65 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.04 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 5.62800 REMARK 3 B22 (A**2) : 5.62800 REMARK 3 B33 (A**2) : -15.53000 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: 0.4810 REMARK 3 OPERATOR: H,-K,-L REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.016 761 REMARK 3 ANGLE : 1.933 1024 REMARK 3 CHIRALITY : 0.103 116 REMARK 3 PLANARITY : 0.008 127 REMARK 3 DIHEDRAL : 21.949 285 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 2 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN A REMARK 3 ORIGIN FOR THE GROUP (A): 5.6027 -2.8007 -3.8011 REMARK 3 T TENSOR REMARK 3 T11: 0.2097 T22: 0.0305 REMARK 3 T33: 0.0982 T12: -0.0243 REMARK 3 T13: 0.0399 T23: 0.0001 REMARK 3 L TENSOR REMARK 3 L11: 1.5303 L22: 0.6058 REMARK 3 L33: 1.2517 L12: -0.2599 REMARK 3 L13: -0.1968 L23: 0.1448 REMARK 3 S TENSOR REMARK 3 S11: -0.3947 S12: 0.0305 S13: -0.1248 REMARK 3 S21: 0.0779 S22: 0.0922 S23: 0.2384 REMARK 3 S31: 0.0651 S32: -0.0038 S33: 0.3164 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN B REMARK 3 ORIGIN FOR THE GROUP (A): 5.7167 2.3428 3.7106 REMARK 3 T TENSOR REMARK 3 T11: 0.3127 T22: 0.0693 REMARK 3 T33: 0.0437 T12: 0.0488 REMARK 3 T13: -0.0324 T23: -0.0097 REMARK 3 L TENSOR REMARK 3 L11: 0.7812 L22: 0.2758 REMARK 3 L33: 0.5308 L12: -0.1887 REMARK 3 L13: 0.0044 L23: -1.0586 REMARK 3 S TENSOR REMARK 3 S11: -0.3087 S12: 0.0083 S13: 0.0555 REMARK 3 S21: 0.1310 S22: 0.1638 S23: -0.0637 REMARK 3 S31: 0.2135 S32: -0.1904 S33: 0.0712 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 3FT7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-JAN-09. REMARK 100 THE DEPOSITION ID IS D_1000051012. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-JUL-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-002 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA 3.2.25 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6218 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 85.749 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : 0.08000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.3070 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.20 REMARK 200 R MERGE FOR SHELL (I) : 0.62300 REMARK 200 R SYM FOR SHELL (I) : 0.62300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.200 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: PDB ENTRY 1MYK, 1PAR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16-22% PEG 4000, 100MM HEPES PH 7.5 , REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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,X,Z+3/4 REMARK 290 4555 Y,-X,Z+1/4 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 42.84500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 64.26750 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 21.42250 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3660 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 5540 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -27.0 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 GLY A 2 REMARK 465 ARG A 3 REMARK 465 PRO A 4 REMARK 465 TYR A 5 REMARK 465 LYS A 6 REMARK 465 LEU A 7 REMARK 465 LYS A 53 REMARK 465 GLN A 54 REMARK 465 LYS A 55 REMARK 465 LYS A 56 REMARK 465 GLY B 2 REMARK 465 ARG B 3 REMARK 465 PRO B 4 REMARK 465 TYR B 5 REMARK 465 LYS B 6 REMARK 465 LYS B 53 REMARK 465 GLN B 54 REMARK 465 LYS B 55 REMARK 465 LYS B 56 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 ASP A 52 CG OD1 OD2 REMARK 470 ASP B 52 CG OD1 OD2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ASP A 52 C REMARK 480 ASP B 52 N 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 ND2 ASN A 9 O LEU B 7 3554 2.15 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 ASN A 9 -157.24 -110.89 REMARK 500 HIS A 22 -64.05 -29.00 REMARK 500 LYS A 30 -75.40 -51.52 REMARK 500 GLU A 31 -29.66 -32.23 REMARK 500 ASN B 9 -147.30 -51.92 REMARK 500 ASN B 33 78.40 46.16 REMARK 500 ASN B 50 29.46 -66.37 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 57 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2K9I RELATED DB: PDB REMARK 900 NMR STRUCTURE DBREF 3FT7 A 2 56 UNP Q54323 Q54323_SULIS 2 56 DBREF 3FT7 B 2 56 UNP Q54323 Q54323_SULIS 2 56 SEQRES 1 A 55 GLY ARG PRO TYR LYS LEU LEU ASN GLY ILE LYS LEU GLY SEQRES 2 A 55 VAL TYR ILE PRO GLN GLU TRP HIS ASP ARG LEU MET GLU SEQRES 3 A 55 ILE ALA LYS GLU LYS ASN LEU THR LEU SER ASP VAL CYS SEQRES 4 A 55 ARG LEU ALA ILE LYS GLU TYR LEU ASP ASN HIS ASP LYS SEQRES 5 A 55 GLN LYS LYS SEQRES 1 B 55 GLY ARG PRO TYR LYS LEU LEU ASN GLY ILE LYS LEU GLY SEQRES 2 B 55 VAL TYR ILE PRO GLN GLU TRP HIS ASP ARG LEU MET GLU SEQRES 3 B 55 ILE ALA LYS GLU LYS ASN LEU THR LEU SER ASP VAL CYS SEQRES 4 B 55 ARG LEU ALA ILE LYS GLU TYR LEU ASP ASN HIS ASP LYS SEQRES 5 B 55 GLN LYS LYS HET GOL A 57 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *41(H2 O) HELIX 1 1 PRO A 18 ASN A 33 1 16 HELIX 2 2 THR A 35 HIS A 51 1 17 HELIX 3 3 PRO B 18 LYS B 32 1 15 HELIX 4 4 THR B 35 ASN B 50 1 16 SHEET 1 A 2 TYR A 16 ILE A 17 0 SHEET 2 A 2 ILE B 11 LYS B 12 -1 O ILE B 11 N ILE A 17 SITE 1 AC1 2 ASP A 38 ARG A 41 CRYST1 33.030 33.030 85.690 90.00 90.00 90.00 P 43 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 0.030276 0.000000 0.000000 0.00000 SCALE2 0.000000 0.030276 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011670 0.00000