HEADER DNA BINDING PROTEIN 05-DEC-23 8XAQ TITLE THE THERMOSTABLE AND ACID-TOLERANT DNA-BINDING PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA/RNA-BINDING PROTEIN ALBA; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SULFOLOBUS ACIDOCALDARIUS DSM 639; SOURCE 3 ORGANISM_TAXID: 330779; SOURCE 4 GENE: ALBA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS THERMOSTABLE, ACID-TOLERANT DNA-BINDING PROTEIN, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.Y.CHEN,C.H.HUANG REVDAT 1 11-DEC-24 8XAQ 0 JRNL AUTH C.Y.CHEN,C.H.HUANG JRNL TITL CRYSTAL STRUCTURES OF THE THERMOSTABLE AND ACID-TOLERANT JRNL TITL 2 DNA-BINDING PROTEINS, SAC10B1, SAC10B2 AND SAC10B1-F59A FROM JRNL TITL 3 SULFOLOBUS ACIDOCALDARIUS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.5 REMARK 3 NUMBER OF REFLECTIONS : 32457 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.320 REMARK 3 FREE R VALUE TEST SET COUNT : 1728 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 25.0300 - 3.2000 0.97 2982 147 0.2092 0.2425 REMARK 3 2 3.2000 - 2.5400 1.00 2909 221 0.2223 0.2521 REMARK 3 3 2.5400 - 2.2200 0.99 2924 170 0.2201 0.2559 REMARK 3 4 2.2200 - 2.0200 0.99 2970 163 0.2098 0.2643 REMARK 3 5 2.0200 - 1.8700 0.99 2924 165 0.2312 0.2491 REMARK 3 6 1.8700 - 1.7600 0.99 2881 176 0.2363 0.2750 REMARK 3 7 1.7600 - 1.6700 0.97 2888 136 0.2328 0.2575 REMARK 3 8 1.6700 - 1.6000 0.88 2585 128 0.2337 0.2839 REMARK 3 9 1.6000 - 1.5400 0.78 2292 147 0.2355 0.2463 REMARK 3 10 1.5400 - 1.4900 0.69 2026 94 0.2190 0.2215 REMARK 3 11 1.4900 - 1.4400 0.60 1789 79 0.2369 0.2250 REMARK 3 12 1.4400 - 1.4000 0.53 1559 102 0.2394 0.2981 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 : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 28.590 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.44 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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): 10.0814 19.3958 10.9892 REMARK 3 T TENSOR REMARK 3 T11: 0.0731 T22: 0.0654 REMARK 3 T33: 0.0818 T12: 0.0027 REMARK 3 T13: -0.0026 T23: -0.0029 REMARK 3 L TENSOR REMARK 3 L11: 1.0461 L22: 1.4867 REMARK 3 L33: 1.1520 L12: -0.0699 REMARK 3 L13: -0.3788 L23: 0.1065 REMARK 3 S TENSOR REMARK 3 S11: -0.0054 S12: 0.0972 S13: 0.0332 REMARK 3 S21: -0.0363 S22: 0.0287 S23: 0.0743 REMARK 3 S31: 0.0125 S32: -0.1143 S33: -0.0182 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 8XAQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 12-DEC-23. REMARK 100 THE DEPOSITION ID IS D_1300043058. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSRRC REMARK 200 BEAMLINE : TPS 05A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.99984 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36860 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 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 (%) : 98.4 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.5400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.45 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.41000 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: 7DI4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% (W/V) PEG 1000, 0.1M IMIDAZOLE, PH REMARK 280 8.0, 0.2M CA(OAC)2, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z REMARK 290 4555 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 47.53700 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.44750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 47.53700 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 19.44750 REMARK 290 SMTRY3 4 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 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: 1480 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 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 SER A 2 REMARK 465 SER A 3 REMARK 465 PRO A 61 REMARK 465 LYS A 96 REMARK 465 ALA A 97 REMARK 465 MET B 1 REMARK 465 SER B 2 REMARK 465 SER B 3 REMARK 465 PRO B 61 REMARK 465 LYS B 96 REMARK 465 ALA B 97 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 B 176 O HOH B 201 2.10 REMARK 500 O HOH A 186 O HOH B 176 2.12 REMARK 500 O HOH B 185 O HOH B 187 2.14 REMARK 500 O HOH B 129 O HOH B 197 2.14 REMARK 500 O HOH A 180 O HOH A 181 2.16 REMARK 500 NZ LYS B 15 O HOH B 101 2.16 REMARK 500 OE2 GLU A 90 O HOH A 101 2.17 REMARK 500 NH1 ARG B 43 O HOH B 102 2.17 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 B 109 O HOH B 166 4546 2.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 8XAO RELATED DB: PDB REMARK 900 RELATED ID: 8XAP RELATED DB: PDB DBREF 8XAQ A 1 97 UNP Q4J973 ALBA_SULAC 1 97 DBREF 8XAQ B 1 97 UNP Q4J973 ALBA_SULAC 1 97 SEQADV 8XAQ ALA A 59 UNP Q4J973 PHE 59 ENGINEERED MUTATION SEQADV 8XAQ ALA B 59 UNP Q4J973 PHE 59 ENGINEERED MUTATION SEQRES 1 A 97 MET SER SER GLY ALA THR PRO SER ASN VAL VAL LEU VAL SEQRES 2 A 97 GLY LYS LYS PRO VAL MET ASN TYR VAL LEU ALA ALA LEU SEQRES 3 A 97 THR LEU LEU ASN GLN GLY VAL SER GLU ILE THR ILE LYS SEQRES 4 A 97 ALA ARG GLY ARG ALA ILE SER LYS ALA VAL ASP THR VAL SEQRES 5 A 97 GLU ILE VAL ARG ASN ARG ALA LEU PRO ASP LYS ILE GLU SEQRES 6 A 97 VAL LYS GLU ILE ARG ILE GLY SER GLN VAL VAL THR SER SEQRES 7 A 97 GLN ASP GLY ARG GLN SER ARG VAL SER THR ILE GLU ILE SEQRES 8 A 97 GLY ILE ARG LYS LYS ALA SEQRES 1 B 97 MET SER SER GLY ALA THR PRO SER ASN VAL VAL LEU VAL SEQRES 2 B 97 GLY LYS LYS PRO VAL MET ASN TYR VAL LEU ALA ALA LEU SEQRES 3 B 97 THR LEU LEU ASN GLN GLY VAL SER GLU ILE THR ILE LYS SEQRES 4 B 97 ALA ARG GLY ARG ALA ILE SER LYS ALA VAL ASP THR VAL SEQRES 5 B 97 GLU ILE VAL ARG ASN ARG ALA LEU PRO ASP LYS ILE GLU SEQRES 6 B 97 VAL LYS GLU ILE ARG ILE GLY SER GLN VAL VAL THR SER SEQRES 7 B 97 GLN ASP GLY ARG GLN SER ARG VAL SER THR ILE GLU ILE SEQRES 8 B 97 GLY ILE ARG LYS LYS ALA FORMUL 3 HOH *195(H2 O) HELIX 1 AA1 PRO A 17 GLN A 31 1 15 HELIX 2 AA2 ARG A 43 ALA A 59 1 17 HELIX 3 AA3 PRO B 17 GLN B 31 1 15 HELIX 4 AA4 ARG B 43 ALA B 59 1 17 SHEET 1 AA1 4 VAL A 10 LEU A 12 0 SHEET 2 AA1 4 GLU A 35 ARG A 41 1 O THR A 37 N VAL A 11 SHEET 3 AA1 4 GLN A 83 ARG A 94 -1 O ILE A 91 N ILE A 38 SHEET 4 AA1 4 GLU A 65 THR A 77 -1 N VAL A 76 O SER A 84 SHEET 1 AA2 4 VAL B 10 LEU B 12 0 SHEET 2 AA2 4 GLU B 35 ARG B 41 1 O THR B 37 N VAL B 11 SHEET 3 AA2 4 GLN B 83 ARG B 94 -1 O ILE B 91 N ILE B 38 SHEET 4 AA2 4 GLU B 65 THR B 77 -1 N VAL B 76 O SER B 84 CRYST1 95.074 38.895 69.120 90.00 131.66 90.00 C 1 2 1 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 0.010518 0.000000 0.009357 0.00000 SCALE2 0.000000 0.025710 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019364 0.00000