HEADER UNKNOWN FUNCTION 22-JUN-23 8T8K TITLE STRUCTURE OF DOMAIN OF UNKNOWN FUNCTION 507 (DUF507) IN SPACE GROUP TITLE 2 C222(1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DUF507 FAMILY PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AQUIFEX AEOLICUS; SOURCE 3 ORGANISM_TAXID: 63363; SOURCE 4 GENE: AQ_1752; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DUF507, 4-HELIX BUNDLE, UNKNOWN FUNCTION EXPDTA X-RAY DIFFRACTION AUTHOR J.J.TANNER,C.E.MCKAY REVDAT 1 30-AUG-23 8T8K 0 JRNL AUTH C.E.MCKAY,J.CHENG,J.J.TANNER JRNL TITL CRYSTAL STRUCTURE OF DOMAIN OF UNKNOWN FUNCTION 507 (DUF507) JRNL TITL 2 REVEALS A NEW PROTEIN FOLD. JRNL REF SCI REP V. 13 13496 2023 JRNL REFN ESSN 2045-2322 JRNL PMID 37596303 JRNL DOI 10.1038/S41598-023-40558-Y REMARK 2 REMARK 2 RESOLUTION. 1.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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) : 1.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.53 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 3 NUMBER OF REFLECTIONS : 20563 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 987 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 45.5300 - 3.5900 1.00 2966 124 0.1755 0.1883 REMARK 3 2 3.5900 - 2.8500 1.00 2824 152 0.2048 0.2348 REMARK 3 3 2.8500 - 2.4900 1.00 2824 137 0.2143 0.2514 REMARK 3 4 2.4900 - 2.2600 0.98 2747 122 0.2335 0.2828 REMARK 3 5 2.2600 - 2.1000 0.99 2744 156 0.2709 0.3387 REMARK 3 6 2.1000 - 1.9800 0.99 2780 145 0.2753 0.3090 REMARK 3 7 1.9800 - 1.8800 0.97 2691 151 0.3853 0.4129 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 : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 30.880 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) : 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 : 0.003 1532 REMARK 3 ANGLE : 0.468 2049 REMARK 3 CHIRALITY : 0.037 232 REMARK 3 PLANARITY : 0.005 263 REMARK 3 DIHEDRAL : 11.843 629 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 113 THROUGH 183 ) REMARK 3 ORIGIN FOR THE GROUP (A): 46.6427 29.2450 41.1780 REMARK 3 T TENSOR REMARK 3 T11: 0.3823 T22: 0.1731 REMARK 3 T33: 0.2122 T12: 0.0458 REMARK 3 T13: 0.0044 T23: -0.0041 REMARK 3 L TENSOR REMARK 3 L11: 1.1646 L22: 1.1188 REMARK 3 L33: 6.4448 L12: 0.1119 REMARK 3 L13: -0.5497 L23: 0.6878 REMARK 3 S TENSOR REMARK 3 S11: -0.0267 S12: 0.2474 S13: -0.0394 REMARK 3 S21: -0.1090 S22: -0.0023 S23: -0.0940 REMARK 3 S31: 0.3074 S32: -0.0309 S33: 0.0404 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 25 ) REMARK 3 ORIGIN FOR THE GROUP (A): 46.0616 36.8772 51.3868 REMARK 3 T TENSOR REMARK 3 T11: 0.5972 T22: 0.2704 REMARK 3 T33: 0.2050 T12: 0.0872 REMARK 3 T13: -0.0377 T23: 0.0106 REMARK 3 L TENSOR REMARK 3 L11: 2.6193 L22: 1.8961 REMARK 3 L33: 7.1453 L12: -1.1550 REMARK 3 L13: -2.3201 L23: 3.4540 REMARK 3 S TENSOR REMARK 3 S11: 0.2329 S12: 0.4601 S13: 0.0531 REMARK 3 S21: -0.7092 S22: -0.3745 S23: 0.2930 REMARK 3 S31: -0.5962 S32: -0.2828 S33: 0.0651 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 26 THROUGH 70 ) REMARK 3 ORIGIN FOR THE GROUP (A): 61.3149 23.3010 45.7796 REMARK 3 T TENSOR REMARK 3 T11: 0.5234 T22: 0.2232 REMARK 3 T33: 0.1763 T12: 0.0010 REMARK 3 T13: 0.0096 T23: 0.0208 REMARK 3 L TENSOR REMARK 3 L11: 2.3112 L22: 7.4502 REMARK 3 L33: 3.2928 L12: -3.7057 REMARK 3 L13: -2.2842 L23: 4.6898 REMARK 3 S TENSOR REMARK 3 S11: 0.1305 S12: -0.1327 S13: 0.2407 REMARK 3 S21: -0.4544 S22: 0.1934 S23: -0.3818 REMARK 3 S31: -0.2628 S32: 0.2355 S33: -0.2933 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 71 THROUGH 112 ) REMARK 3 ORIGIN FOR THE GROUP (A): 56.0922 17.5658 49.6590 REMARK 3 T TENSOR REMARK 3 T11: 0.5517 T22: 0.2059 REMARK 3 T33: 0.2060 T12: 0.0630 REMARK 3 T13: 0.0065 T23: 0.0055 REMARK 3 L TENSOR REMARK 3 L11: 0.3386 L22: 7.2010 REMARK 3 L33: 6.6600 L12: -2.3356 REMARK 3 L13: -2.2747 L23: 7.1583 REMARK 3 S TENSOR REMARK 3 S11: -0.1680 S12: -0.0089 S13: -0.0504 REMARK 3 S21: 0.2691 S22: 0.0838 S23: 0.2448 REMARK 3 S31: 0.0564 S32: -0.1811 S33: 0.0652 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 8T8K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1000275272. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-22 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0722 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CMOS REMARK 200 DETECTOR MANUFACTURER : RDI CMOS_8M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 20928 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.870 REMARK 200 RESOLUTION RANGE LOW (A) : 45.530 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : 0.08100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.87 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 6.80 REMARK 200 R MERGE FOR SHELL (I) : 0.61800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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 (%): 56.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.01 M CO(II)CL2 HEXAHYDRATE, 0.1 M REMARK 280 SODIUM ACETATE PH 4.6, AND 1.0 M 1,6-HEXANEDIOL, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 286K 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 39.56950 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 39.56950 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 36.35700 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.26700 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 36.35700 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.26700 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.56950 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 36.35700 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 43.26700 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 39.56950 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 36.35700 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 43.26700 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 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 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 309 LIES ON A SPECIAL POSITION. 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 SER A 0 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 MET A 1 CG SD CE REMARK 470 GLU A 5 CG CD OE1 OE2 REMARK 470 LYS A 36 CE NZ REMARK 470 LYS A 127 CD CE NZ REMARK 470 GLU A 131 CG CD OE1 OE2 REMARK 470 LYS A 138 CE NZ REMARK 470 LYS A 152 CG CD CE NZ REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: SASDSX6 RELATED DB: SASBDB DBREF 8T8K A 1 183 UNP O67633 O67633_AQUAE 1 183 SEQADV 8T8K SER A 0 UNP O67633 EXPRESSION TAG SEQRES 1 A 184 SER MET ARG LEU PRO GLU ARG LEU VAL GLU ALA ILE ALA SEQRES 2 A 184 GLU SER ILE ILE GLN LYS LEU GLY LYS GLU GLU GLY ILE SEQRES 3 A 184 LEU GLU LEU GLU ASP PRO ALA THR PHE LYS LYS LYS ILE SEQRES 4 A 184 ILE SER LEU PHE LYS GLU ALA ASP ARG GLU GLU LYS GLU SEQRES 5 A 184 LEU GLU GLU LYS ALA LYS ALA VAL LEU ARG GLU ASN LEU SEQRES 6 A 184 GLU VAL LEU GLU ARG GLU ASN ILE ASP TYR ARG THR ALA SEQRES 7 A 184 PHE LEU ALA VAL LYS ARG LYS LEU ALA GLU GLU MET ASN SEQRES 8 A 184 ILE ASN VAL ASP ARG ARG GLU ARG LEU ASN GLN ILE ILE SEQRES 9 A 184 ASN ARG ILE MET ASP LEU ILE MET LYS ASP GLU SER VAL SEQRES 10 A 184 GLU ILE TYR GLU ASP PRO PRO VAL ILE ARG LYS LYS ILE SEQRES 11 A 184 ARG GLU ILE VAL LEU GLY ALA LEU LYS ILE GLU GLU GLU SEQRES 12 A 184 ILE GLU LYS THR VAL ARG GLN ARG ILE LYS LYS TYR SER SEQRES 13 A 184 ARG ASP LEU LEU GLU GLY SER PRO GLU TRP GLN ILE LEU SEQRES 14 A 184 TRP LYS ARG ILE TYR GLU ASP GLU LEU LYS LYS ARG GLY SEQRES 15 A 184 LEU ALA HET HEZ A 201 8 HETNAM HEZ HEXANE-1,6-DIOL FORMUL 2 HEZ C6 H14 O2 FORMUL 3 HOH *91(H2 O) HELIX 1 AA1 PRO A 4 GLY A 20 1 17 HELIX 2 AA2 ASP A 30 ASN A 63 1 34 HELIX 3 AA3 ASN A 63 ASN A 71 1 9 HELIX 4 AA4 ASP A 73 MET A 89 1 17 HELIX 5 AA5 ASP A 94 ASP A 113 1 20 HELIX 6 AA6 ASP A 121 LYS A 152 1 32 HELIX 7 AA7 LYS A 153 SER A 155 5 3 HELIX 8 AA8 SER A 162 ARG A 180 1 19 SHEET 1 AA1 2 LEU A 26 LEU A 28 0 SHEET 2 AA1 2 VAL A 116 ILE A 118 -1 O GLU A 117 N GLU A 27 CRYST1 72.714 86.534 79.139 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 0.013753 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011556 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012636 0.00000