HEADER RNA BINDING PROTEIN 08-MAY-24 9F9U TITLE CRYSTAL STRUCTURE OF SACCHAROLOBUS SOLFATARICUS NUSA2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTION ELONGATION FACTOR NUSA; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SACCHAROLOBUS SOLFATARICUS P2; SOURCE 3 ORGANISM_TAXID: 273057; SOURCE 4 STRAIN: P2; SOURCE 5 ATCC: 35092; SOURCE 6 GENE: SSO0172; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_VARIANT: PLYSS; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS CRENARCHAEA, ZINC-FINGER PROTEIN, ALPHA-BETA FOLD, RNA-BINDING KEYWDS 2 PROTEIN, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.PILOTTTO,D.K.PHUNG,F.WERNER REVDAT 1 02-OCT-24 9F9U 0 JRNL AUTH D.K.PHUNG,S.PILOTTTO,D.MATELSKA,F.BLOMBACH,N.PINOTSIS, JRNL AUTH 2 L.HOVAN,F.L.GERVASIO,F.WERNER JRNL TITL ARCHAEAL NUSA2 IS THE EVOLUTIONARY PRECURSOR OF THE JRNL TITL 2 RIBOSOMAL PROTEIN ES7 IN EUKARYOTES JRNL REF STRUCTURE 2024 JRNL REFN ISSN 0969-2126 REMARK 2 REMARK 2 RESOLUTION. 1.68 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.68 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.72 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.050 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.4 REMARK 3 NUMBER OF REFLECTIONS : 20507 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.217 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.630 REMARK 3 FREE R VALUE TEST SET COUNT : 950 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 38.7200 - 3.2100 1.00 3079 166 0.1895 0.1935 REMARK 3 2 3.2100 - 2.5500 1.00 3069 135 0.2241 0.2396 REMARK 3 3 2.5500 - 2.2300 0.98 3010 148 0.2289 0.2751 REMARK 3 4 2.2300 - 2.0200 0.97 2951 148 0.2158 0.2723 REMARK 3 5 2.0200 - 1.8800 0.91 2780 123 0.2717 0.3408 REMARK 3 6 1.8800 - 1.7700 0.86 2627 123 0.2977 0.3393 REMARK 3 7 1.7700 - 1.6800 0.67 2041 107 0.3246 0.3924 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) : 0.256 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.320 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 27.34 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 34.53 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 : 0.008 1412 REMARK 3 ANGLE : 1.012 1912 REMARK 3 CHIRALITY : 0.062 232 REMARK 3 PLANARITY : 0.009 238 REMARK 3 DIHEDRAL : 5.248 195 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 9F9U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-MAY-24. REMARK 100 THE DEPOSITION ID IS D_1292138366. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P14 (MX2) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.2826 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X CDTE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21422 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.680 REMARK 200 RESOLUTION RANGE LOW (A) : 72.880 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.3 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.68 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.74 REMARK 200 COMPLETENESS FOR SHELL (%) : 75.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 1.08600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHELXDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% W/V PEG 20,000, 2% V/V 1,4 REMARK 280 -DIOXANE, 100 MM BICINE PH 9.0, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 36.40650 REMARK 290 SMTRY3 2 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 9400 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 NZ LYS A 107 O HOH A 301 1.92 REMARK 500 OG1 THR A 47 O HOH A 302 2.03 REMARK 500 OE1 GLN A 112 O HOH A 303 2.10 REMARK 500 NH1 ARG A 143 O HOH A 304 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 LYS A 50 CD - CE - NZ ANGL. DEV. = -15.1 DEGREES 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 THR A 47 -31.91 -132.75 REMARK 500 HIS A 58 -68.34 -91.31 REMARK 500 ASP A 64 -122.64 54.85 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 201 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 8 OD2 REMARK 620 2 CYS A 11 SG 110.9 REMARK 620 3 CYS A 18 SG 95.4 112.0 REMARK 620 4 CYS A 21 SG 96.7 122.3 114.6 REMARK 620 N 1 2 3 DBREF 9F9U A 1 170 UNP Q980V4 Q980V4_SACS2 1 170 SEQRES 1 A 170 MET LYS MET LYS ILE PRO LEU ASP TYR VAL CYS VAL ARG SEQRES 2 A 170 SER GLY LEU LEU CYS ASN ARG CYS GLN SER LEU ILE ASP SEQRES 3 A 170 SER GLY GLU VAL PHE GLU TYR GLU VAL GLU ILE ILE LYS SEQRES 4 A 170 ILE LEU LEU ASP LEU GLU GLU THR GLN PHE LYS GLU LEU SEQRES 5 A 170 LYS ASP SER THR TYR HIS LYS ALA TYR LYS VAL ASP ASP SEQRES 6 A 170 LEU LEU ILE LEU LEU VAL THR SER GLY GLN GLU MET THR SEQRES 7 A 170 GLN GLN LYS TRP ILE LYS ILE ALA ARG ILE LEU GLN GLU SEQRES 8 A 170 LYS LEU ASN ILE LYS VAL ARG VAL LEU GLU LYS THR ASN SEQRES 9 A 170 SER ILE LYS ASN SER ALA VAL GLN LEU LEU SER PRO ALA SEQRES 10 A 170 ARG VAL LEU GLY VAL ASN THR VAL TRP MET PRO ASP GLY SEQRES 11 A 170 SER VAL GLN TYR VAL ILE ARG VAL SER ARG SER GLU ARG SEQRES 12 A 170 ARG LEU LEU PRO ALA GLU ALA GLN LEU LEU GLU SER ALA SEQRES 13 A 170 LEU THR LYS ILE HIS SER THR PRO VAL ARG ILE ARG VAL SEQRES 14 A 170 GLU HET ZN A 201 1 HETNAM ZN ZINC ION FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *141(H2 O) HELIX 1 AA1 ASP A 8 GLY A 15 1 8 HELIX 2 AA2 CYS A 18 SER A 27 1 10 HELIX 3 AA3 PHE A 31 GLN A 48 1 18 HELIX 4 AA4 PHE A 49 ASP A 54 5 6 HELIX 5 AA5 THR A 78 ASN A 94 1 17 HELIX 6 AA6 SER A 105 SER A 115 1 11 HELIX 7 AA7 ARG A 140 LEU A 146 5 7 HELIX 8 AA8 GLU A 149 SER A 162 1 14 SHEET 1 AA1 4 LYS A 2 MET A 3 0 SHEET 2 AA1 4 THR A 56 VAL A 63 1 O TYR A 57 N LYS A 2 SHEET 3 AA1 4 LEU A 66 THR A 72 -1 O ILE A 68 N TYR A 61 SHEET 4 AA1 4 LYS A 96 GLU A 101 1 O LEU A 100 N LEU A 69 SHEET 1 AA2 3 VAL A 119 TRP A 126 0 SHEET 2 AA2 3 VAL A 132 VAL A 138 -1 O GLN A 133 N VAL A 125 SHEET 3 AA2 3 VAL A 165 VAL A 169 1 O ARG A 166 N ILE A 136 LINK OD2 ASP A 8 ZN ZN A 201 1555 1555 2.33 LINK SG CYS A 11 ZN ZN A 201 1555 1555 2.30 LINK SG CYS A 18 ZN ZN A 201 1555 1555 2.31 LINK SG CYS A 21 ZN ZN A 201 1555 1555 2.31 CISPEP 1 SER A 115 PRO A 116 0 7.08 CRYST1 35.467 72.813 41.746 90.00 111.95 90.00 P 1 21 1 2 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 0.028195 0.000000 0.011363 0.00000 SCALE2 0.000000 0.013734 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025827 0.00000