HEADER RNA BINDING PROTEIN 31-JAN-22 7QZP TITLE IDENTIFICATION AND CHARACTERIZATION OF AN RRM-CONTAINING, ELAV-LIKE, TITLE 2 RNA BINDING PROTEIN IN ACINETOBACTER BAUMANNII COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYPOTHETICAL RNA BINDING PROTEIN FROM ACINETOBACTER COMPND 3 BAUMANNII; COMPND 4 CHAIN: A; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACINETOBACTER BAUMANNII; SOURCE 3 ORGANISM_TAXID: 470; SOURCE 4 GENE: HMPREF0022_00746; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RNA, ACINETOBACTER, RRM, HUR, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.CIANI,A.PEREZ-RAFOLS,I.BONOMO,M.MICAELLI,A.ESPOSITO,C.ZUCAL, AUTHOR 2 R.BELLI,V.G.D'AGOSTINO,I.BIANCONI,V.CALDERONE,L.CEROFOLINI,M.FRAGAI, AUTHOR 3 A.PROVENZANI REVDAT 3 31-JAN-24 7QZP 1 REMARK REVDAT 2 10-AUG-22 7QZP 1 JRNL REVDAT 1 13-JUL-22 7QZP 0 JRNL AUTH C.CIANI,A.PEREZ-RAFOLS,I.BONOMO,M.MICAELLI,A.ESPOSITO, JRNL AUTH 2 C.ZUCAL,R.BELLI,V.G.D'AGOSTINO,I.BIANCONI,V.CALDERONE, JRNL AUTH 3 L.CEROFOLINI,O.MASSIDDA,M.B.WHALEN,M.FRAGAI,A.PROVENZANI JRNL TITL IDENTIFICATION AND CHARACTERIZATION OF AN RRM-CONTAINING, JRNL TITL 2 RNA BINDING PROTEIN IN ACINETOBACTER BAUMANNII . JRNL REF BIOMOLECULES V. 12 2022 JRNL REFN ESSN 2218-273X JRNL PMID 35883478 JRNL DOI 10.3390/BIOM12070922 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20RC1_4392 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.87 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 87.1 REMARK 3 NUMBER OF REFLECTIONS : 8214 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.213 REMARK 3 R VALUE (WORKING SET) : 0.212 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 411 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 18.8700 - 2.3900 1.00 3035 160 0.2006 0.2209 REMARK 3 2 2.3800 - 1.8900 0.97 2879 152 0.2298 0.2472 REMARK 3 3 1.8900 - 1.6500 0.64 1889 99 0.2679 0.2685 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) : 0.240 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.380 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.75 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): 31.3397 25.2325 -7.0562 REMARK 3 T TENSOR REMARK 3 T11: 0.1900 T22: 0.2232 REMARK 3 T33: 0.1877 T12: -0.0321 REMARK 3 T13: -0.0155 T23: -0.0026 REMARK 3 L TENSOR REMARK 3 L11: 4.1903 L22: 4.0087 REMARK 3 L33: 1.6959 L12: 0.3817 REMARK 3 L13: -0.3457 L23: -0.2780 REMARK 3 S TENSOR REMARK 3 S11: 0.0597 S12: -0.2113 S13: 0.0735 REMARK 3 S21: 0.2780 S22: -0.0650 S23: -0.3950 REMARK 3 S31: -0.1050 S32: 0.3988 S33: 0.0160 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 7QZP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-JAN-22. REMARK 100 THE DEPOSITION ID IS D_1292118887. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-MAR-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : SEALED TUBE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : BRUKER D8 QUEST REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : BRUKER PHOTON III REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8220 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 19.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.1 REMARK 200 DATA REDUNDANCY : 11.70 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07900 REMARK 200 FOR THE DATA SET : 18.7600 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.75 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.85000 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: MOLREP REMARK 200 STARTING MODEL: 1FXL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 31.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.79 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE TRIHYDRATE, 3 M REMARK 280 SODIUM CHLORIDE, PH 4.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,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 34.78000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 34.78000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 16.23000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 34.78000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 8.11500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 34.78000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 24.34500 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 34.78000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.78000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 16.23000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 34.78000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 24.34500 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 34.78000 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 8.11500 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 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 HIS A 0 REMARK 465 MET A 1 REMARK 465 ILE A 2 REMARK 465 LEU A 3 REMARK 465 LYS A 4 REMARK 465 CYS A 5 REMARK 465 ILE A 6 REMARK 465 LEU A 7 REMARK 465 ALA A 8 REMARK 465 PHE A 9 REMARK 465 LEU A 10 REMARK 465 LEU A 11 REMARK 465 MET A 12 REMARK 465 VAL A 13 REMARK 465 ASN A 14 REMARK 465 GLU A 15 REMARK 465 GLY A 16 REMARK 465 TRP A 17 REMARK 465 LYS A 18 REMARK 465 GLU A 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 OD2 ASP A 27 OG SER A 29 2.09 REMARK 500 NH2 ARG A 91 O HOH A 101 2.10 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 LYS A 58 62.31 -62.29 REMARK 500 SER A 59 -27.83 172.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FXL RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUD AND AU-RICH ELEMENT OF THE C-FOS RNA DBREF1 7QZP A 12 97 UNP A0A828SWT5_ACIBA DBREF2 7QZP A A0A828SWT5 1 86 SEQADV 7QZP HIS A 0 UNP A0A828SWT EXPRESSION TAG SEQADV 7QZP MET A 1 UNP A0A828SWT EXPRESSION TAG SEQADV 7QZP ILE A 2 UNP A0A828SWT EXPRESSION TAG SEQADV 7QZP LEU A 3 UNP A0A828SWT EXPRESSION TAG SEQADV 7QZP LYS A 4 UNP A0A828SWT EXPRESSION TAG SEQADV 7QZP CYS A 5 UNP A0A828SWT EXPRESSION TAG SEQADV 7QZP ILE A 6 UNP A0A828SWT EXPRESSION TAG SEQADV 7QZP LEU A 7 UNP A0A828SWT EXPRESSION TAG SEQADV 7QZP ALA A 8 UNP A0A828SWT EXPRESSION TAG SEQADV 7QZP PHE A 9 UNP A0A828SWT EXPRESSION TAG SEQADV 7QZP LEU A 10 UNP A0A828SWT EXPRESSION TAG SEQADV 7QZP LEU A 11 UNP A0A828SWT EXPRESSION TAG SEQRES 1 A 98 HIS MET ILE LEU LYS CYS ILE LEU ALA PHE LEU LEU MET SEQRES 2 A 98 VAL ASN GLU GLY TRP LYS MET LYS ILE LEU VAL ARG ASN SEQRES 3 A 98 LEU ASP ARG SER VAL THR GLU ALA GLU VAL LEU GLU LEU SEQRES 4 A 98 PHE LYS ALA TYR GLY LYS VAL GLU SER CYS VAL VAL VAL SEQRES 5 A 98 THR ASP LYS ASP THR GLY LYS SER LYS GLY PHE GLY PHE SEQRES 6 A 98 VAL GLU MET PRO ASN PRO ARG GLU ALA ILE LYS ALA ILE SEQRES 7 A 98 LYS GLY LEU ASN THR LEU LYS VAL LYS GLY TYR GLY ILE SEQRES 8 A 98 ARG VAL LYS ALA ALA GLU GLU FORMUL 2 HOH *45(H2 O) HELIX 1 AA1 THR A 31 ALA A 41 1 11 HELIX 2 AA2 ASN A 69 ASN A 81 1 13 SHEET 1 AA1 4 SER A 47 VAL A 51 0 SHEET 2 AA1 4 GLY A 61 GLU A 66 -1 O PHE A 62 N VAL A 51 SHEET 3 AA1 4 LYS A 20 LEU A 26 -1 N ILE A 21 O VAL A 65 SHEET 4 AA1 4 ARG A 91 ALA A 94 -1 O LYS A 93 N LEU A 22 SHEET 1 AA2 2 LYS A 84 VAL A 85 0 SHEET 2 AA2 2 TYR A 88 GLY A 89 -1 O TYR A 88 N VAL A 85 CRYST1 69.560 69.560 32.460 90.00 90.00 90.00 I 41 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 0.014376 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014376 0.000000 0.00000 SCALE3 0.000000 0.000000 0.030807 0.00000