HEADER RNA BINDING PROTEIN 11-FEB-11 2Y90 TITLE CRYSTAL STRUCTURE OF HFQ RIBOREGULATOR FROM E. COLI (P6 SPACE GROUP) COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN HFQ; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: HF-1, HOST FACTOR-I PROTEIN, HF-I; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) STAR; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PETM11 KEYWDS RNA-BINDING PROTEIN, SM-LIKE, RNA CHAPERONE, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.BASQUIN,C.SAUTER REVDAT 4 20-DEC-23 2Y90 1 REMARK REVDAT 3 15-MAY-19 2Y90 1 REMARK REVDAT 2 08-MAY-19 2Y90 1 REMARK REVDAT 1 21-DEC-11 2Y90 0 JRNL AUTH L.BONNEFOND,P.SCHELLENBERGER,J.BASQUIN,G.DEMANGEAT, JRNL AUTH 2 C.RITZENTHALER,R.CHENEVERT,C.BALG,M.FRUGIER, JRNL AUTH 3 J.RUDINGER-THIRION,R.GIEGE,L.LORBER,C.SAUTER JRNL TITL EXPLOITING PROTEIN ENGINEERING AND CRYSTAL POLYMORPHISM FOR JRNL TITL 2 SUCCESSFUL X-RAY STRUCTURE DETERMINATION JRNL REF CRYST. GROWTH DES. V. 11 4334 2011 JRNL REFN ISSN 1528-7483 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.SAUTER,J.BASQUIN,D.SUCK REMARK 1 TITL SM-LIKE PROTEINS IN EUBACTERIA: THE CRYSTAL STRUCTURE OF THE REMARK 1 TITL 2 HFQ PROTEIN FROM ESCHERICHIA COLI. REMARK 1 REF NUCLEIC ACIDS RES. V. 31 4091 2003 REMARK 1 REFN ISSN 0305-1048 REMARK 1 PMID 12853626 REMARK 2 REMARK 2 RESOLUTION. 2.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) 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) : 2.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 53.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 2979 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.800 REMARK 3 FREE R VALUE TEST SET COUNT : 232 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 24.9582 - 2.2608 0.91 2713 232 0.1832 0.2262 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.33 REMARK 3 B_SOL : 25.04 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.430 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.66400 REMARK 3 B22 (A**2) : -2.66400 REMARK 3 B33 (A**2) : 5.32790 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: 0.3130 REMARK 3 OPERATOR: H,-H-K,-L REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.007 519 REMARK 3 ANGLE : 1.164 704 REMARK 3 CHIRALITY : 0.077 85 REMARK 3 PLANARITY : 0.005 89 REMARK 3 DIHEDRAL : 14.250 197 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: THE FULL LENGTH HFQ PROTEIN REMARK 3 CRYSTALLIZED AFTER PROTEOLYTIC DEGRADATION AS INDICATED BY THE REMARK 3 CRYSTAL SOLVENT SOLVENT CONTENT (SEE REF1). THE RESULTING REMARK 3 MONOMER LACKS RESIDUES 70-102. THE LATTER ARE EITHER DISORDERED REMARK 3 IN THE CRYSTAL OR ABSENT DUE TO BY PROTEOLYSIS. REMARK 4 REMARK 4 2Y90 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-FEB-11. REMARK 100 THE DEPOSITION ID IS D_1290047347. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL 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 : ESRF REMARK 200 BEAMLINE : ID14-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 2979 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.250 REMARK 200 RESOLUTION RANGE LOW (A) : 54.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : 0.06000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.30 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.17000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1HK9 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS WERE OBTAINED BY VAPOR REMARK 280 DIFFUSION IN 2UL HANGING DROPS AT 20C. THE RESERVOIR CONTAINED REMARK 280 1.6 M AMMONIUM SULFATE, 0.1 M TRIS-HCL PH 8.0., VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 6 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z REMARK 290 6555 X-Y,X,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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 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 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8520 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18490 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -71.1 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 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 -0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 3 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 5 -0.500000 -0.866025 0.000000 0.00000 REMARK 350 BIOMT2 5 0.866025 -0.500000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 6 0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 6 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 -1 REMARK 465 ALA A 0 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 LYS A 3 REMARK 465 GLY A 4 REMARK 465 GLN A 5 REMARK 465 HIS A 70 REMARK 465 HIS A 71 REMARK 465 SER A 72 REMARK 465 ASN A 73 REMARK 465 ASN A 74 REMARK 465 ALA A 75 REMARK 465 GLY A 76 REMARK 465 GLY A 77 REMARK 465 GLY A 78 REMARK 465 THR A 79 REMARK 465 SER A 80 REMARK 465 SER A 81 REMARK 465 ASN A 82 REMARK 465 TYR A 83 REMARK 465 HIS A 84 REMARK 465 HIS A 85 REMARK 465 GLY A 86 REMARK 465 SER A 87 REMARK 465 SER A 88 REMARK 465 ALA A 89 REMARK 465 GLN A 90 REMARK 465 ASN A 91 REMARK 465 THR A 92 REMARK 465 SER A 93 REMARK 465 ALA A 94 REMARK 465 GLN A 95 REMARK 465 GLN A 96 REMARK 465 ASP A 97 REMARK 465 SER A 98 REMARK 465 GLU A 99 REMARK 465 GLU A 100 REMARK 465 THR A 101 REMARK 465 GLU A 102 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 48 -117.47 -128.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1M7C RELATED DB: PDB REMARK 900 STUCTURAL MODEL OF E. COLI HFQ REMARK 900 RELATED ID: 1OOU RELATED DB: PDB REMARK 900 STRUCTURAL MODELLING OF E. COLI HFQ REMARK 900 RELATED ID: 1HK9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HFQ PROTEIN FROM ESCHERICHIA COLI REMARK 900 RELATED ID: 1OOV RELATED DB: PDB REMARK 900 COMPLEX OF E. COLI HFQ WITH A RA7 OLIGONUCLEOTIDE REMARK 999 REMARK 999 SEQUENCE REMARK 999 TWO AMINO ACIDS ADDED IN N-TERMINUS AND PROBABLE REMARK 999 PROTEOLYTIC DEGRADATION AFTER RESIDUE 69. RESIDUES 70-102 ARE REMARK 999 EITHER DISORDERED IN THE CRYSTAL OR ABSENT DUE TO PROTEOLYSIS. DBREF 2Y90 A 1 102 UNP P0A6X3 HFQ_ECOLI 1 102 SEQADV 2Y90 GLY A -1 UNP P0A6X3 EXPRESSION TAG SEQADV 2Y90 ALA A 0 UNP P0A6X3 EXPRESSION TAG SEQRES 1 A 104 GLY ALA MET ALA LYS GLY GLN SER LEU GLN ASP PRO PHE SEQRES 2 A 104 LEU ASN ALA LEU ARG ARG GLU ARG VAL PRO VAL SER ILE SEQRES 3 A 104 TYR LEU VAL ASN GLY ILE LYS LEU GLN GLY GLN ILE GLU SEQRES 4 A 104 SER PHE ASP GLN PHE VAL ILE LEU LEU LYS ASN THR VAL SEQRES 5 A 104 SER GLN MET VAL TYR LYS HIS ALA ILE SER THR VAL VAL SEQRES 6 A 104 PRO SER ARG PRO VAL SER HIS HIS SER ASN ASN ALA GLY SEQRES 7 A 104 GLY GLY THR SER SER ASN TYR HIS HIS GLY SER SER ALA SEQRES 8 A 104 GLN ASN THR SER ALA GLN GLN ASP SER GLU GLU THR GLU FORMUL 2 HOH *11(H2 O) HELIX 1 1 LEU A 7 GLU A 18 1 12 SHEET 1 AA 5 SER A 51 TYR A 55 0 SHEET 2 AA 5 VAL A 43 LYS A 47 -1 O ILE A 44 N VAL A 54 SHEET 3 AA 5 LYS A 31 PHE A 39 -1 O GLN A 35 N LYS A 47 SHEET 4 AA 5 VAL A 22 LEU A 26 -1 O VAL A 22 N GLY A 34 SHEET 5 AA 5 ILE A 59 PRO A 64 -1 N SER A 60 O TYR A 25 CRYST1 61.500 61.500 28.250 90.00 90.00 120.00 P 6 6 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 0.016260 0.009388 0.000000 0.00000 SCALE2 0.000000 0.018776 0.000000 0.00000 SCALE3 0.000000 0.000000 0.035398 0.00000