HEADER RNA BINDING PROTEIN 21-MAR-13 4JRK TITLE CRYSTAL STRUCTURE OF ESCHERICHIA COLI HFQ SURFACE MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN HFQ; COMPND 3 CHAIN: A, B, C; COMPND 4 FRAGMENT: UNP RESIDUES 2-69; COMPND 5 SYNONYM: HF-1, HOST FACTOR-I PROTEIN, HF-I; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: HFQ, B4172, JW4130 KEYWDS RIBOREGULATOR, POST-TRANSCRIPTIONAL REGULATOR, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.E.ROBINSON,J.ORANS REVDAT 4 28-FEB-24 4JRK 1 SEQADV REVDAT 3 15-NOV-17 4JRK 1 REMARK REVDAT 2 12-MAR-14 4JRK 1 JRNL REVDAT 1 11-DEC-13 4JRK 0 JRNL AUTH K.E.ROBINSON,J.ORANS,A.R.KOVACH,T.M.LINK,R.G.BRENNAN JRNL TITL MAPPING HFQ-RNA INTERACTION SURFACES USING TRYPTOPHAN JRNL TITL 2 FLUORESCENCE QUENCHING. JRNL REF NUCLEIC ACIDS RES. V. 42 2736 2014 JRNL REFN ISSN 0305-1048 JRNL PMID 24288369 JRNL DOI 10.1093/NAR/GKT1171 REMARK 2 REMARK 2 RESOLUTION. 1.89 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8_1069) 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 : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.89 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.9 REMARK 3 NUMBER OF REFLECTIONS : 15335 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 765 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 24.4318 - 3.2367 0.97 3057 148 0.1642 0.2002 REMARK 3 2 3.2367 - 2.5700 1.00 2960 145 0.1879 0.2113 REMARK 3 3 2.5700 - 2.2454 1.00 2925 171 0.1820 0.2419 REMARK 3 4 2.2454 - 2.0402 0.99 2899 157 0.1789 0.2166 REMARK 3 5 2.0402 - 1.8940 0.94 2729 144 0.1968 0.2424 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.760 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 : 0.007 1667 REMARK 3 ANGLE : 1.213 2285 REMARK 3 CHIRALITY : 0.081 271 REMARK 3 PLANARITY : 0.004 291 REMARK 3 DIHEDRAL : 14.582 662 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 4JRK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-MAR-13. REMARK 100 THE DEPOSITION ID IS D_1000078414. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15335 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.894 REMARK 200 RESOLUTION RANGE LOW (A) : 24.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06800 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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) : 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: CCP4 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.92 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.15450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.55300 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 33.15450 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 42.55300 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 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 33.15450 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 42.55300 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 C 107 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 108 LIES ON A SPECIAL POSITION. REMARK 375 HOH C 110 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 ALA A 2 REMARK 465 LYS A 3 REMARK 465 VAL A 68 REMARK 465 SER A 69 REMARK 465 VAL B 68 REMARK 465 SER B 69 REMARK 465 ALA C 2 REMARK 465 LYS C 3 REMARK 465 GLY C 4 REMARK 465 PRO C 67 REMARK 465 VAL C 68 REMARK 465 SER C 69 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 A 114 O HOH A 147 2.19 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 170 O HOH C 127 2555 2.18 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 GLN A 5 -26.00 160.84 REMARK 500 GLN A 5 -24.57 160.32 REMARK 500 SER A 6 130.77 -34.79 REMARK 500 ASP A 40 -154.37 -137.97 REMARK 500 ASN A 48 -114.93 -131.63 REMARK 500 ASP B 40 -153.73 -136.53 REMARK 500 ASN B 48 -109.23 -126.95 REMARK 500 ASN B 48 -113.06 -123.87 REMARK 500 ASP C 40 -155.18 -141.00 REMARK 500 ASN C 48 -115.70 -128.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4JLI RELATED DB: PDB REMARK 900 RELATED ID: 4JRI RELATED DB: PDB DBREF 4JRK A 2 69 UNP P0A6X3 P0A6X3_ECO1E 2 69 DBREF 4JRK B 2 69 UNP P0A6X3 P0A6X3_ECO1E 2 69 DBREF 4JRK C 2 69 UNP P0A6X3 P0A6X3_ECO1E 2 69 SEQADV 4JRK TRP A 11 UNP P0A6X3 PHE 11 ENGINEERED MUTATION SEQADV 4JRK TRP B 11 UNP P0A6X3 PHE 11 ENGINEERED MUTATION SEQADV 4JRK TRP C 11 UNP P0A6X3 PHE 11 ENGINEERED MUTATION SEQRES 1 A 68 ALA LYS GLY GLN SER LEU GLN ASP PRO TRP LEU ASN ALA SEQRES 2 A 68 LEU ARG ARG GLU ARG VAL PRO VAL SER ILE TYR LEU VAL SEQRES 3 A 68 ASN GLY ILE LYS LEU GLN GLY GLN ILE GLU SER PHE ASP SEQRES 4 A 68 GLN PHE VAL ILE LEU LEU LYS ASN THR VAL SER GLN MET SEQRES 5 A 68 VAL TYR LYS HIS ALA ILE SER THR VAL VAL PRO SER ARG SEQRES 6 A 68 PRO VAL SER SEQRES 1 B 68 ALA LYS GLY GLN SER LEU GLN ASP PRO TRP LEU ASN ALA SEQRES 2 B 68 LEU ARG ARG GLU ARG VAL PRO VAL SER ILE TYR LEU VAL SEQRES 3 B 68 ASN GLY ILE LYS LEU GLN GLY GLN ILE GLU SER PHE ASP SEQRES 4 B 68 GLN PHE VAL ILE LEU LEU LYS ASN THR VAL SER GLN MET SEQRES 5 B 68 VAL TYR LYS HIS ALA ILE SER THR VAL VAL PRO SER ARG SEQRES 6 B 68 PRO VAL SER SEQRES 1 C 68 ALA LYS GLY GLN SER LEU GLN ASP PRO TRP LEU ASN ALA SEQRES 2 C 68 LEU ARG ARG GLU ARG VAL PRO VAL SER ILE TYR LEU VAL SEQRES 3 C 68 ASN GLY ILE LYS LEU GLN GLY GLN ILE GLU SER PHE ASP SEQRES 4 C 68 GLN PHE VAL ILE LEU LEU LYS ASN THR VAL SER GLN MET SEQRES 5 C 68 VAL TYR LYS HIS ALA ILE SER THR VAL VAL PRO SER ARG SEQRES 6 C 68 PRO VAL SER FORMUL 4 HOH *192(H2 O) HELIX 1 1 LEU A 7 GLU A 18 1 12 HELIX 2 2 LEU B 7 ARG B 19 1 13 HELIX 3 3 LEU C 7 GLU C 18 1 12 SHEET 1 A15 SER B 51 TYR B 55 0 SHEET 2 A15 VAL B 43 LYS B 47 -1 N ILE B 44 O VAL B 54 SHEET 3 A15 LYS B 31 PHE B 39 -1 N SER B 38 O LEU B 45 SHEET 4 A15 PRO B 21 LEU B 26 -1 N ILE B 24 O LEU B 32 SHEET 5 A15 ILE B 59 PRO B 64 -1 O SER B 60 N TYR B 25 SHEET 6 A15 SER A 51 TYR A 55 -1 N TYR A 55 O SER B 60 SHEET 7 A15 VAL A 43 LYS A 47 -1 N ILE A 44 O VAL A 54 SHEET 8 A15 LYS A 31 PHE A 39 -1 N GLN A 35 O LYS A 47 SHEET 9 A15 PRO A 21 LEU A 26 -1 N ILE A 24 O LEU A 32 SHEET 10 A15 ILE A 59 PRO A 64 -1 O VAL A 63 N SER A 23 SHEET 11 A15 SER C 51 TYR C 55 -1 O TYR C 55 N SER A 60 SHEET 12 A15 VAL C 43 LYS C 47 -1 N ILE C 44 O VAL C 54 SHEET 13 A15 LYS C 31 PHE C 39 -1 N GLU C 37 O LEU C 45 SHEET 14 A15 PRO C 21 LEU C 26 -1 N ILE C 24 O LEU C 32 SHEET 15 A15 ILE C 59 PRO C 64 -1 O SER C 60 N TYR C 25 CRYST1 33.410 66.309 85.106 90.00 90.00 90.00 P 2 21 21 12 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 0.029931 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015081 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011750 0.00000