HEADER MEMBRANE PROTEIN 17-OCT-15 5EB0 TITLE CRYSTAL FORM II OF YFIB BELONGING TO P41 COMPND MOL_ID: 1; COMPND 2 MOLECULE: YFIB; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 34-168; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PSEUDOMONAS AERUGINOSA PAO1; SOURCE 3 ORGANISM_TAXID: 208964; SOURCE 4 STRAIN: PAO1; SOURCE 5 GENE: YFIB, PA1119; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-CODONPLUS(DE3)-RIPL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PETDUET-1 KEYWDS OMPA/PAL-LIKE OUTER-MEMBRANE LIPOPROTEIN, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.XU,X.YANG,X.-A.YANG,L.ZHOU,T.-Z.LIU,Z.FAN,T.JIANG REVDAT 3 08-NOV-23 5EB0 1 REMARK REVDAT 2 15-JUN-16 5EB0 1 JRNL REVDAT 1 18-MAY-16 5EB0 0 JRNL AUTH M.XU,X.YANG,X.-A.YANG,L.ZHOU,T.-Z.LIU,Z.FAN,T.JIANG JRNL TITL STRUCTURAL INSIGHTS INTO THE REGULATORY MECHANISM OF THE JRNL TITL 2 PSEUDOMONAS AERUGINOSA YFIBNR SYSTEM JRNL REF PROTEIN CELL V. 7 403 2016 JRNL REFN ESSN 1674-8018 JRNL PMID 27113583 JRNL DOI 10.1007/S13238-016-0264-7 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 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) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.95 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.410 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 8009 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.265 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.610 REMARK 3 FREE R VALUE TEST SET COUNT : 369 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 46.9596 - 4.0353 0.93 2450 110 0.1880 0.2184 REMARK 3 2 4.0353 - 3.2031 0.99 2584 137 0.1853 0.2998 REMARK 3 3 3.2031 - 2.7983 1.00 2606 122 0.2094 0.2923 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) : 0.280 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.20 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.60 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 : 0.009 2114 REMARK 3 ANGLE : 1.132 2844 REMARK 3 CHIRALITY : 0.069 310 REMARK 3 PLANARITY : 0.004 386 REMARK 3 DIHEDRAL : 14.117 810 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 5EB0 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 22-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214477. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-SEP-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8105 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 11.10 REMARK 200 R MERGE (I) : 0.14600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.50 REMARK 200 R MERGE FOR SHELL (I) : 0.49700 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: PHENIX REMARK 200 STARTING MODEL: 3KHN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.95 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.86 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE MONOHYDRATE, 0.1 REMARK 280 M TRIS-HCL, 30%(W/V) POLYETHYLENE GLYCOL 4000, PH 8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 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 -Y,X,Z+1/4 REMARK 290 4555 Y,-X,Z+3/4 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 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 77.12100 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 38.56050 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 115.68150 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 O VAL B 137 O HOH B 301 2.18 REMARK 500 OE2 GLU A 45 O HOH A 201 2.19 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 ASP A 93 19.88 -142.15 REMARK 500 ASP A 102 -165.03 -78.66 REMARK 500 GLU A 127 5.14 -64.88 REMARK 500 THR A 151 139.96 -171.56 REMARK 500 ALA A 167 34.30 -84.03 REMARK 500 ARG B 51 -150.81 -120.64 REMARK 500 LEU B 69 -68.27 -100.35 REMARK 500 LYS B 94 149.12 -177.01 REMARK 500 ASP B 102 -164.19 -78.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 201 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5EAZ RELATED DB: PDB REMARK 900 RELATED ID: 5EB1 RELATED DB: PDB REMARK 900 RELATED ID: 5EB2 RELATED DB: PDB REMARK 900 RELATED ID: 5EB3 RELATED DB: PDB DBREF 5EB0 A 34 168 UNP Q9I4L6 Q9I4L6_PSEAE 34 168 DBREF 5EB0 B 34 168 UNP Q9I4L6 Q9I4L6_PSEAE 34 168 SEQRES 1 A 135 GLY LEU SER ALA GLU GLN ILE ALA VAL LEU GLN GLU GLN SEQRES 2 A 135 GLY PHE GLU LEU ARG ASP GLU GLY TRP GLU PHE GLY MET SEQRES 3 A 135 SER SER LYS VAL LEU PHE GLY ASN ASN LEU ASP ARG LEU SEQRES 4 A 135 ASN PRO ASP SER ARG ASN THR LEU THR LYS ILE ALA ARG SEQRES 5 A 135 ALA LEU LEU ALA VAL ASP ILE ASP LYS VAL ARG LEU GLU SEQRES 6 A 135 GLY HIS THR ASP ASN TYR GLY ASP GLU GLY TYR ASN GLN SEQRES 7 A 135 LYS LEU SER GLU ARG ARG ALA GLU SER VAL ALA ALA VAL SEQRES 8 A 135 PHE ARG GLU ALA GLY MET PRO ALA ALA ASN ILE GLU VAL SEQRES 9 A 135 ARG GLY LEU GLY MET SER LYS PRO VAL ALA ASP ASN LYS SEQRES 10 A 135 THR ARG ALA GLY ARG SER GLU ASN ARG ARG VAL ALA ILE SEQRES 11 A 135 ILE VAL PRO ALA GLU SEQRES 1 B 135 GLY LEU SER ALA GLU GLN ILE ALA VAL LEU GLN GLU GLN SEQRES 2 B 135 GLY PHE GLU LEU ARG ASP GLU GLY TRP GLU PHE GLY MET SEQRES 3 B 135 SER SER LYS VAL LEU PHE GLY ASN ASN LEU ASP ARG LEU SEQRES 4 B 135 ASN PRO ASP SER ARG ASN THR LEU THR LYS ILE ALA ARG SEQRES 5 B 135 ALA LEU LEU ALA VAL ASP ILE ASP LYS VAL ARG LEU GLU SEQRES 6 B 135 GLY HIS THR ASP ASN TYR GLY ASP GLU GLY TYR ASN GLN SEQRES 7 B 135 LYS LEU SER GLU ARG ARG ALA GLU SER VAL ALA ALA VAL SEQRES 8 B 135 PHE ARG GLU ALA GLY MET PRO ALA ALA ASN ILE GLU VAL SEQRES 9 B 135 ARG GLY LEU GLY MET SER LYS PRO VAL ALA ASP ASN LYS SEQRES 10 B 135 THR ARG ALA GLY ARG SER GLU ASN ARG ARG VAL ALA ILE SEQRES 11 B 135 ILE VAL PRO ALA GLU HET SO4 B 201 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 O4 S 2- FORMUL 4 HOH *52(H2 O) HELIX 1 AA1 SER A 36 GLY A 47 1 12 HELIX 2 AA2 SER A 61 PHE A 65 1 5 HELIX 3 AA3 ASN A 73 VAL A 90 1 18 HELIX 4 AA4 ASP A 106 GLU A 127 1 22 HELIX 5 AA5 PRO A 131 ALA A 133 5 3 HELIX 6 AA6 THR A 151 ARG A 159 1 9 HELIX 7 AA7 SER B 36 GLN B 46 1 11 HELIX 8 AA8 SER B 61 GLY B 66 1 6 HELIX 9 AA9 ASN B 73 ALA B 89 1 17 HELIX 10 AB1 ASP B 106 ALA B 128 1 23 HELIX 11 AB2 PRO B 131 ALA B 133 5 3 HELIX 12 AB3 THR B 151 ARG B 159 1 9 SHEET 1 AA1 5 GLU A 49 ARG A 51 0 SHEET 2 AA1 5 GLY A 54 SER A 60 -1 O GLY A 54 N ARG A 51 SHEET 3 AA1 5 ARG A 160 VAL A 165 -1 O VAL A 161 N MET A 59 SHEET 4 AA1 5 VAL A 95 HIS A 100 -1 N GLU A 98 O ALA A 162 SHEET 5 AA1 5 ILE A 135 GLY A 141 1 O GLU A 136 N LEU A 97 SHEET 1 AA2 5 GLU B 49 LEU B 50 0 SHEET 2 AA2 5 GLY B 54 SER B 60 -1 O GLU B 56 N GLU B 49 SHEET 3 AA2 5 ARG B 160 PRO B 166 -1 O ILE B 163 N PHE B 57 SHEET 4 AA2 5 VAL B 95 HIS B 100 -1 N ARG B 96 O ILE B 164 SHEET 5 AA2 5 ILE B 135 GLY B 139 1 O GLU B 136 N LEU B 97 SITE 1 AC1 4 ARG A 116 ASN B 67 HOH B 303 HOH B 304 CRYST1 46.953 46.953 154.242 90.00 90.00 90.00 P 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 0.021298 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021298 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006483 0.00000