HEADER MEMBRANE PROTEIN 25-AUG-11 3VHJ TITLE CRYSTAL STRUCTURE OF THE CYTOPLASMIC DOMAIN OF BFPC COMPND MOL_ID: 1; COMPND 2 MOLECULE: BFPC; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: N TERMINAL DOMAIN, UNP RESIDUES 1-165; COMPND 5 SYNONYM: PUTATIVE UNCHARACTERIZED PROTEIN BFPC; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: BFPC, MAR006; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: B834; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PRPA302 KEYWDS TYPE IV PILUS BIOGENESIS, BFPD, MEMBRANE, MEMBRANE PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.YAMAGATA,J.A.TAINER,M.S.DONNENBERG REVDAT 2 30-OCT-24 3VHJ 1 SEQADV LINK REVDAT 1 23-MAY-12 3VHJ 0 JRNL AUTH A.YAMAGATA,E.MILGOTINA,K.SCANLON,L.CRAIG,J.A.TAINER, JRNL AUTH 2 M.S.DONNENBERG JRNL TITL STRUCTURE OF AN ESSENTIAL TYPE IV PILUS BIOGENESIS PROTEIN JRNL TITL 2 PROVIDES INSIGHTS INTO PILUS AND TYPE II SECRETION SYSTEMS JRNL REF J.MOL.BIOL. V. 419 110 2012 JRNL REFN ISSN 0022-2836 JRNL PMID 22387466 JRNL DOI 10.1016/J.JMB.2012.02.041 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.2 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 164402.400 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.0 REMARK 3 NUMBER OF REFLECTIONS : 16509 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 810 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.80 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2457 REMARK 3 BIN R VALUE (WORKING SET) : 0.2370 REMARK 3 BIN FREE R VALUE : 0.2620 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 115 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1265 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 119 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.14 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.08700 REMARK 3 B22 (A**2) : -8.21200 REMARK 3 B33 (A**2) : 7.12500 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.22 REMARK 3 ESD FROM SIGMAA (A) : 0.12 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.24 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.16 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 24.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.670 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.250 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.929 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.206 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.292 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.45 REMARK 3 BSOL : 63.74 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : WATER.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3VHJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-SEP-11. REMARK 100 THE DEPOSITION ID IS D_1000095051. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791, 0.9793, 0.9639 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16999 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.57 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.0M AMMONIUM SULFATE, PH 5.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 21.41850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.13550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.91800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.13550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.41850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.91800 REMARK 290 SMTRY3 4 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 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 MSE A 1 REMARK 465 VAL A 2 REMARK 465 GLY A 165 REMARK 465 SER A 166 REMARK 465 HIS A 167 REMARK 465 HIS A 168 REMARK 465 HIS A 169 REMARK 465 HIS A 170 REMARK 465 HIS A 171 REMARK 465 HIS A 172 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 27 -131.74 56.32 REMARK 500 ASN A 93 50.07 -112.88 REMARK 500 ASP A 110 87.49 -153.70 REMARK 500 VAL A 127 -61.73 -103.97 REMARK 500 REMARK 500 REMARK: NULL DBREF 3VHJ A 1 165 UNP Q57029 Q57029_ECOLX 1 165 SEQADV 3VHJ VAL A 2 UNP Q57029 ILE 2 ENGINEERED MUTATION SEQADV 3VHJ SER A 166 UNP Q57029 EXPRESSION TAG SEQADV 3VHJ HIS A 167 UNP Q57029 EXPRESSION TAG SEQADV 3VHJ HIS A 168 UNP Q57029 EXPRESSION TAG SEQADV 3VHJ HIS A 169 UNP Q57029 EXPRESSION TAG SEQADV 3VHJ HIS A 170 UNP Q57029 EXPRESSION TAG SEQADV 3VHJ HIS A 171 UNP Q57029 EXPRESSION TAG SEQADV 3VHJ HIS A 172 UNP Q57029 EXPRESSION TAG SEQRES 1 A 172 MSE VAL LYS ASN ASN LEU GLY VAL ALA VAL ILE GLY SER SEQRES 2 A 172 LYS GLN TYR ALA VAL ASN LEU LEU TRP GLY SER SER GLN SEQRES 3 A 172 ASP THR GLU THR THR ASN GLN ALA LEU ASN LYS SER LEU SEQRES 4 A 172 THR LEU MSE SER SER LYS LEU TYR SER VAL ILE GLY ARG SEQRES 5 A 172 PHE GLN GLY GLU GLN PHE ALA VAL GLY ASP LYS ASN ILE SEQRES 6 A 172 GLY HIS LYS ARG GLY GLN VAL THR LEU LEU SER ALA ILE SEQRES 7 A 172 ASP PHE ASP GLY SER SER PHE CYS GLY LEU PHE PRO ALA SEQRES 8 A 172 ASP ASN GLU LEU TRP LEU VAL ILE GLY VAL ASP LYS ASP SEQRES 9 A 172 GLY MSE VAL HIS PHE ASP LYS SER PHE HIS SER LYS ASP SEQRES 10 A 172 ASP ALA LYS LYS PHE PHE PHE ASP HIS VAL ALA TYR GLY SEQRES 11 A 172 TYR PRO TRP ASP ARG THR TYR SER PRO SER ASP VAL GLY SEQRES 12 A 172 VAL GLY GLU SER ARG SER ILE SER GLU LEU SER LEU ILE SEQRES 13 A 172 LYS GLY LYS LYS LEU LYS GLU LYS GLY SER HIS HIS HIS SEQRES 14 A 172 HIS HIS HIS MODRES 3VHJ MSE A 42 MET SELENOMETHIONINE MODRES 3VHJ MSE A 106 MET SELENOMETHIONINE HET MSE A 42 8 HET MSE A 106 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 HOH *119(H2 O) HELIX 1 1 THR A 30 SER A 43 1 14 HELIX 2 2 ASP A 62 GLY A 66 5 5 HELIX 3 3 LEU A 74 ILE A 78 1 5 HELIX 4 4 SER A 115 VAL A 127 1 13 HELIX 5 5 SER A 149 LEU A 153 5 5 SHEET 1 A 3 VAL A 8 ILE A 11 0 SHEET 2 A 3 LYS A 14 ALA A 17 -1 O TYR A 16 N ALA A 9 SHEET 3 A 3 VAL A 72 THR A 73 1 O VAL A 72 N ALA A 17 SHEET 1 B 4 LEU A 21 GLY A 23 0 SHEET 2 B 4 GLY A 55 VAL A 60 -1 O PHE A 58 N GLY A 23 SHEET 3 B 4 LEU A 46 ARG A 52 -1 N ILE A 50 O GLN A 57 SHEET 4 B 4 LYS A 162 GLU A 163 -1 O LYS A 162 N TYR A 47 SHEET 1 C 4 VAL A 107 PHE A 113 0 SHEET 2 C 4 TRP A 96 VAL A 101 -1 N TRP A 96 O PHE A 113 SHEET 3 C 4 PHE A 85 PRO A 90 -1 N PHE A 89 O LEU A 97 SHEET 4 C 4 ARG A 135 TYR A 137 1 O TYR A 137 N LEU A 88 LINK C LEU A 41 N MSE A 42 1555 1555 1.33 LINK C MSE A 42 N SER A 43 1555 1555 1.33 LINK C GLY A 105 N MSE A 106 1555 1555 1.33 LINK C MSE A 106 N VAL A 107 1555 1555 1.33 CRYST1 42.837 61.836 78.271 90.00 90.00 90.00 P 21 21 21 4 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 0.023344 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016172 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012776 0.00000