HEADER CELL ADHESION 08-OCT-08 3ETW TITLE CRYSTAL STRUCTURE OF BACTERIAL ADHESIN FADA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADHESIN A; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FUSOBACTERIUM NUCLEATUM; SOURCE 3 ORGANISM_TAXID: 851; SOURCE 4 GENE: FADA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET21(B) KEYWDS ANTIPARALLEL HELIX-LOOP-HELIX, LEUCINE CHAIN, CELL ADHESIN, CELL KEYWDS 2 ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR S.NITHIANANTHAM,M.XU,N.WU,M.SHOHAM,Y.W.HAN REVDAT 4 27-DEC-23 3ETW 1 REMARK SEQADV REVDAT 3 25-OCT-17 3ETW 1 REMARK REVDAT 2 24-FEB-09 3ETW 1 JRNL REVDAT 1 02-DEC-08 3ETW 0 SPRSDE 02-DEC-08 3ETW 2AVR JRNL AUTH S.NITHIANANTHAM,M.XU,M.YAMADA,A.IKEGAMI,M.SHOHAM,Y.W.HAN JRNL TITL CRYSTAL STRUCTURE OF FADA ADHESIN FROM FUSOBACTERIUM JRNL TITL 2 NUCLEATUM REVEALS A NOVEL OLIGOMERIZATION MOTIF, THE LEUCINE JRNL TITL 3 CHAIN. JRNL REF J.BIOL.CHEM. V. 284 3865 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 18996848 JRNL DOI 10.1074/JBC.M805503200 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH S.NITHIANANTHAM,M.XU,N.WU,Y.W.HAN,M.SHOHAM REMARK 1 TITL CRYSTALLIZATION AND PRELIMINARY X-RAY DATA OF THE FADA REMARK 1 TITL 2 ADHESIN FROM FUSOBACTERIUM NUCLEATUM REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 62 1215 2006 REMARK 1 REFN ESSN 1744-3091 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 15819 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) : 0.225 REMARK 3 FREE R VALUE : 0.254 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.200 REMARK 3 FREE R VALUE TEST SET COUNT : 1563 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.02 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3380 REMARK 3 BIN FREE R VALUE : 0.3120 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 28 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 873 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 162 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.80 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.11 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 12.05500 REMARK 3 B22 (A**2) : 12.05500 REMARK 3 B33 (A**2) : -24.11100 REMARK 3 B12 (A**2) : 2.45900 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) : 0.27 REMARK 3 ESD FROM SIGMAA (A) : 0.35 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) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.39 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 BOND ANGLES (DEGREES) : 1.140 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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) : 1.985 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.775 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 3.687 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.625 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 58.71 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 : CNS_TOPPAR:PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : SCN.PARAM REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : CNS_TOPPAR:PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : SCN.TOP REMARK 3 TOPOLOGY FILE 3 : CNS_TOPPAR:WATER.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3ETW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-OCT-08. REMARK 100 THE DEPOSITION ID IS D_1000049761. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-AUG-05; 14-JAN-05 REMARK 200 TEMPERATURE (KELVIN) : 100; 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : APS; ALS REMARK 200 BEAMLINE : 19-BM; 4.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0332; 0.92871, 0.91999, REMARK 200 0.91979 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL (SI-111); DOUBLE REMARK 200 CRYSTAL (SI-111) REMARK 200 OPTICS : 3 X 3 MOSAIC; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : SBC-2; NOIR-1 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15871 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 29.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 6.600 REMARK 200 R MERGE (I) : 0.04500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 63.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.90 REMARK 200 R MERGE FOR SHELL (I) : 0.27500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.813 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: SOLVE 2.06 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 73.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M SODIUM CITRATE PH 5.6, 0.5M REMARK 280 POTASSIUM THIOCYANATE, 5% DIOXANE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 61 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+5/6 REMARK 290 6555 X-Y,X,Z+1/6 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 42.12467 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 84.24933 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 63.18700 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 105.31167 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 21.06233 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 ALA A 1 REMARK 465 THR A 2 REMARK 465 ASP A 3 REMARK 465 GLU A 113 REMARK 465 HIS A 114 REMARK 465 HIS A 115 REMARK 465 HIS A 116 REMARK 465 HIS A 117 REMARK 465 HIS A 118 REMARK 465 HIS A 119 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 ALA A 64 -19.15 -48.40 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 SCN A 130 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ETX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BACTERIAL ADHESIN FADA L14A MUTANT REMARK 900 RELATED ID: 3ETY RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BACTERIAL ADHESIN FADA L14A MUTANT REMARK 900 RELATED ID: 3ETZ RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF BACTERIAL ADHESIN FADA L76A MUTANT DBREF 3ETW A 1 111 UNP Q5I6B0 Q5I6B0_FUSNU 19 129 SEQADV 3ETW LEU A 112 UNP Q5I6B0 EXPRESSION TAG SEQADV 3ETW GLU A 113 UNP Q5I6B0 EXPRESSION TAG SEQADV 3ETW HIS A 114 UNP Q5I6B0 EXPRESSION TAG SEQADV 3ETW HIS A 115 UNP Q5I6B0 EXPRESSION TAG SEQADV 3ETW HIS A 116 UNP Q5I6B0 EXPRESSION TAG SEQADV 3ETW HIS A 117 UNP Q5I6B0 EXPRESSION TAG SEQADV 3ETW HIS A 118 UNP Q5I6B0 EXPRESSION TAG SEQADV 3ETW HIS A 119 UNP Q5I6B0 EXPRESSION TAG SEQRES 1 A 119 ALA THR ASP ALA ALA SER LEU VAL GLY GLU LEU GLN ALA SEQRES 2 A 119 LEU ASP ALA GLU TYR GLN ASN LEU ALA ASN GLN GLU GLU SEQRES 3 A 119 ALA ARG PHE ASN GLU GLU ARG ALA GLN ALA ASP ALA ALA SEQRES 4 A 119 ARG GLN ALA LEU ALA GLN ASN GLU GLN VAL TYR ASN GLU SEQRES 5 A 119 LEU SER GLN ARG ALA GLN ARG LEU GLN ALA GLU ALA ASN SEQRES 6 A 119 THR ARG PHE TYR LYS SER GLN TYR GLN GLU LEU ALA SER SEQRES 7 A 119 LYS TYR GLU ASP ALA LEU LYS LYS LEU GLU ALA GLU MET SEQRES 8 A 119 GLU GLN GLN LYS ALA VAL ILE SER ASP PHE GLU LYS ILE SEQRES 9 A 119 GLN ALA LEU ARG ALA GLY ASN LEU GLU HIS HIS HIS HIS SEQRES 10 A 119 HIS HIS HET SCN A 130 3 HETNAM SCN THIOCYANATE ION FORMUL 2 SCN C N S 1- FORMUL 3 HOH *162(H2 O) HELIX 1 1 ALA A 4 ALA A 64 1 61 HELIX 2 2 TYR A 69 GLY A 110 1 42 SITE 1 AC1 5 PHE A 29 ARG A 33 GLU A 75 SER A 78 SITE 2 AC1 5 GLN A 105 CRYST1 59.340 59.340 126.374 90.00 90.00 120.00 P 61 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 0.016852 0.009730 0.000000 0.00000 SCALE2 0.000000 0.019459 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007913 0.00000