HEADER CELL ADHESION 30-AUG-05 2AVR OBSLTE 02-DEC-08 2AVR 3ETW TITLE CRYSTAL STRUCTURE OF BACTERIAL ADHESIN FADA COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADHESION A; COMPND 3 CHAIN: X; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: FUSOBACTERIUM NUCLEATUM; SOURCE 3 ORGANISM_TAXID: 851; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21 KEYWDS ANTIPARALLEL HELIX-LOOP-HELIX, LEUCINE CHAIN, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR S.NITHIANANTHAM,M.XU,N.WU,M.SHOHAM,Y.W.HAN REVDAT 2 02-DEC-08 2AVR 1 OBSLTE REVDAT 1 03-OCT-06 2AVR 0 JRNL AUTH S.NITHIANANTHAM,M.XU,N.WU,M.SHOHAM,Y.W.HAN JRNL TITL CRYSTAL STRUCTURE OF BACTERIAL ADHESIN FADA JRNL REF TO BE PUBLISHED JRNL REFN REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.90 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) (%) : 86.2 REMARK 3 NUMBER OF REFLECTIONS : 17095 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.234 REMARK 3 FREE R VALUE : 0.257 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.600 REMARK 3 FREE R VALUE TEST SET COUNT : 1703 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.97 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.4535 REMARK 3 BIN FREE R VALUE : 0.3563 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 19 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 : 27 REMARK 3 SOLVENT ATOMS : 268 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 11.72700 REMARK 3 B22 (A**2) : 11.72700 REMARK 3 B33 (A**2) : -23.45300 REMARK 3 B12 (A**2) : 1.53600 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : NULL REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.603 ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.375 ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : 2.994 ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.589 ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 72.99 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 : TRIS.PARAM REMARK 3 PARAMETER FILE 3 : CNS_TOPPAR:WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : CIT.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : CNS_TOPPAR:PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : TRIS.TOP REMARK 3 TOPOLOGY FILE 3 : CNS_TOPPAR:WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : CIT.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2AVR COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 31-AUG-05. REMARK 100 THE RCSB ID CODE IS RCSB034370. 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 : GRAPHITE; GRAPHITE REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ENRAF-NONIUS CAD4; ENRAF- REMARK 200 NONIUS CAD4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17144 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 27.900 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.2 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : 0.04900 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) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 43.1 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : 0.39600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH; 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 (%): 73.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM CITRATE, GLYCEROL, SODIUM REMARK 280 THIOCYANATE, PH 5.6, VAPOR DIFFUSION, HANGING 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 42.15300 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 84.30600 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 63.22950 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 105.38250 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 21.07650 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 300 REMARK 300 REMARK: MONOMER 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 APPLY THE FOLLOWING TO CHAINS: X 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 X 1 REMARK 465 THR X 2 REMARK 465 ASP X 3 REMARK 465 GLU X 113 REMARK 465 HIS X 114 REMARK 465 HIS X 115 REMARK 465 HIS X 116 REMARK 465 HIS X 117 REMARK 465 HIS X 118 REMARK 465 HIS X 119 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH X5162 DISTANCE = 5.49 ANGSTROMS REMARK 525 HOH X5184 DISTANCE = 6.19 ANGSTROMS REMARK 525 HOH X5220 DISTANCE = 8.74 ANGSTROMS REMARK 525 HOH X5228 DISTANCE = 7.09 ANGSTROMS REMARK 525 HOH X5233 DISTANCE = 9.52 ANGSTROMS REMARK 525 HOH X5234 DISTANCE = 8.64 ANGSTROMS REMARK 525 HOH X5241 DISTANCE = 7.80 ANGSTROMS REMARK 525 HOH X5242 DISTANCE = 9.36 ANGSTROMS REMARK 525 HOH X5251 DISTANCE = 11.30 ANGSTROMS REMARK 525 HOH X5252 DISTANCE = 8.68 ANGSTROMS REMARK 525 HOH X5256 DISTANCE = 9.34 ANGSTROMS REMARK 525 HOH X5260 DISTANCE = 10.44 ANGSTROMS REMARK 525 HOH X5262 DISTANCE = 12.94 ANGSTROMS REMARK 525 HOH X5265 DISTANCE = 14.43 ANGSTROMS REMARK 525 HOH X5266 DISTANCE = 10.28 ANGSTROMS REMARK 525 HOH X5269 DISTANCE = 11.46 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE FLC X 601 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SCN X 603 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SCN X 604 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE TRS X 5006 DBREF 2AVR X 1 111 GB 57117488 AAW33965 19 129 SEQADV 2AVR LEU X 112 GB 57117488 EXPRESSION TAG SEQADV 2AVR GLU X 113 GB 57117488 EXPRESSION TAG SEQADV 2AVR HIS X 114 GB 57117488 EXPRESSION TAG SEQADV 2AVR HIS X 115 GB 57117488 EXPRESSION TAG SEQADV 2AVR HIS X 116 GB 57117488 EXPRESSION TAG SEQADV 2AVR HIS X 117 GB 57117488 EXPRESSION TAG SEQADV 2AVR HIS X 118 GB 57117488 EXPRESSION TAG SEQADV 2AVR HIS X 119 GB 57117488 EXPRESSION TAG SEQRES 1 X 119 ALA THR ASP ALA ALA SER LEU VAL GLY GLU LEU GLN ALA SEQRES 2 X 119 LEU ASP ALA GLU TYR GLN ASN LEU ALA ASN GLN GLU GLU SEQRES 3 X 119 ALA ARG PHE ASN GLU GLU ARG ALA GLN ALA ASP ALA ALA SEQRES 4 X 119 ARG GLN ALA LEU ALA GLN ASN GLU GLN VAL TYR ASN GLU SEQRES 5 X 119 LEU SER GLN ARG ALA GLN ARG LEU GLN ALA GLU ALA ASN SEQRES 6 X 119 THR ARG PHE TYR LYS SER GLN TYR GLN GLU LEU ALA SER SEQRES 7 X 119 LYS TYR GLU ASP ALA LEU LYS LYS LEU GLU ALA GLU MET SEQRES 8 X 119 GLU GLN GLN LYS ALA VAL ILE SER ASP PHE GLU LYS ILE SEQRES 9 X 119 GLN ALA LEU ARG ALA GLY ASN LEU GLU HIS HIS HIS HIS SEQRES 10 X 119 HIS HIS HET SCN X 603 3 HET SCN X 604 3 HET FLC X 601 13 HET TRS X5006 8 HETNAM SCN THIOCYANATE ION HETNAM FLC CITRATE ANION HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN TRS TRIS BUFFER FORMUL 2 SCN 2(C N S 1-) FORMUL 4 FLC C6 H5 O7 3- FORMUL 5 TRS C4 H12 N O3 1+ FORMUL 6 HOH *268(H2 O) HELIX 1 1 ALA X 4 ALA X 64 1 61 HELIX 2 2 TYR X 69 GLY X 110 1 42 SITE 1 AC1 8 GLN X 41 ALA X 44 HOH X5013 HOH X5029 SITE 2 AC1 8 HOH X5032 HOH X5045 HOH X5048 HOH X5062 SITE 1 AC2 3 PHE X 29 GLN X 105 HOH X5108 SITE 1 AC3 3 ALA X 22 ARG X 108 HOH X5053 SITE 1 AC4 6 GLU X 52 ARG X 56 ARG X 59 HOH X5069 SITE 2 AC4 6 HOH X5084 HOH X5120 CRYST1 59.344 59.344 126.459 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 0.016851 0.009729 0.000000 0.00000 SCALE2 0.000000 0.019458 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007908 0.00000