HEADER METAL BINDING PROTEIN 31-DEC-10 3Q69 TITLE X-RAY CRYSTAL STRUCTURE OF A MUCBP DOMAIN OF THE PROTEIN LBA1460 FROM TITLE 2 LACTOBACILLUS ACIDOPHILUS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TITLE 3 TARGET LAR80A COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROBABLE ZN BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PUTATIVE MUCUS BINDING PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LACTOBACILLUS ACIDOPHILUS; SOURCE 3 ORGANISM_TAXID: 1579; SOURCE 4 GENE: LBA1460 KEYWDS STRUCTURAL GENOMICS, PSI-BIOLOGY, PROTEIN STRUCTURE INITIATIVE, KEYWDS 2 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM, NESG, DOMAIN FAMILY KEYWDS 3 PF06458, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.SEETHARAMAN,S.LEW,F.FOROUHAR,D.WANG,C.CICCOSANTI,S.SAHDEV,R.NAIR, AUTHOR 2 B.ROST,T.B.ACTON,R.XIAO,J.K.EVERETT,G.T.MONTELIONE,L.TONG,J.F.HUNT, AUTHOR 3 NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG) REVDAT 3 22-FEB-12 3Q69 1 VERSN KEYWDS REVDAT 2 18-MAY-11 3Q69 1 REVDAT 1 06-APR-11 3Q69 0 JRNL AUTH J.SEETHARAMAN,S.LEW,F.FOROUHAR,D.WANG,C.CICCOSANTI,S.SAHDEV, JRNL AUTH 2 R.NAIR,B.ROST,T.B.ACTON,R.XIAO,J.K.EVERETT,G.T.MONTELIONE, JRNL AUTH 3 L.TONG,J.F.HUNT JRNL TITL X-RAY CRYSTAL STRUCTURE OF A MUCBP DOMAIN OF THE PROTEIN JRNL TITL 2 LBA1460 FROM LACTOBACILLUS ACIDOPHILUS, NORTHEAST STRUCTURAL JRNL TITL 3 GENOMICS CONSORTIUM TARGET LAR80A JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.40 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 : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.29 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 937353.920 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.3 REMARK 3 NUMBER OF REFLECTIONS : 8945 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) : 0.234 REMARK 3 FREE R VALUE : 0.292 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.300 REMARK 3 FREE R VALUE TEST SET COUNT : 835 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.55 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 95.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1328 REMARK 3 BIN R VALUE (WORKING SET) : 0.2790 REMARK 3 BIN FREE R VALUE : 0.3400 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 9.80 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 145 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.028 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 840 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 63 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 33.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.87000 REMARK 3 B22 (A**2) : 13.81000 REMARK 3 B33 (A**2) : -7.94000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.05000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM SIGMAA (A) : 0.26 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) : 0.44 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.38 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 27.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.76 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) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 40.57 REMARK 3 REMARK 3 NCS MODEL : NONE 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_REP.PARAM REMARK 3 PARAMETER FILE 3 : ION.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : ION.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3Q69 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JAN-11. REMARK 100 THE RCSB ID CODE IS RCSB063246. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9462 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : 0.06300 REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.44 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.6 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: SAD 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 (%): 42.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, .1M KBR .1M BIS TRIS REMARK 280 PROPANE PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z 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 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 30.89450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 12.42750 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 30.89450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 12.42750 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 THR A 106 REMARK 465 ILE A 107 REMARK 465 THR A 108 REMARK 465 GLN A 109 REMARK 465 ASN A 110 REMARK 465 LYS A 111 REMARK 465 LYS A 112 REMARK 465 ASP A 113 REMARK 465 GLY A 114 REMARK 465 LEU A 115 REMARK 465 GLU A 116 REMARK 465 HIS A 117 REMARK 465 HIS A 118 REMARK 465 HIS A 119 REMARK 465 HIS A 120 REMARK 465 HIS A 121 REMARK 465 HIS A 122 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: LAR80A RELATED DB: TARGETDB DBREF 3Q69 A 2 114 UNP Q5FJ43 Q5FJ43_LACAC 182 294 SEQADV 3Q69 MSE A 1 UNP Q5FJ43 EXPRESSION TAG SEQADV 3Q69 LEU A 115 UNP Q5FJ43 EXPRESSION TAG SEQADV 3Q69 GLU A 116 UNP Q5FJ43 EXPRESSION TAG SEQADV 3Q69 HIS A 117 UNP Q5FJ43 EXPRESSION TAG SEQADV 3Q69 HIS A 118 UNP Q5FJ43 EXPRESSION TAG SEQADV 3Q69 HIS A 119 UNP Q5FJ43 EXPRESSION TAG SEQADV 3Q69 HIS A 120 UNP Q5FJ43 EXPRESSION TAG SEQADV 3Q69 HIS A 121 UNP Q5FJ43 EXPRESSION TAG SEQADV 3Q69 HIS A 122 UNP Q5FJ43 EXPRESSION TAG SEQRES 1 A 122 MSE ILE GLU PRO ILE LYS ARG THR GLN VAL VAL THR GLN SEQRES 2 A 122 THR ILE HIS TYR ARG TYR GLU ASP GLY ALA VAL ALA HIS SEQRES 3 A 122 ASP ASP HIS VAL VAL SER LEU ILE PHE THR GLN SER GLY SEQRES 4 A 122 LYS ARG ASP LEU THR ASN GLY LYS GLU ILE TRP ASP SER SEQRES 5 A 122 LYS TRP SER LEU THR GLN THR PHE GLU ALA LEU PRO SER SEQRES 6 A 122 PRO VAL ILE ILE GLY TYR THR ALA ASP LYS PRO MSE VAL SEQRES 7 A 122 GLY PRO ASP GLU VAL THR VAL ASP SER LYS ASN PHE LEU SEQRES 8 A 122 ASP LYS GLN ASN ARG GLU GLU THR VAL ILE TYR SER ALA SEQRES 9 A 122 ASN THR ILE THR GLN ASN LYS LYS ASP GLY LEU GLU HIS SEQRES 10 A 122 HIS HIS HIS HIS HIS MODRES 3Q69 MSE A 1 MET SELENOMETHIONINE MODRES 3Q69 MSE A 77 MET SELENOMETHIONINE HET MSE A 1 8 HET MSE A 77 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 2(C5 H11 N O2 SE) FORMUL 2 HOH *63(H2 O) HELIX 1 1 LYS A 88 PHE A 90 5 3 SHEET 1 A 5 GLU A 48 ILE A 49 0 SHEET 2 A 5 VAL A 24 ASP A 42 -1 N LYS A 40 O ILE A 49 SHEET 3 A 5 ILE A 2 TYR A 19 -1 N GLN A 9 O PHE A 35 SHEET 4 A 5 ARG A 96 ALA A 104 1 O GLU A 98 N HIS A 16 SHEET 5 A 5 TYR A 71 ALA A 73 -1 N THR A 72 O SER A 103 SHEET 1 B 2 SER A 55 PHE A 60 0 SHEET 2 B 2 ASP A 81 ASP A 86 -1 O VAL A 83 N GLN A 58 SHEET 1 C 2 LEU A 63 PRO A 64 0 SHEET 2 C 2 MSE A 77 VAL A 78 -1 O VAL A 78 N LEU A 63 LINK C MSE A 1 N ILE A 2 1555 1555 1.33 LINK C PRO A 76 N MSE A 77 1555 1555 1.33 LINK C MSE A 77 N VAL A 78 1555 1555 1.32 CISPEP 1 GLY A 79 PRO A 80 0 0.20 CRYST1 61.789 24.855 83.363 90.00 108.53 90.00 C 1 2 1 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 0.016184 0.000000 0.005424 0.00000 SCALE2 0.000000 0.040233 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012651 0.00000 HETATM 1 N MSE A 1 20.126 20.919 14.313 1.00 36.25 N HETATM 2 CA MSE A 1 20.755 21.592 15.485 1.00 37.61 C HETATM 3 C MSE A 1 19.831 21.428 16.693 1.00 34.31 C HETATM 4 O MSE A 1 18.693 21.897 16.678 1.00 33.41 O HETATM 5 CB MSE A 1 20.947 23.078 15.178 1.00 42.70 C HETATM 6 CG MSE A 1 22.022 23.759 16.012 1.00 50.12 C HETATM 7 SE MSE A 1 23.794 23.566 15.211 1.00 62.04 SE HETATM 8 CE MSE A 1 23.838 25.182 14.172 1.00 57.21 C