PDB Short entry for 1BSO HEADER TRANSPORT PROTEIN 29-AUG-98 1BSO TITLE 12-BROMODODECANOIC ACID BINDS INSIDE THE CALYX OF BOVINE BETA- TITLE 2 LACTOGLOBULIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (BOVINE BETA-LACTOGLOBULIN A); COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 VARIANT: VARIANT A; SOURCE 6 ORGAN: BREAST; SOURCE 7 TISSUE: MAMMARY GLAND; SOURCE 8 SECRETION: MILK KEYWDS BETA-LACTOGLOBULIN, LIGAND BINDING, X-RAY CRYSTAL STRUCTURE, KEYWDS 2 TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR B.Y.QIN,L.K.CREAMER,E.N.BAKER,G.B.JAMESON REVDAT 4 03-APR-24 1BSO 1 REMARK SEQADV REVDAT 3 24-FEB-09 1BSO 1 VERSN REVDAT 2 12-JAN-00 1BSO 4 HEADER COMPND REMARK JRNL REVDAT 2 2 4 ATOM SOURCE SEQRES REVDAT 1 02-SEP-99 1BSO 0 JRNL AUTH B.Y.QIN,L.K.CREAMER,E.N.BAKER,G.B.JAMESON JRNL TITL 12-BROMODODECANOIC ACID BINDS INSIDE THE CALYX OF BOVINE JRNL TITL 2 BETA-LACTOGLOBULIN. JRNL REF FEBS LETT. V. 438 272 1998 JRNL REFN ISSN 0014-5793 JRNL PMID 9827560 JRNL DOI 10.1016/S0014-5793(98)01199-5 REMARK 2 REMARK 2 RESOLUTION. 2.23 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.851 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.23 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 100000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0100 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 92.7 REMARK 3 NUMBER OF REFLECTIONS : 8980 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) : 0.235 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 476 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.013 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.23 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.33 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 81.40 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 57 REMARK 3 BIN R VALUE (WORKING SET) : 0.3050 REMARK 3 BIN FREE R VALUE : 0.3990 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.90 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 903 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1286 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 66 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 45.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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) : 0.50 REMARK 3 ESD FROM SIGMAA (A) : 0.31 REMARK 3 LOW RESOLUTION CUTOFF (A) : 15.0 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.57 REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 26.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.320 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : OVERALL 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 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 : PARHCSDX.PRO REMARK 3 PARAMETER FILE 2 : WATER.PAR REMARK 3 PARAMETER FILE 3 : BRC.PAR REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : TOPHCSDX.PRO REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : BRC.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1BSO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB. REMARK 100 THE DEPOSITION ID IS D_1000008422. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-MAR-98 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 7.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NI REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9695 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.230 REMARK 200 RESOLUTION RANGE LOW (A) : 15.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 2.620 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : 0.04800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 18.7300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.23 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.8 REMARK 200 DATA REDUNDANCY IN SHELL : 2.64 REMARK 200 R MERGE FOR SHELL (I) : 0.54800 REMARK 200 R SYM FOR SHELL (I) : 0.54800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.040 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: BLGA IN LATTICE Z AT PH 7.1 REMARK 200 REMARK 200 REMARK: DATA WERE COLLECTED USING OSCILLATION METHOD REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.62 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN WAS CRYSTALLIZED FROM AMMONIUM REMARK 280 SULFATE, PH 7.3 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 74.78867 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 37.39433 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 37.39433 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 74.78867 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 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 350 BIOMT1 2 -0.500000 0.866025 0.000000 0.00000 REMARK 350 BIOMT2 2 0.866025 0.500000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 112.18300 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PRO A 113 C - N - CA ANGL. DEV. = 9.4 DEGREES 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 33 -90.40 -37.80 REMARK 500 GLU A 62 -80.29 -100.12 REMARK 500 ASN A 63 -92.57 -72.22 REMARK 500 ASP A 64 35.66 -149.18 REMARK 500 ALA A 86 -175.54 168.32 REMARK 500 THR A 97 143.61 -174.57 REMARK 500 TYR A 99 -37.80 68.79 REMARK 500 CYS A 160 19.12 59.29 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 BRC A 388 DBREF 1BSO A 1 162 UNP P02754 LACB_BOVIN 17 178 SEQADV 1BSO ASP A 64 UNP P02754 GLY 80 CONFLICT SEQADV 1BSO VAL A 118 UNP P02754 ALA 134 CONFLICT SEQRES 1 A 162 LEU ILE VAL THR GLN THR MET LYS GLY LEU ASP ILE GLN SEQRES 2 A 162 LYS VAL ALA GLY THR TRP TYR SER LEU ALA MET ALA ALA SEQRES 3 A 162 SER ASP ILE SER LEU LEU ASP ALA GLN SER ALA PRO LEU SEQRES 4 A 162 ARG VAL TYR VAL GLU GLU LEU LYS PRO THR PRO GLU GLY SEQRES 5 A 162 ASP LEU GLU ILE LEU LEU GLN LYS TRP GLU ASN ASP GLU SEQRES 6 A 162 CYS ALA GLN LYS LYS ILE ILE ALA GLU LYS THR LYS ILE SEQRES 7 A 162 PRO ALA VAL PHE LYS ILE ASP ALA LEU ASN GLU ASN LYS SEQRES 8 A 162 VAL LEU VAL LEU ASP THR ASP TYR LYS LYS TYR LEU LEU SEQRES 9 A 162 PHE CYS MET GLU ASN SER ALA GLU PRO GLU GLN SER LEU SEQRES 10 A 162 VAL CYS GLN CYS LEU VAL ARG THR PRO GLU VAL ASP ASP SEQRES 11 A 162 GLU ALA LEU GLU LYS PHE ASP LYS ALA LEU LYS ALA LEU SEQRES 12 A 162 PRO MET HIS ILE ARG LEU SER PHE ASN PRO THR GLN LEU SEQRES 13 A 162 GLU GLU GLN CYS HIS ILE HET BRC A 388 15 HETNAM BRC 12-BROMODODECANOIC ACID FORMUL 2 BRC C12 H23 BR O2 FORMUL 3 HOH *66(H2 O) HELIX 1 4 ILE A 29 LEU A 32 1 4 HELIX 2 5 ASP A 130 LEU A 140 1 11 HELIX 3 6 PRO A 153 LEU A 156 1 4 SHEET 1 A 6 ILE A 147 SER A 150 0 SHEET 2 A 6 TYR A 20 ALA A 26 -1 N ALA A 26 O ILE A 147 SHEET 3 A 6 VAL A 118 VAL A 123 -1 N VAL A 123 O TYR A 20 SHEET 4 A 6 TYR A 102 ASN A 109 -1 N MET A 107 O VAL A 118 SHEET 5 A 6 ASN A 90 THR A 97 -1 N ASP A 96 O LEU A 104 SHEET 6 A 6 VAL A 81 ILE A 84 -1 N ILE A 84 O ASN A 90 SHEET 1 B 3 CYS A 66 ALA A 73 0 SHEET 2 B 3 LEU A 54 TRP A 61 -1 N LYS A 60 O ALA A 67 SHEET 3 B 3 VAL A 41 PRO A 48 -1 N LYS A 47 O GLU A 55 SHEET 1 C 9 ILE A 147 SER A 150 0 SHEET 2 C 9 TYR A 20 ALA A 26 -1 N ALA A 26 O ILE A 147 SHEET 3 C 9 VAL A 118 VAL A 123 -1 N VAL A 123 O TYR A 20 SHEET 4 C 9 TYR A 102 ASN A 109 -1 N MET A 107 O VAL A 118 SHEET 5 C 9 ASN A 90 THR A 97 -1 N ASP A 96 O LEU A 104 SHEET 6 C 9 VAL A 81 ILE A 84 -1 N ILE A 84 O ASN A 90 SHEET 7 C 9 CYS A 66 LYS A 75 -1 N GLU A 74 O LYS A 83 SHEET 8 C 9 LEU A 54 TRP A 61 -1 N LYS A 60 O ALA A 67 SHEET 9 C 9 VAL A 41 PRO A 48 -1 N LYS A 47 O GLU A 55 SSBOND 1 CYS A 66 CYS A 160 1555 1555 2.03 SSBOND 2 CYS A 106 CYS A 119 1555 1555 2.02 SITE 1 AC1 6 ILE A 56 LYS A 60 LYS A 69 ILE A 71 SITE 2 AC1 6 PHE A 105 MET A 107 CRYST1 54.026 54.026 112.183 90.00 90.00 120.00 P 32 2 1 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 0.018510 0.010687 0.000000 0.00000 SCALE2 0.000000 0.021373 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008914 0.00000