PDB Short entry for 1B0O HEADER LIPOCALIN 11-NOV-98 1B0O TITLE BOVINE BETA-LACTOGLOBULIN COMPLEXED WITH PALMITATE, LATTICE Z COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-LACTOGLOBULIN; 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: GENETIC VARIANT B; SOURCE 6 ORGAN: MAMMARY GLAND; SOURCE 7 SECRETION: MILK; SOURCE 8 CELLULAR_LOCATION: EXTRACELLULAR; SOURCE 9 OTHER_DETAILS: PROTEIN PURCHASED FROM SIGMA CHEMICALS, LOT 13H7150 KEYWDS LIPOCALIN, MILK WHEY PROTEIN, BOVINE, PALMITATE-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR S.-Y.WU,L.SAWYER REVDAT 4 02-AUG-23 1B0O 1 REMARK REVDAT 3 24-FEB-09 1B0O 1 VERSN REVDAT 2 06-APR-99 1B0O 3 HET REMARK TITLE DBREF REVDAT 2 2 3 JRNL SCALE REVDAT 1 02-FEB-99 1B0O 0 JRNL AUTH S.Y.WU,M.D.PEREZ,P.PUYOL,L.SAWYER JRNL TITL BETA-LACTOGLOBULIN BINDS PALMITATE WITHIN ITS CENTRAL JRNL TITL 2 CAVITY. JRNL REF J.BIOL.CHEM. V. 274 170 1999 JRNL REFN ISSN 0021-9258 JRNL PMID 9867826 JRNL DOI 10.1074/JBC.274.1.170 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.Y.QIN,M.C.BEWLEY,L.K.CREAMER,H.M.BAKER,E.N.BAKER, REMARK 1 AUTH 2 G.B.JAMESON REMARK 1 TITL STRUCTURAL BASIS OF THE TANFORD TRANSITION OF BOVINE REMARK 1 TITL 2 BETA-LACTOGLOBULIN REMARK 1 REF BIOCHEMISTRY V. 37 14014 1998 REMARK 1 REFN ISSN 0006-2960 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.BROWNLOW,J.H.MORAIS CABRAL,R.COOPER,D.R.FLOWER, REMARK 1 AUTH 2 S.J.YEWDALL,I.POLIKARPOV,A.C.NORTH,L.SAWYER REMARK 1 TITL BOVINE BETA-LACTOGLOBULIN AT 1.8 A RESOLUTION--STILL AN REMARK 1 TITL 2 ENIGMATIC LIPOCALIN REMARK 1 REF STRUCTURE V. 5 481 1997 REMARK 1 REFN ISSN 0969-2126 REMARK 1 REFERENCE 3 REMARK 1 AUTH B.Y.QIN,L.K.CREAMER,E.N.BAKER,G.B.JAMESON REMARK 1 TITL 12-BROMODODECANOIC ACID BINDS INSIDE THE CALYX OF BOVINE REMARK 1 TITL 2 BETA-LACTOGLOBULIN REMARK 1 REF FEBS LETT. V. 438 272 1998 REMARK 1 REFN ISSN 0014-5793 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.205 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 336 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 6685 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.197 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 319 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 5873 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1272 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 18 REMARK 3 SOLVENT ATOMS : 105 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 1395.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 0 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 5583 REMARK 3 NUMBER OF RESTRAINTS : 5396 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.004 REMARK 3 ANGLE DISTANCES (A) : 0.018 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.007 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.280 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.020 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.028 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.024 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : NULL REMARK 3 SIMILAR ADP COMPONENTS (A**2) : NULL REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1B0O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000171464. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-NOV-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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 : ENRAF-NONIUS FR571 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE(002) REMARK 200 OPTICS : COLLIMATOR REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6888 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 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 : 14.10 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 21.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.16 REMARK 200 R MERGE FOR SHELL (I) : 0.36600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.950 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: 1BEB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.78 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 7.5 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 74.42667 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 37.21333 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 37.21333 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 74.42667 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 111.64000 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 LEU A 1 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 ARG A 148 NE - CZ - NH1 ANGL. DEV. = -3.1 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 GLU A 44 -70.92 -96.43 REMARK 500 ASP A 53 -179.86 -66.72 REMARK 500 TRP A 61 108.71 -53.00 REMARK 500 THR A 76 -169.04 -128.80 REMARK 500 ASP A 85 30.83 -78.44 REMARK 500 ASN A 88 31.80 93.95 REMARK 500 GLU A 89 76.00 31.02 REMARK 500 THR A 97 155.11 178.99 REMARK 500 TYR A 99 -32.14 75.69 REMARK 500 ALA A 111 -6.87 72.18 REMARK 500 PRO A 113 -107.70 -69.03 REMARK 500 GLU A 114 -30.73 -30.40 REMARK 500 ARG A 148 117.75 -160.84 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: PBS REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: FATTY ACID (PALMITATE ) BINDING SITE REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PLM A 180 DBREF 1B0O A 1 162 UNP P02754 LACB_BOVIN 17 178 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 GLY 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 ALA 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 PLM A 180 18 HETNAM PLM PALMITIC ACID FORMUL 2 PLM C16 H32 O2 FORMUL 3 HOH *105(H2 O) HELIX 1 1 ILE A 12 VAL A 15 5 4 HELIX 2 2 ILE A 29 LEU A 31 5 3 HELIX 3 3 ASP A 130 LYS A 141 1 12 HELIX 4 4 PRO A 153 LEU A 156 1 4 SHEET 1 A 9 ILE A 147 SER A 150 0 SHEET 2 A 9 TYR A 20 ALA A 26 -1 N ALA A 26 O ILE A 147 SHEET 3 A 9 LEU A 117 VAL A 123 -1 N VAL A 123 O TYR A 20 SHEET 4 A 9 TYR A 102 GLU A 108 -1 N MET A 107 O ALA A 118 SHEET 5 A 9 ASN A 90 THR A 97 -1 N ASP A 96 O LEU A 104 SHEET 6 A 9 VAL A 81 ILE A 84 -1 N ILE A 84 O ASN A 90 SHEET 7 A 9 CYS A 66 LYS A 75 -1 N GLU A 74 O LYS A 83 SHEET 8 A 9 LEU A 54 TRP A 61 -1 N LYS A 60 O ALA A 67 SHEET 9 A 9 TYR A 42 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 2.04 SITE 1 PBS 11 LEU A 46 PHE A 105 MET A 107 VAL A 41 SITE 2 PBS 11 LYS A 69 LYS A 60 ILE A 71 ILE A 84 SITE 3 PBS 11 ILE A 56 LEU A 103 VAL A 94 SITE 1 AC1 10 VAL A 41 LEU A 46 LEU A 54 LYS A 60 SITE 2 AC1 10 GLU A 62 LYS A 69 ILE A 84 VAL A 94 SITE 3 AC1 10 PHE A 105 MET A 107 CRYST1 53.480 53.480 111.640 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 0.018699 0.010796 0.000000 0.00000 SCALE2 0.000000 0.021591 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008957 0.00000