HEADER BLOOD CLOTTING, CELL ADHESION 13-DEC-07 3BN6 TITLE CRYSTAL STRUCTURE OF THE C2 DOMAIN OF BOVINE LACTADHERIN AT 1.67 TITLE 2 ANGSTROM RESOLUTION COMPND MOL_ID: 1; COMPND 2 MOLECULE: LACTADHERIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: F5/8 TYPE C 2, C2, RESIDUES 270-427; COMPND 5 SYNONYM: MILK FAT GLOBULE-EGF FACTOR 8, MFG-E8, MGP57/53, PAS-6/PAS-7 COMPND 6 GLYCOPROTEIN, MFGM, SPERM SURFACE PROTEIN SP47, BP47, COMPONENTS COMPND 7 15/16; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 GENE: MFGE8; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS ANTICOAGULATION, ANTI-COAGULATION, ANTICOAGULANT, ANTI-COAGULANT, KEYWDS 2 MEMBRANE BINDING, PHOSPHATIDYL-SERINE BINDING, PHOSPHATIDYLSERINE KEYWDS 3 BINDING, BLOOD COAGULATION FACTOR V C2 HOMOLOGUE, BLOOD COAGULATION KEYWDS 4 FACTOR VIII C2 HOMOLOGUE, MILK FAT GLOBULE, APOPTOSIS, DISCOIDIN KEYWDS 5 DOMAIN, FA58C, F5_F8_TYPE_C, ALTERNATIVE SPLICING, CELL ADHESION, KEYWDS 6 EGF-LIKE DOMAIN, FERTILIZATION, GLYCOPROTEIN, BLOOD CLOTTING EXPDTA X-RAY DIFFRACTION AUTHOR C.SHAO,V.A.NOVAKOVIC,J.F.HEAD,B.A.SEATON,G.E.GILBERT REVDAT 7 13-NOV-24 3BN6 1 REMARK REVDAT 6 20-SEP-23 3BN6 1 REMARK REVDAT 5 31-MAY-23 3BN6 1 REMARK REVDAT 4 25-OCT-17 3BN6 1 REMARK REVDAT 3 24-FEB-09 3BN6 1 VERSN REVDAT 2 05-AUG-08 3BN6 1 JRNL REVDAT 1 25-DEC-07 3BN6 0 JRNL AUTH C.SHAO,V.A.NOVAKOVIC,J.F.HEAD,B.A.SEATON,G.E.GILBERT JRNL TITL CRYSTAL STRUCTURE OF LACTADHERIN C2 DOMAIN AT 1.7A JRNL TITL 2 RESOLUTION WITH MUTATIONAL AND COMPUTATIONAL ANALYSES OF ITS JRNL TITL 3 MEMBRANE-BINDING MOTIF. JRNL REF J.BIOL.CHEM. V. 283 7230 2008 JRNL REFN ISSN 0021-9258 JRNL PMID 18160406 JRNL DOI 10.1074/JBC.M705195200 REMARK 2 REMARK 2 RESOLUTION. 1.67 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.67 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 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) (%) : 97.4 REMARK 3 NUMBER OF REFLECTIONS : 16784 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 7.700 REMARK 3 FREE R VALUE TEST SET COUNT : 1322 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) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 1274 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 233 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.63700 REMARK 3 B22 (A**2) : 1.30100 REMARK 3 B33 (A**2) : 2.33700 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) : 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) : 1.168 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.809 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 1.959 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 2.891 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : 45.56 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : ION.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 TOPOLOGY FILE 2 : NULL REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 3BN6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000045723. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-MAR-06 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 : RIGAKU RU300 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17121 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.670 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.9 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.67 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.72 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.00 REMARK 200 R MERGE FOR SHELL (I) : 0.33400 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR 2.5 REMARK 200 STARTING MODEL: PDB ENTRY 1CZT REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.98 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18% (W/V) PEG4000, 0.1 M HEPES, PH REMARK 280 7.5, 0.2 M MGCL2, 10% ISOPROPANOL, MICRO-SEEDING, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 290K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 15.95450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.83500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.01650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.83500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 15.95450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 28.01650 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 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 TRP A 26 49.04 33.35 REMARK 500 PHE A 31 44.51 -109.36 REMARK 500 TRP A 33 71.67 -108.21 REMARK 500 ASN A 147 -60.97 67.31 REMARK 500 REMARK 500 REMARK: NULL DBREF 3BN6 A 1 158 UNP Q95114 MFGM_BOVIN 270 427 SEQRES 1 A 158 CYS THR GLU PRO LEU GLY LEU LYS ASP ASN THR ILE PRO SEQRES 2 A 158 ASN LYS GLN ILE THR ALA SER SER TYR TYR LYS THR TRP SEQRES 3 A 158 GLY LEU SER ALA PHE SER TRP PHE PRO TYR TYR ALA ARG SEQRES 4 A 158 LEU ASP ASN GLN GLY LYS PHE ASN ALA TRP THR ALA GLN SEQRES 5 A 158 THR ASN SER ALA SER GLU TRP LEU GLN ILE ASP LEU GLY SEQRES 6 A 158 SER GLN LYS ARG VAL THR GLY ILE ILE THR GLN GLY ALA SEQRES 7 A 158 ARG ASP PHE GLY HIS ILE GLN TYR VAL ALA ALA TYR ARG SEQRES 8 A 158 VAL ALA TYR GLY ASP ASP GLY VAL THR TRP THR GLU TYR SEQRES 9 A 158 LYS ASP PRO GLY ALA SER GLU SER LYS ILE PHE PRO GLY SEQRES 10 A 158 ASN MET ASP ASN ASN SER HIS LYS LYS ASN ILE PHE GLU SEQRES 11 A 158 THR PRO PHE GLN ALA ARG PHE VAL ARG ILE GLN PRO VAL SEQRES 12 A 158 ALA TRP HIS ASN ARG ILE THR LEU ARG VAL GLU LEU LEU SEQRES 13 A 158 GLY CYS FORMUL 2 HOH *233(H2 O) HELIX 1 1 PRO A 13 LYS A 15 5 3 HELIX 2 2 LYS A 24 SER A 32 5 9 HELIX 3 3 PHE A 34 ALA A 38 5 5 SHEET 1 A 8 GLU A 3 PRO A 4 0 SHEET 2 A 8 THR A 150 GLY A 157 -1 O GLY A 157 N GLU A 3 SHEET 3 A 8 TRP A 49 THR A 50 -1 N TRP A 49 O LEU A 151 SHEET 4 A 8 THR A 150 GLY A 157 -1 O LEU A 151 N TRP A 49 SHEET 5 A 8 LEU A 60 GLN A 76 -1 N GLY A 72 O LEU A 156 SHEET 6 A 8 LYS A 125 HIS A 146 -1 O VAL A 138 N ILE A 62 SHEET 7 A 8 HIS A 83 GLY A 95 -1 N ALA A 89 O VAL A 143 SHEET 8 A 8 PHE A 115 PRO A 116 -1 O PHE A 115 N TYR A 90 SHEET 1 B 7 ILE A 17 ALA A 19 0 SHEET 2 B 7 LEU A 60 GLN A 76 -1 O GLN A 61 N THR A 18 SHEET 3 B 7 LYS A 125 HIS A 146 -1 O VAL A 138 N ILE A 62 SHEET 4 B 7 HIS A 83 GLY A 95 -1 N ALA A 89 O VAL A 143 SHEET 5 B 7 ALA A 78 ASP A 80 -1 N ALA A 78 O GLN A 85 SHEET 6 B 7 HIS A 83 GLY A 95 -1 O GLN A 85 N ALA A 78 SHEET 7 B 7 THR A 102 GLU A 103 -1 O THR A 102 N TYR A 94 SSBOND 1 CYS A 1 CYS A 158 1555 1555 2.04 CRYST1 31.909 56.033 79.670 90.00 90.00 90.00 P 21 21 21 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 0.031339 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017847 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012552 0.00000