HEADER LIPID BINDING PROTEIN 10-FEB-98 1A44 TITLE PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN FROM CALF BRAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHATIDYLETHANOLAMINE-BINDING PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PEBP, PBP SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 ORGAN: BRAIN; SOURCE 6 CELLULAR_LOCATION: CYTOPLASM; SOURCE 7 OTHER_DETAILS: CALF KEYWDS LIPID-BINDING, LIPID-BINDING PROTEIN, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.SERRE,B.VALLEE,C.ZELWER,F.SCHOENTGEN REVDAT 3 07-FEB-24 1A44 1 KEYWDS REMARK REVDAT 2 24-FEB-09 1A44 1 VERSN REVDAT 1 13-JAN-99 1A44 0 JRNL AUTH L.SERRE,B.VALLEE,N.BUREAUD,F.SCHOENTGEN,C.ZELWER JRNL TITL CRYSTAL STRUCTURE OF THE PHOSPHATIDYLETHANOLAMINE-BINDING JRNL TITL 2 PROTEIN FROM BOVINE BRAIN: A NOVEL STRUCTURAL CLASS OF JRNL TITL 3 PHOSPHOLIPID-BINDING PROTEINS. JRNL REF STRUCTURE V. 6 1255 1998 JRNL REFN ISSN 0969-2126 JRNL PMID 9782057 JRNL DOI 10.1016/S0969-2126(98)00126-9 REMARK 2 REMARK 2 RESOLUTION. 1.84 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.84 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 14517 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : RFREE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1466 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 4 REMARK 3 SOLVENT ATOMS : 244 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 9.74 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.89 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.010 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.027 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.031 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; 0.050 REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.030 ; 0.040 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.131 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.177 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.245 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.106 ; 0.300 REMARK 3 H-BOND (X-H...Y) (A) : 0.000 ; 0.300 REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : 0.000 ; 15.000 REMARK 3 PLANAR (DEGREES) : 5.300 ; 7.000 REMARK 3 STAGGERED (DEGREES) : 15.800; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 23.200; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.772 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.354 ; 5.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 4.089 ; 6.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 5.170 ; 8.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1A44 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_1000170368. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NOV-97 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LURE REMARK 200 BEAMLINE : DW32 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14517 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.840 REMARK 200 RESOLUTION RANGE LOW (A) : 36.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.03900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.84 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.09300 REMARK 200 <I/SIGMA(I)> FOR SHELL : 8.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MULTIPLE ISOMORPHOUS REMARK 200 REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.99 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.6 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 41.35000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 16.77500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 41.35000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 16.77500 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 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: 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 TYR A 28 CB - CG - CD2 ANGL. DEV. = -4.1 DEGREES REMARK 500 GLU A 32 CB - CG - CD ANGL. DEV. = 24.7 DEGREES REMARK 500 ASP A 34 N - CA - CB ANGL. DEV. = -11.9 DEGREES REMARK 500 THR A 53 CB - CA - C ANGL. DEV. = -16.2 DEGREES REMARK 500 THR A 53 N - CA - CB ANGL. DEV. = 14.2 DEGREES REMARK 500 ARG A 81 CA - C - N ANGL. DEV. = 16.0 DEGREES REMARK 500 ARG A 81 O - C - N ANGL. DEV. = -15.6 DEGREES REMARK 500 ARG A 140 CD - NE - CZ ANGL. DEV. = 8.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 THR A 53 -10.39 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 ACT A 201 DBREF 1A44 A 1 185 UNP P13696 PEBP_BOVIN 1 185 SEQRES 1 A 185 PRO VAL ASP LEU SER LYS TRP SER GLY PRO LEU SER LEU SEQRES 2 A 185 GLN GLU VAL ASP GLU ARG PRO GLN HIS PRO LEU GLN VAL SEQRES 3 A 185 LYS TYR GLY GLY ALA GLU VAL ASP GLU LEU GLY LYS VAL SEQRES 4 A 185 LEU THR PRO THR GLN VAL LYS ASN ARG PRO THR SER ILE SEQRES 5 A 185 THR TRP ASP GLY LEU ASP PRO GLY LYS LEU TYR THR LEU SEQRES 6 A 185 VAL LEU THR ASP PRO ASP ALA PRO SER ARG LYS ASP PRO SEQRES 7 A 185 LYS TYR ARG GLU TRP HIS HIS PHE LEU VAL VAL ASN MET SEQRES 8 A 185 LYS GLY ASN ASN ILE SER SER GLY THR VAL LEU SER ASP SEQRES 9 A 185 TYR VAL GLY SER GLY PRO PRO LYS GLY THR GLY LEU HIS SEQRES 10 A 185 ARG TYR VAL TRP LEU VAL TYR GLU GLN GLU GLY PRO LEU SEQRES 11 A 185 LYS CYS ASP GLU PRO ILE LEU SER ASN ARG SER GLY ASP SEQRES 12 A 185 HIS ARG GLY LYS PHE LYS VAL ALA SER PHE ARG LYS LYS SEQRES 13 A 185 TYR GLU LEU GLY ALA PRO VAL ALA GLY THR CYS TYR GLN SEQRES 14 A 185 ALA GLU TRP ASP ASP TYR VAL PRO LYS LEU TYR GLU GLN SEQRES 15 A 185 LEU SER GLY HET ACT A 201 4 HETNAM ACT ACETATE ION FORMUL 2 ACT C2 H3 O2 1- FORMUL 3 HOH *244(H2 O) HELIX 1 1 LEU A 4 LYS A 6 5 3 HELIX 2 2 LEU A 13 GLU A 15 5 3 HELIX 3 3 ILE A 96 SER A 98 5 3 HELIX 4 4 VAL A 150 LYS A 156 1 7 HELIX 5 5 VAL A 176 LEU A 183 1 8 SHEET 1 A 3 SER A 51 THR A 53 0 SHEET 2 A 3 GLN A 25 TYR A 28 -1 N LYS A 27 O SER A 51 SHEET 3 A 3 ALA A 31 VAL A 33 -1 N VAL A 33 O VAL A 26 SHEET 1 B 5 ALA A 164 ALA A 170 0 SHEET 2 B 5 HIS A 117 GLU A 125 -1 N VAL A 123 O ALA A 164 SHEET 3 B 5 TYR A 63 ASP A 69 -1 N THR A 68 O VAL A 120 SHEET 4 B 5 TRP A 83 VAL A 89 -1 N VAL A 88 O LEU A 65 SHEET 5 B 5 THR A 100 SER A 103 -1 N SER A 103 O LEU A 87 CISPEP 1 ALA A 72 PRO A 73 0 -5.12 CISPEP 2 ARG A 81 GLU A 82 0 -25.95 SITE 1 AC1 7 HIS A 85 GLY A 109 TYR A 180 HOH A 234 SITE 2 AC1 7 HOH A 242 HOH A 248 HOH A 298 CRYST1 82.700 33.550 60.070 90.00 97.71 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 0.012092 0.000000 0.001637 0.00000 SCALE2 0.000000 0.029806 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016799 0.00000